Contacts of the helix formed by residues 1385 - 1407 (chain B) in PDB entry 5WBY


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLU1385 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1386B  ARG*     1.3    69.6    +      -       +      +
   1387B  ALA*     3.3     5.2    -      -       -      +
   1388B  ALA*     3.1    21.6    +      -       -      +
   1389B  LYS*     3.2    37.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1385B  GLU*     1.3    78.6    -      -       +      +
   1387B  ALA*     1.3    63.8    +      -       -      +
   1389B  LYS*     3.5    38.5    +      -       +      +
   1390B  CYS*     3.7     9.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1387 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1385B  GLU      3.3     3.5    -      -       -      +
   1386B  ARG*     1.3    76.9    -      -       -      +
   1388B  ALA*     1.3    59.5    +      -       -      +
   1390B  CYS*     3.2    27.8    -      -       -      -
   1391B  ARG*     3.7     6.1    +      -       -      +
   2311B  GLU*     5.2     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1388 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1385B  GLU*     3.1    15.1    +      -       -      +
   1387B  ALA*     1.3    76.3    -      -       -      +
   1389B  LYS*     1.3    61.9    +      -       -      +
   1390B  CYS      3.5     0.2    -      -       -      -
   1391B  ARG*     3.5    21.6    -      -       +      +
   1392B  ALA*     3.4    19.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS1389 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1385B  GLU*     3.2    32.8    +      -       -      +
   1386B  ARG*     3.7    34.6    -      -       +      +
   1387B  ALA      3.3     0.8    -      -       -      -
   1388B  ALA*     1.3    76.2    -      -       -      +
   1390B  CYS*     1.3    63.5    +      -       -      +
   1392B  ALA*     3.4    14.9    +      -       -      +
   1393B  TYR*     3.1    30.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with CYS1390 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1386B  ARG      3.7     7.6    +      -       -      +
   1387B  ALA*     3.2    27.1    -      -       -      -
   1389B  LYS*     1.3    75.6    -      -       -      +
   1391B  ARG*     1.3    59.2    +      -       -      +
   1393B  TYR*     3.5     6.1    +      -       -      -
   1394B  ALA*     3.0    26.4    +      -       -      +
   1422B  LYS      6.1     0.2    -      -       -      +
   1423B  LEU*     3.4    28.1    -      -       +      +
   2311B  GLU*     4.5    17.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1391 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1387B  ALA      3.7     5.4    +      -       -      +
   1388B  ALA*     3.5    24.4    +      -       -      +
   1390B  CYS*     1.3    80.3    -      -       -      +
   1392B  ALA*     1.3    64.8    +      -       -      +
   1394B  ALA*     3.3     2.4    +      -       -      -
   1395B  LYS*     3.1    13.8    +      -       +      +
   2308B  PRO      4.9     2.8    +      -       -      -
   2309B  SER*     3.7    22.6    -      -       -      -
   2310B  SER*     2.8    31.8    +      -       -      +
   2311B  GLU*     3.3    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1392 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1388B  ALA      3.4     9.7    +      -       -      +
   1389B  LYS*     3.6    11.2    -      -       -      +
   1390B  CYS      3.4     0.2    -      -       -      -
   1391B  ARG*     1.3    78.3    -      -       -      +
   1393B  TYR*     1.3    65.6    +      -       +      +
   1395B  LYS*     4.1     4.8    -      -       -      +
   1396B  ALA*     3.2    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1393 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1389B  LYS*     3.1    33.1    +      -       +      -
   1390B  CYS*     3.5    10.2    +      -       -      +
   1391B  ARG      3.3     0.4    -      -       -      -
   1392B  ALA*     1.3    79.2    -      -       +      +
   1394B  ALA*     1.3    59.3    +      -       -      +
   1396B  ALA*     3.4     4.7    +      -       +      -
   1397B  LEU*     2.8    29.6    +      -       -      +
   1419B  ILE*     3.4    25.5    -      -       +      +
   1422B  LYS*     4.0    47.9    -      -       +      +
   1423B  LEU*     4.1    11.4    -      -       +      -
   1578B  MET*     3.7    26.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1394 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1390B  CYS      3.0    18.3    +      -       -      +
   1391B  ARG      3.3     0.2    +      -       -      -
   1393B  TYR*     1.3    76.4    -      -       -      +
   1395B  LYS*     1.3    59.8    +      -       -      +
   1397B  LEU*     3.4     5.7    +      -       -      +
   1398B  HIS*     3.3    17.0    +      -       -      +
   1423B  LEU*     4.1    18.8    -      -       +      +
   2310B  SER*     3.6    34.7    -      -       -      +
   2311B  GLU*     4.0     6.7    -      -       -      +
   2313B  TRP*     3.9    11.4    -      -       -      -
   2314B  PHE*     4.6     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1395 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1391B  ARG*     3.1    16.1    +      -       +      +
   1392B  ALA*     4.1     4.7    -      -       -      +
   1394B  ALA*     1.3    74.0    -      -       -      +
   1396B  ALA*     1.3    64.2    -      -       -      +
   1398B  HIS*     3.4    13.8    +      -       -      +
   1399B  TYR*     3.2    54.5    +      -       +      -
   2304B  TRP*     4.7    12.1    -      -       +      -
   2310B  SER*     3.4    15.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1396 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1392B  ALA      3.2    17.7    +      -       -      +
   1393B  TYR*     3.6     3.8    -      -       +      +
   1394B  ALA      3.3     0.2    -      -       -      -
   1395B  LYS*     1.3    75.5    -      -       -      +
   1397B  LEU*     1.3    61.0    +      -       -      +
   1399B  TYR*     3.6     7.0    +      -       -      +
   1400B  LYS*     3.0    30.1    +      -       -      +
   1419B  ILE*     3.5    18.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1397 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1393B  TYR      2.8    17.6    +      -       -      +
   1394B  ALA*     3.5     7.2    -      -       -      +
   1395B  LYS      3.3     0.2    -      -       -      -
   1396B  ALA*     1.3    73.9    -      -       -      +
   1398B  HIS*     1.3    56.0    +      -       -      +
   1400B  LYS*     3.2     2.0    +      -       -      -
   1401B  GLU*     2.7    64.3    +      -       +      +
   1416B  LEU*     4.0    16.4    -      -       +      -
   1419B  ILE*     3.3    20.3    -      -       +      +
   1420B  ASN*     3.4    31.4    -      -       -      +
   1423B  LEU*     4.0     9.0    -      -       +      -
   2313B  TRP*     4.9     2.2    -      -       +      -
   2314B  PHE*     3.5    31.0    -      -       +      -
   2317B  ARG*     4.3     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1398 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1394B  ALA      3.3     8.1    +      -       -      +
   1395B  LYS      3.4     8.9    +      -       -      +
   1397B  LEU*     1.3    78.2    -      -       -      +
   1399B  TYR*     1.3    76.2    +      +       -      +
   1401B  GLU*     3.5     5.4    +      -       -      +
   1402B  LEU*     3.0    46.1    +      -       +      +
   2301B  LYS*     6.4     2.0    -      -       +      -
   2304B  TRP*     3.3    77.1    +      +       +      -
   2313B  TRP*     3.8    23.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR1399 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1395B  LYS*     3.2    56.2    +      -       +      -
   1396B  ALA*     4.1     6.3    -      -       -      +
   1397B  LEU      3.3     0.2    -      -       -      -
   1398B  HIS*     1.3    93.1    -      +       -      +
   1400B  LYS*     1.3    60.2    +      -       -      +
   1402B  LEU*     3.2    15.2    +      -       +      +
   1403B  GLU*     2.8    29.3    +      -       -      +
   2304B  TRP*     4.5     8.8    +      +       -      -
----------------------------------------------------------
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Residues in contact with LYS1400 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1396B  ALA      3.0    20.1    +      -       -      +
   1397B  LEU*     3.6     7.4    -      -       -      +
   1399B  TYR*     1.3    75.2    -      -       -      +
   1401B  GLU*     1.3    59.0    +      -       -      +
   1403B  GLU*     3.4    27.4    +      -       -      +
   1404B  PHE*     3.1    19.9    +      -       -      +
   1412B  ILE*     3.6    16.7    -      -       +      +
   1415B  SER*     3.2    44.1    +      -       -      +
   1416B  LEU*     3.7    19.2    -      -       +      +
   1419B  ILE*     4.8     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1401 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1397B  LEU*     2.7    43.1    +      -       +      +
   1398B  HIS*     3.7     4.8    +      -       -      +
   1400B  LYS*     1.3    71.2    -      -       -      +
   1402B  LEU*     1.3    59.5    +      -       -      +
   1403B  GLU      3.1     0.2    -      -       -      -
   1404B  PHE*     3.1    10.8    +      -       -      +
   1405B  GLN*     2.9    31.2    +      -       -      +
   1416B  LEU*     4.1     5.0    -      -       +      +
   1420B  ASN*     5.4     1.2    +      -       -      -
   2313B  TRP*     4.0     6.8    -      -       -      -
   2317B  ARG*     2.7    44.0    +      -       -      -
   2388B  GLU*     3.6    12.3    -      -       -      +
   2389B  VAL*     3.6    33.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1402 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1398B  HIS*     3.0    41.1    +      -       +      +
   1399B  TYR*     3.2    16.6    +      -       +      +
   1401B  GLU*     1.3    72.6    -      -       -      +
   1403B  GLU*     1.3    62.0    +      -       -      +
   1405B  GLN*     3.6    22.5    -      -       +      +
   1406B  LYS*     3.5    29.4    +      -       -      +
   2297B  ASP*     5.9     2.0    -      -       -      +
   2301B  LYS*     5.3    20.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1403 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1399B  TYR      2.8    12.6    +      -       -      +
   1400B  LYS*     3.4    38.3    +      -       -      +
   1402B  LEU*     1.3    75.6    -      -       -      +
   1404B  PHE*     1.3    64.8    +      -       -      +
   1406B  LYS*     3.1    19.3    +      -       +      +
   1407B  GLY      3.2    12.1    +      -       -      +
   1412B  ILE*     3.7    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1404 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1400B  LYS      3.1    10.5    +      -       -      +
   1401B  GLU*     3.1    11.4    +      -       -      +
   1403B  GLU*     1.3    77.6    -      -       -      +
   1405B  GLN*     1.3    70.0    +      -       -      +
   1407B  GLY      4.4     0.4    -      -       -      -
   1408B  PRO*     3.2    45.3    -      -       +      +
   1412B  ILE*     3.9    21.2    -      -       +      +
   1413B  LEU*     3.8    19.3    -      -       +      -
   1416B  LEU*     4.2    16.4    -      -       +      -
   1435B  TYR*     3.6    42.8    -      +       -      -
   2389B  VAL*     3.7    33.7    -      -       +      -
   2390B  THR*     4.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1405 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1401B  GLU      2.9    17.9    +      -       -      +
   1402B  LEU*     3.6    29.0    -      -       +      +
   1404B  PHE*     1.3    82.9    -      -       -      +
   1406B  LYS*     1.3    61.1    +      -       +      +
   1407B  GLY*     3.4     1.0    +      -       -      -
   1408B  PRO*     4.9     2.6    -      -       -      +
   2297B  ASP*     5.4     3.0    -      -       -      +
   2385B  ASN*     3.5    33.2    +      -       -      +
   2389B  VAL*     3.9    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1406 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1402B  LEU*     3.6    17.0    -      -       -      +
   1403B  GLU*     3.1    12.1    +      -       +      +
   1405B  GLN*     1.3    79.5    -      -       +      +
   1407B  GLY*     1.3    57.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1407 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1403B  GLU      3.2     5.1    +      -       -      +
   1404B  PHE      3.5     2.7    -      -       -      -
   1405B  GLN      3.3     2.6    -      -       -      -
   1406B  LYS*     1.3    79.7    -      -       -      +
   1408B  PRO*     1.4    72.7    -      -       -      +
   1409B  THR*     3.2    13.1    +      -       -      +
   1412B  ILE*     3.3    18.5    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il