Contacts of the strand formed by residues 1345 - 1352 (chain E) in PDB entry 6BAA


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 ILE1345 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343E  GLY      3.8     2.7    +      -       -      +
   1344E  LYS*     1.3    75.3    -      -       -      +
   1346E  GLN*     1.3    59.2    +      -       -      +
   1347E  ILE*     6.2     1.8    -      -       +      -
   1368E  LEU*     3.3     2.6    -      -       -      +
   1369E  ILE*     2.4    59.4    +      -       +      +
   1392E  PHE*     6.0     5.8    -      -       +      -
   1404E  ILE      3.9    16.2    -      -       -      +
   1405E  ILE*     5.3     0.9    -      -       -      -
   1406E  ASP      5.2     2.7    -      -       -      +
   1532E  THR*     5.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1346 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345E  ILE*     1.3    75.0    -      -       -      +
   1347E  ILE*     1.3    66.1    +      -       -      +
   1348E  GLN*     4.1     2.4    +      -       +      -
   1367E  THR      3.3     9.0    -      -       -      +
   1368E  LEU*     4.3    11.2    -      -       +      -
   1402E  ARG      4.3     1.7    -      -       -      +
   1404E  ILE*     3.7    30.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1347 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345E  ILE*     6.1     2.2    -      -       +      -
   1346E  GLN*     1.3    82.5    -      -       -      +
   1348E  GLN*     1.3    62.9    +      -       -      +
   1350E  LEU*     3.7    22.4    -      -       +      -
   1365E  VAL*     3.4    33.2    -      -       +      +
   1366E  ASN*     3.3     6.9    -      -       -      +
   1367E  THR*     2.6    40.7    +      -       -      +
   1402E  ARG      4.0     1.3    -      -       -      +
   1403E  ILE*     3.8    28.0    -      -       +      -
   1404E  ILE      4.5     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1348 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1346E  GLN*     4.1     2.6    +      -       +      +
   1347E  ILE*     1.3    74.7    -      -       -      +
   1349E  ASN*     1.3    69.6    +      -       +      +
   1350E  LEU      3.4     1.3    -      -       -      -
   1366E  ASN*     4.9     2.0    -      -       -      +
   1401E  GLY*     3.2    19.4    -      -       -      -
   1402E  ARG*     3.2    16.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN1349 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1348E  GLN*     1.3    72.2    -      -       +      +
   1350E  LEU*     1.3    61.3    +      -       -      +
   1351E  SER*     3.4     4.5    +      -       -      -
   1364E  HIS*     4.2    17.0    -      -       +      +
   1365E  VAL      2.9    15.7    +      -       -      -
   1366E  ASN*     4.6     4.6    -      -       -      +
   1400E  GLU*     3.2    15.9    -      -       +      +
   1401E  GLY*     3.3     8.3    -      -       -      +
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Residues in contact with LEU1350 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347E  ILE*     3.7    25.1    -      -       +      -
   1348E  GLN      3.4     1.7    +      -       -      -
   1349E  ASN*     1.3    75.8    -      -       -      +
   1351E  SER*     1.3    59.1    +      -       -      +
   1362E  LEU*     3.6    23.6    -      -       +      +
   1364E  HIS      3.5     4.9    +      -       -      -
   1365E  VAL*     3.2    25.1    +      -       +      +
   1398E  MET*     4.8     8.7    -      -       +      -
   1400E  GLU      3.3     7.9    -      -       -      +
   1401E  GLY*     4.4     0.4    -      -       -      -
   1402E  ARG      4.7     9.4    -      -       -      +
   1403E  ILE*     5.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1351 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1349E  ASN      3.4     3.8    +      -       -      -
   1350E  LEU*     1.3    76.5    +      -       -      +
   1352E  VAL*     1.3    55.9    +      -       -      +
   1360E  PRO*     5.8     2.5    -      -       -      -
   1362E  LEU      3.3     9.3    +      -       -      -
   1363E  LYS*     4.3     1.6    -      -       -      -
   1364E  HIS*     3.8    13.2    +      -       -      -
   1398E  MET*     3.2     5.0    -      -       -      -
   1399E  PHE*     2.4    39.8    +      -       -      -
   1400E  GLU*     3.0    25.5    +      -       -      +
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Residues in contact with VAL1352 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1351E  SER*     1.3    75.5    -      -       -      +
   1353E  ARG*     1.3    62.2    +      -       -      +
   1354E  TYR*     5.1     3.8    -      -       +      +
   1360E  PRO*     3.4     5.3    -      -       -      +
   1361E  VAL*     2.4    41.0    +      -       +      -
   1362E  LEU*     3.2    40.7    +      -       +      +
   1387E  SER*     4.6     7.0    -      -       -      +
   1391E  ALA*     5.6     5.4    -      -       +      -
   1396E  VAL*     3.7    21.3    -      -       +      +
   1397E  ASP      3.3    25.6    -      -       -      +
   1398E  MET*     4.3     3.6    -      -       +      -
   1399E  PHE*     4.1     6.9    -      -       -      +
----------------------------------------------------------
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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