Contacts of the strand formed by residues 1362 - 1369 (chain F) in PDB entry 5YWB


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 LEU1362 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1350F  LEU*     4.3    18.8    -      -       +      -
   1351F  SER*     2.7    28.3    +      -       -      -
   1352F  VAL*     3.4    30.7    -      -       +      +
   1360F  PRO*     3.8     8.5    -      -       -      +
   1361F  VAL*     1.3    82.9    -      -       -      +
   1363F  LYS*     1.3    62.1    +      -       -      +
   1365F  VAL*     3.7    25.8    -      -       +      -
   1383F  SER      4.5     5.6    -      -       -      +
   1384F  GLY      4.5     2.0    -      -       -      +
   1387F  SER*     4.0    16.4    -      -       -      +
   1388F  PHE*     4.5    21.1    -      -       +      -
   1391F  ALA*     5.5     0.7    -      -       +      -
   1552F  LEU*     4.1    19.3    -      -       +      -
   1555F  GLY      3.7    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS1363 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1350F  LEU      4.1     1.1    +      -       -      -
   1351F  SER*     4.5     7.2    -      -       -      +
   1360F  PRO*     5.4    13.2    -      -       +      -
   1362F  LEU*     1.3    80.8    -      -       -      +
   1364F  HIS*     1.3   105.1    +      -       +      +
   1365F  VAL*     3.4     2.0    +      -       -      +
   1555F  GLY*     3.5    16.5    +      -       -      +
   1556F  ALA*     3.9    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS1364 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1349F  ASN*     4.1    30.0    +      -       -      +
   1350F  LEU      3.5     6.2    +      -       -      -
   1351F  SER*     5.0     1.4    -      -       -      -
   1363F  LYS*     1.3   111.9    -      -       +      +
   1365F  VAL*     1.3    63.3    +      -       -      +
   1366F  ASN*     3.7     5.2    +      -       -      +
   1556F  ALA*     4.8     7.4    -      -       +      +
   1557F  ILE      5.6     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1365 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347F  ILE*     3.7     7.0    -      -       +      +
   1348F  GLN      3.6     1.2    -      -       -      -
   1349F  ASN      2.8    15.1    +      -       -      -
   1350F  LEU*     2.8    60.8    +      -       +      +
   1362F  LEU*     3.7    37.2    -      -       +      -
   1363F  LYS      4.2     4.9    -      -       -      +
   1364F  HIS*     1.3    76.5    -      -       -      +
   1366F  ASN*     1.3    60.4    +      -       -      +
   1367F  ALA*     5.1     1.3    -      -       +      +
   1388F  PHE*     4.6    11.4    -      -       +      -
   1555F  GLY      4.8     1.3    -      -       -      +
   1556F  ALA*     5.4     0.2    -      -       -      -
   1557F  ILE*     3.6    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN1366 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1347F  ILE      3.2     9.4    -      -       -      +
   1348F  GLN*     4.3    15.6    -      -       -      +
   1349F  ASN*     4.4     4.3    -      -       -      +
   1364F  HIS      3.7     6.4    +      -       -      +
   1365F  VAL*     1.3    76.4    -      -       -      +
   1367F  ALA*     1.3    70.0    +      -       -      +
   1368F  LEU*     5.9     1.7    -      -       -      +
   1557F  ILE*     5.1     6.9    -      -       -      +
   1559F  GLU*     4.7     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1367 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1346F  GLN*     3.4     3.4    -      -       -      +
   1347F  ILE*     2.9    44.8    +      -       +      +
   1365F  VAL*     5.3     2.5    -      -       +      -
   1366F  ASN*     1.3    81.7    +      -       -      +
   1368F  LEU*     1.3    61.5    +      -       -      +
   1369F  ILE*     5.7     1.6    -      -       +      -
   1388F  PHE*     5.5     1.6    -      -       +      -
   1550F  MET*     4.0    21.3    -      -       +      -
   1557F  ILE*     5.2     7.0    -      -       +      -
   1559F  GLU*     3.1    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1368 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1345F  ILE      3.5     9.6    -      -       -      +
   1346F  GLN*     4.2    11.7    -      -       +      +
   1366F  ASN*     5.9     1.8    -      -       -      +
   1367F  ALA*     1.3    75.1    -      -       -      +
   1369F  ILE*     1.3    72.2    +      -       -      +
   1370F  SER*     4.5    15.5    -      -       -      +
   1548F  LEU*     4.4    12.4    -      -       +      +
   1559F  GLU*     3.3    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1369 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1343F  GLY      4.2     2.0    -      -       -      +
   1344F  LYS*     3.2     9.6    -      -       -      +
   1345F  ILE*     2.9    64.9    +      -       +      +
   1347F  ILE*     6.6     0.2    -      -       +      -
   1367F  ALA*     5.7     1.6    -      -       +      -
   1368F  LEU*     1.3    84.2    -      -       -      +
   1370F  SER*     1.3    70.7    +      -       -      +
   1375F  ILE*     3.6    54.5    -      -       +      -
   1388F  PHE*     6.0     3.6    -      -       +      -
   1392F  PHE*     6.0     0.9    -      -       +      -
   1532F  THR*     3.8    14.8    -      -       +      -
   1534F  VAL*     4.0     9.6    -      -       +      -
   1548F  LEU*     5.1     1.6    -      -       -      -
   1550F  MET*     4.4    13.7    -      -       +      -
   1559F  GLU*     5.3     0.2    -      -       -      +
----------------------------------------------------------
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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