Contacts of the strand formed by residues 434 - 442 (chain D) in PDB entry 7C97


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 ILE 434 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1270C  PHE*     4.5    20.4    -      -       +      -
   1274C  GLU*     4.6    11.7    -      -       +      +
   1277C  ALA*     4.5    16.8    -      -       +      -
   1278C  LEU*     4.5    14.8    -      -       +      -
   1281C  TYR*     2.6    32.8    +      -       +      -
    422D  LEU*     4.7     9.4    -      -       +      -
    423D  LEU      3.8     4.0    -      -       -      +
    424D  ASN*     3.4    35.9    -      -       +      +
    428D  THR*     4.6     2.4    -      -       +      +
    431D  ARG      3.7     2.7    +      -       -      +
    433D  GLY*     1.3    78.3    -      -       -      +
    435D  GLN*     1.3    63.1    +      -       -      +
    469D  HIS*     5.4     3.4    -      -       +      -
    484D  MET*     3.5    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 435 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1281C  TYR*     4.4     4.7    -      -       -      +
    422D  LEU*     4.7     2.2    -      -       -      -
    423D  LEU      3.3    26.9    +      -       -      +
    432D  LEU*     3.2    26.5    +      -       -      +
    434D  ILE*     1.3    83.6    -      -       -      +
    436D  ALA*     1.3    68.8    +      -       -      +
    437D  PHE*     3.9     2.9    -      -       +      -
    453D  VAL*     3.6    24.1    -      -       -      +
    456D  ALA*     3.7    12.1    -      -       -      +
    457D  TYR*     3.4    18.8    +      -       -      +
    484D  MET*     3.8     8.5    -      -       -      +
    486D  SER*     3.1    32.5    +      -       -      +
    489D  ASN*     4.4    18.9    +      -       -      +
    499D  ILE*     6.3     0.2    -      -       -      +
    500D  ILE*     5.9     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 436 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420D  PRO*     4.3     4.5    -      -       +      -
    421D  VAL      3.0    14.4    -      -       -      +
    422D  LEU*     3.5    16.9    -      -       +      +
    435D  GLN*     1.3    74.8    -      -       -      +
    437D  PHE*     1.3    76.1    +      -       -      +
    480D  ALA*     3.2    30.7    -      -       +      +
    484D  MET*     3.2    17.4    +      -       +      +
    485D  MET*     4.4     5.4    -      -       -      -
    486D  SER*     3.6    14.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 437 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363D  LEU      3.9    11.0    -      -       -      -
    364D  HIS      4.1     1.8    -      -       -      -
    365D  GLN      4.0    20.2    -      -       -      -
    366D  CYS*     3.9    24.7    -      -       +      +
    420D  PRO*     3.3     4.5    -      -       -      +
    421D  VAL*     2.9    33.1    +      -       +      +
    423D  LEU*     3.6    27.8    -      -       +      -
    435D  GLN*     3.9     5.8    -      -       +      -
    436D  ALA*     1.3    83.2    -      -       -      +
    438D  GLU*     1.3    64.9    +      -       -      +
    439D  PRO*     3.5     1.8    -      -       -      +
    449D  LEU*     4.3     9.6    -      -       +      -
    450D  HIS*     5.8     3.4    -      -       +      -
    453D  VAL*     4.0    20.2    -      -       +      -
    457D  TYR*     3.3    27.8    -      +       -      -
    485D  MET*     4.8     4.0    -      -       -      -
    486D  SER*     3.3    32.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 438 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364D  HIS*     3.2    30.1    +      -       -      +
    365D  GLN*     3.0    29.6    -      -       +      +
    366D  CYS      3.4     0.6    +      -       -      -
    417D  ARG      4.6     3.6    -      -       -      +
    418D  GLU*     3.6    21.5    -      -       -      +
    419D  HIS      5.9     0.4    -      -       -      +
    420D  PRO*     4.6     9.2    -      -       +      -
    437D  PHE*     1.3    74.1    -      -       -      +
    439D  PRO*     1.3    70.3    -      -       +      +
    481D  ARG*     2.8    38.8    +      -       -      +
    485D  MET*     3.7    21.8    -      -       +      +
      3E  ARG      3.6     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 439 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365D  GLN*     5.5     0.7    -      -       -      +
    366D  CYS*     3.2    11.7    -      -       -      +
    368D  LEU*     4.1    27.1    -      -       +      -
    377D  PHE*     5.1     0.7    -      -       +      -
    416D  ILE*     3.2    40.7    -      -       +      +
    419D  HIS      3.4    24.7    -      -       -      +
    421D  VAL*     4.3    18.4    -      -       +      -
    437D  PHE      3.5     6.2    -      -       -      +
    438D  GLU*     1.3    90.8    -      -       +      +
    440D  VAL*     1.3    61.0    +      -       -      +
    441D  LEU*     5.4     1.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 440 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360D  TYR*     5.3     2.5    -      -       +      +
    361D  LEU*     4.3    19.3    -      -       +      -
    365D  GLN*     5.0    14.4    -      -       +      +
    366D  CYS      3.1    17.2    +      -       -      +
    367D  GLY*     3.5     8.9    -      -       -      +
    368D  LEU      3.2    17.7    +      -       -      -
    438D  GLU      4.9     0.7    -      -       -      +
    439D  PRO*     1.3    74.9    -      -       -      +
    441D  LEU*     1.3    74.5    +      -       -      +
    442D  ILE*     3.2     8.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 441 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  THR*     5.8     2.3    -      -       -      +
    368D  LEU*     3.5    15.3    -      -       +      +
    369D  PRO      4.6     3.1    -      -       -      +
    370D  LYS*     4.0    29.1    +      -       +      +
    373D  ALA*     3.6    31.4    -      -       +      -
    412D  LEU*     4.9    11.9    -      -       +      +
    413D  ASP*     4.8    17.0    -      -       +      +
    416D  ILE*     4.4    29.6    -      -       +      -
    439D  PRO*     5.4     0.7    -      -       +      +
    440D  VAL*     1.3    82.4    -      -       -      +
    442D  ILE*     1.3    61.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 442 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  THR*     5.8     4.0    -      -       -      -
    360D  TYR*     3.6    24.5    -      -       -      +
    367D  GLY*     4.5     5.2    -      -       -      -
    368D  LEU      3.4    22.2    +      -       -      +
    369D  PRO*     3.7     4.7    -      -       +      +
    370D  LYS*     3.2    31.4    +      -       -      +
    440D  VAL*     3.2    14.4    +      -       +      +
    441D  LEU*     1.3    78.8    -      -       -      +
    443D  GLU*     1.3    71.3    +      -       -      +
    444D  GLY*     5.4     1.1    -      -       -      +
    446D  ALA      3.6    25.1    -      -       -      +
    448D  GLN*     3.6    25.1    -      -       +      +
----------------------------------------------------------
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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