Contacts of the strand formed by residues 641 - 645 (chain D) in PDB entry 4G7Z


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 GLN 641 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637D  LEU*     3.2    24.9    -      -       +      +
    638D  LYS*     2.7    36.5    +      -       -      +
    639D  LEU      3.2     0.4    -      -       -      +
    640D  HIS*     1.3   113.2    +      -       +      +
    642D  CYS*     1.3    62.2    +      -       -      +
    716D  PHE*     3.0    17.3    -      -       -      -
    717D  GLN*     3.1    22.1    +      -       -      +
    719D  VAL*     4.0    17.7    -      -       +      +
    729D  HIS*     4.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 642 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637D  LEU*     3.6     8.3    -      -       -      -
    641D  GLN*     1.3    79.7    -      -       -      +
    643D  GLY*     1.3    61.5    +      -       -      +
    644D  LEU*     5.4     2.5    -      -       -      -
    700D  VAL*     4.8     9.6    -      -       -      -
    702D  LEU*     4.3    21.1    -      -       +      -
    716D  PHE*     3.5    31.4    -      -       +      -
    717D  GLN      3.1     5.8    +      -       -      -
    718D  PRO*     3.5    12.3    -      -       -      +
    719D  VAL*     2.7    33.2    +      -       -      -
    726D  ILE*     5.5     1.1    -      -       -      -
    727D  GLN      3.4    14.6    -      -       -      +
    728D  LEU*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 643 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637D  LEU*     3.3     8.1    -      -       -      +
    642D  CYS*     1.3    72.5    -      -       -      +
    644D  LEU*     1.3    59.9    +      -       -      -
    719D  VAL*     3.5     7.9    -      -       -      -
    721D  VAL*     3.9     7.6    -      -       -      -
    726D  ILE*     3.2    15.4    -      -       -      +
    727D  GLN*     2.8    53.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 644 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642D  CYS*     3.6     3.7    +      -       -      +
    643D  GLY*     1.3    73.2    -      -       -      +
    645D  PRO*     1.3    80.6    -      -       +      +
    648D  MET*     3.9    30.5    -      -       +      -
    649D  ALA*     3.7    24.7    -      -       +      +
    652D  LEU*     4.6     8.1    -      -       +      -
    653D  PHE*     4.5    12.3    -      -       +      -
    700D  VAL*     4.9     7.6    -      -       +      -
    718D  PRO*     3.9    29.2    -      -       +      -
    719D  VAL      3.0    10.1    +      -       -      +
    720D  LEU*     3.3     9.6    -      -       +      +
    721D  VAL*     2.8    25.0    +      -       -      +
    726D  ILE*     5.1     2.2    -      -       +      -
    747D  VAL*     4.6    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 645 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1005C  MET*     4.6     1.3    -      -       -      -
    643D  GLY      3.8     2.2    -      -       -      +
    644D  LEU*     1.3    95.9    -      -       +      +
    646D  LYS*     1.3    65.7    -      -       -      +
    647D  ARG*     4.3     4.5    -      -       -      +
    648D  MET*     3.4    21.1    +      -       +      +
    649D  ALA*     3.2    17.2    +      -       -      +
    721D  VAL*     3.4     9.4    -      -       +      +
    723D  GLY      3.2    15.5    -      -       -      +
    724D  GLN*     3.4    10.1    -      -       -      +
    725D  SER      3.1    46.2    -      -       -      +
    726D  ILE*     4.1     6.7    -      -       +      +
----------------------------------------------------------
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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