Contacts of the strand formed by residues 272 - 277 (chain A) in PDB entry 4GDY


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 GLY 272 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  VAL*     3.3     9.7    -      -       -      +
    114A  THR*     2.9    31.2    +      -       -      -
    116A  GLY      3.8    15.9    -      -       -      +
    117A  SER      4.1     1.1    -      -       -      -
    259A  ASP      3.6    11.9    -      -       -      -
    260A  SER*     4.5     3.1    -      -       -      -
    271A  ILE*     1.3    74.3    -      -       -      +
    273A  PHE*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  LEU*     3.7    35.4    -      -       +      -
     90A  LEU*     4.9     7.4    -      -       +      -
     91A  GLN*     3.5    20.4    -      -       -      -
    111A  LEU*     3.7    25.4    -      -       +      -
    112A  CYS      3.2    13.7    -      -       -      +
    113A  VAL*     4.4     0.7    -      -       -      -
    114A  THR*     3.9     3.7    +      -       -      -
    117A  SER*     5.1     1.2    -      -       -      +
    235A  PHE*     5.7     5.6    -      +       -      -
    257A  ARG      3.9     0.5    -      -       -      +
    258A  ALA*     3.6     2.3    -      -       -      +
    259A  ASP*     2.9    73.6    +      -       +      +
    260A  SER      4.9     0.9    -      -       -      -
    261A  PHE*     3.6    36.6    -      +       -      -
    272A  GLY*     1.3    77.8    -      -       -      +
    274A  LEU*     1.3    63.0    +      -       -      +
    275A  THR*     4.3     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  ASP      3.9     0.3    -      -       -      +
    111A  LEU*     3.2     7.7    -      -       -      +
    112A  CYS*     2.9    39.7    +      -       -      -
    114A  THR*     4.7     4.4    +      -       +      +
    117A  SER*     5.0     1.3    -      -       -      +
    120A  GLY*     3.7    26.5    -      -       -      -
    121A  LEU*     4.3     1.6    -      -       +      +
    124A  VAL*     3.6    26.5    -      -       +      -
    256A  ILE*     4.3    11.9    -      -       +      -
    257A  ARG      3.4     5.6    -      -       -      +
    258A  ALA*     3.9    25.4    -      -       +      -
    273A  PHE*     1.3    71.7    -      -       -      +
    275A  THR*     1.3    63.7    +      -       -      +
    281A  ILE*     4.0    17.4    -      -       +      +
    284A  VAL*     3.9    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  GLN*     3.2    26.7    +      -       +      +
    109A  MET*     3.8    25.4    -      -       +      -
    110A  ASP      3.4    10.3    -      -       -      +
    111A  LEU*     3.9    18.0    -      -       +      +
    247A  LEU*     4.3    12.5    -      -       +      +
    255A  VAL      4.0     1.0    -      -       -      +
    256A  ILE*     3.6     2.6    -      -       -      +
    257A  ARG*     2.7    49.1    +      -       -      +
    259A  ASP*     3.9     6.6    +      -       -      -
    273A  PHE*     4.4     2.8    -      -       -      -
    274A  LEU*     1.3    75.5    +      -       -      +
    276A  GLY*     1.3    59.8    +      -       -      +
    281A  ILE*     4.0     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  THR*     6.1     0.2    -      -       -      -
    108A  GLN      3.6     0.7    -      -       -      +
    109A  MET*     3.7     4.7    -      -       -      +
    110A  ASP      2.9    31.8    +      -       -      +
    247A  LEU*     5.5     3.6    -      -       -      -
    255A  VAL      3.6     8.5    -      -       -      -
    256A  ILE*     4.6     2.7    -      -       -      -
    275A  THR*     1.3    77.4    -      -       -      +
    277A  PRO*     1.4    74.0    -      -       -      +
    281A  ILE*     3.5    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  TYR*     3.6    22.0    -      -       +      +
    107A  GLY*     3.7    12.6    -      -       -      +
    108A  GLN      3.5     6.7    -      -       -      +
    250A  ASP*     5.3     0.7    -      -       -      +
    253A  GLY*     3.2    31.6    -      -       -      +
    254A  ARG*     5.2     0.4    -      -       -      -
    255A  VAL      3.6    13.7    -      -       -      +
    256A  ILE*     4.4     5.2    -      -       +      -
    276A  GLY*     1.4    82.0    -      -       -      +
    278A  LYS*     1.4    62.4    +      -       -      +
    279A  PRO*     4.1     2.7    -      -       +      -
    280A  LEU*     3.1    27.0    +      -       +      -
    281A  ILE*     2.9    24.7    +      -       -      +
----------------------------------------------------------
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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