Contacts of the strand formed by residues 473 - 480 (chain A) in PDB entry 1GZD


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 THR 473 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ASP      4.6     1.9    -      -       -      +
     56A  LYS*     3.2    33.8    +      -       -      +
     57A  ASN*     3.6    11.6    -      -       -      +
    402A  PRO*     5.5     0.4    -      -       -      -
    403A  CYS*     3.3    22.7    -      -       +      +
    405A  PHE*     4.4     6.1    -      -       +      -
    432A  THR*     3.6    26.0    +      -       +      +
    435A  LEU*     3.9    30.3    -      -       +      -
    471A  ARG      4.0     6.1    +      -       -      +
    472A  PRO*     1.3    85.9    -      -       -      +
    474A  ASN*     1.3    67.1    +      -       -      +
    475A  SER*     5.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  LEU*     4.6     3.1    -      -       +      -
     53A  ASP      3.7     4.9    -      -       -      +
     54A  TYR*     3.7    16.5    -      -       -      +
     57A  ASN*     2.8    32.2    +      -       -      +
    319A  LEU*     3.7    19.6    -      -       -      +
    322A  LEU*     3.8    11.0    -      -       -      +
    335A  HIS*     5.1     2.4    -      -       -      -
    403A  CYS      2.8     8.2    +      -       -      +
    404A  ASP*     2.7    25.6    -      -       -      +
    405A  PHE*     2.9    27.8    +      -       -      +
    473A  THR*     1.3    76.5    -      -       -      +
    475A  SER*     1.3    61.7    +      -       -      +
    476A  ILE*     4.0    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  LEU      3.5     1.7    -      -       -      +
     53A  ASP*     2.9    50.7    +      -       -      +
     56A  LYS*     4.7     6.3    +      -       -      -
    405A  PHE*     3.4     4.4    -      -       -      +
    428A  PHE*     3.7    23.9    -      -       -      -
    432A  THR*     4.0    20.6    +      -       -      +
    473A  THR*     5.3     0.5    +      -       -      -
    474A  ASN*     1.3    73.8    +      -       -      +
    476A  ILE*     1.3    63.1    +      -       -      +
    477A  VAL*     4.0     6.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     4.0    24.7    -      -       +      -
     51A  LEU      3.2     3.4    -      -       -      +
     52A  LEU*     3.9    21.3    -      -       +      -
    319A  LEU*     5.1     4.7    -      -       +      -
    404A  ASP*     4.3     9.4    -      -       +      -
    405A  PHE      2.8    17.4    +      -       -      +
    406A  LEU*     3.3    13.1    -      -       +      -
    407A  ILE      3.2    22.7    +      -       -      -
    428A  PHE*     4.5     0.2    -      -       -      -
    474A  ASN*     4.0    19.3    -      -       +      -
    475A  SER*     1.3    78.2    -      -       -      +
    477A  VAL*     1.3    61.9    +      -       -      +
    478A  PHE*     3.7    14.5    -      -       +      -
    489A  LEU*     4.3    11.9    -      -       +      -
    492A  MET*     4.5     9.6    -      -       +      -
    493A  TYR*     4.0    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ARG      3.9     0.7    -      -       -      +
     50A  ILE*     3.6     0.4    -      -       -      -
     51A  LEU*     2.7    53.6    +      -       +      +
     53A  ASP*     6.3     0.4    -      -       +      -
    407A  ILE*     3.6    14.8    -      -       +      +
    409A  VAL*     3.6    27.4    -      -       +      -
    425A  LEU*     5.9     2.2    -      -       +      -
    428A  PHE*     3.9    26.2    -      -       +      -
    475A  SER*     4.5     6.7    -      -       -      +
    476A  ILE*     1.3    79.0    -      -       -      +
    478A  PHE*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ARG      2.9    13.9    -      -       -      +
     50A  ILE*     4.0    12.8    -      -       +      -
    344A  LEU*     4.6     7.4    -      -       +      -
    406A  LEU*     4.1    11.9    -      -       +      -
    407A  ILE*     3.3    30.1    +      -       -      -
    408A  PRO*     3.3    27.5    -      -       +      +
    409A  VAL*     3.0    24.0    +      -       -      +
    476A  ILE*     3.7    20.2    -      -       +      -
    477A  VAL*     1.3    77.7    -      -       -      +
    479A  THR*     1.3    66.9    +      -       -      +
    480A  LYS      4.1     7.2    -      -       -      -
    481A  LEU*     3.7    22.9    -      -       +      -
    485A  ILE*     3.9    21.8    -      -       +      -
    489A  LEU*     3.7    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLY*     3.7    12.8    -      -       -      -
     49A  ARG*     2.9    39.4    +      -       -      +
    409A  VAL*     3.3     9.2    +      -       +      +
    410A  GLN*     2.9    51.8    +      -       -      +
    478A  PHE*     1.3    73.3    -      -       -      +
    480A  LYS*     1.3    65.0    +      -       +      +
    485A  ILE*     5.6     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 480 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  TYR*     4.8     3.6    +      -       -      -
    408A  PRO*     4.1     2.7    -      -       -      -
    410A  GLN*     3.6    39.7    -      -       +      +
    411A  THR      4.6     9.4    -      -       -      -
    412A  GLN*     3.9    28.9    +      -       -      +
    478A  PHE*     3.5     5.7    -      -       -      -
    479A  THR*     1.3    85.0    -      -       +      +
    481A  LEU*     1.3    61.7    +      -       -      +
    482A  THR*     3.3    26.7    +      -       +      +
    485A  ILE*     3.6    22.5    -      -       -      +
----------------------------------------------------------
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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