Contacts of the strand formed by residues 476 - 480 (chain A) in PDB entry 3I7H


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 VAL 476 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469A  ILE*     4.3    17.0    -      -       +      -
    470A  GLN      4.0     4.9    -      -       -      -
    471A  ILE*     4.0    24.2    -      -       +      +
    475A  SER*     1.3    68.2    -      -       -      +
    477A  ARG*     1.3    59.7    +      -       -      +
    489A  GLU*     3.9     0.9    -      -       -      -
    490A  TRP*     3.0    58.4    +      -       +      +
    498A  ILE*     3.8    13.1    -      -       +      +
    508A  VAL*     4.9     6.1    -      -       +      -
    510A  VAL*     4.8     7.2    -      -       +      -
    519A  LEU*     3.7    14.4    -      -       +      -
    526A  LEU*     3.8    25.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450A  GLY*     2.7    38.4    +      -       -      -
    451A  PHE      4.1     0.2    -      -       -      -
    452A  VAL*     3.1    41.3    -      -       -      +
    468A  LEU      5.3     0.2    -      -       -      -
    469A  ILE*     3.5     6.9    -      -       -      +
    470A  GLN*     2.7    63.0    +      -       +      +
    472A  THR*     4.3     1.6    -      -       -      -
    475A  SER*     3.1    24.2    -      -       -      +
    476A  VAL*     1.3    72.9    -      -       -      +
    478A  LEU*     1.3    72.9    +      -       -      +
    479A  VAL*     5.1     0.9    -      -       +      +
    486A  LEU*     4.1    15.8    -      -       +      +
    488A  SER      4.0     4.3    -      -       -      -
    489A  GLU*     3.1    32.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463A  VAL*     5.3     4.7    -      -       +      -
    467A  GLN*     3.5    28.0    -      -       +      +
    468A  LEU      4.4     3.4    -      -       -      +
    469A  ILE*     5.3     1.8    -      -       +      -
    476A  VAL*     4.8     1.6    -      -       +      -
    477A  ARG*     1.3    85.9    -      -       -      +
    479A  VAL*     1.3    63.2    +      -       -      +
    480A  SER      4.3     0.2    -      -       -      -
    486A  LEU*     3.1    27.2    -      -       -      +
    487A  VAL*     3.1    23.6    +      -       +      -
    488A  SER*     3.2    19.9    +      -       -      +
    521A  ILE*     3.6    28.9    -      -       +      -
    525A  GLU*     4.5     9.0    -      -       -      +
    526A  LEU*     3.4    43.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     5.6     1.6    -      -       +      -
    449A  MET      3.4    16.8    -      -       -      +
    450A  GLY*     3.0    38.1    -      -       -      +
    451A  PHE*     4.7    11.0    -      -       +      -
    467A  GLN*     4.5     2.0    -      -       -      +
    468A  LEU*     2.7    60.3    +      -       +      +
    477A  ARG*     5.1     1.1    -      -       +      +
    478A  LEU*     1.3    81.2    -      -       -      +
    480A  SER*     1.3    71.1    +      -       -      +
    484A  LYS*     4.8     4.5    -      -       +      -
    485A  ALA      3.3     7.6    -      -       -      +
    486A  LEU*     4.0    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 480 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465A  HIS      4.6     1.6    -      -       -      -
    466A  GLN      3.2    13.0    -      -       -      -
    467A  GLN*     3.7    17.8    -      -       -      +
    468A  LEU*     4.6     0.2    -      -       -      +
    478A  LEU      4.3     0.4    -      -       -      -
    479A  VAL*     1.3    83.3    -      -       -      +
    481A  GLN*     1.3    60.0    +      -       -      +
    483A  PRO*     3.0    35.8    -      -       -      +
    484A  LYS*     3.0    21.7    -      -       -      +
    485A  ALA      3.0    12.1    +      -       -      -
    487A  VAL*     3.3    19.8    -      -       -      +
----------------------------------------------------------
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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