Contacts of the strand formed by residues 332 - 339 (chain A) in PDB entry 6N8P


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 332 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  GLN*     3.8    31.4    +      -       -      +
    313A  HIS*     3.9    18.7    +      -       +      +
    314A  CYS      4.9     0.4    -      -       -      +
    315A  ILE*     3.7    26.7    -      -       +      -
    328A  PHE*     3.6    35.9    -      -       +      -
    331A  ARG*     1.3    73.9    -      -       -      +
    333A  ILE*     1.3    61.9    +      -       -      +
    334A  GLY      3.3    23.1    +      -       -      +
    335A  PHE*     4.5     0.2    -      -       +      -
    355A  VAL*     3.9     7.4    -      -       +      -
    356A  LEU      4.3     2.2    -      -       -      -
    357A  ALA*     4.5     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  PRO*     3.2    47.8    -      -       +      +
     36A  SER*     4.3    15.9    -      -       -      +
     37A  ALA*     4.3     1.6    -      -       -      -
     38A  LEU*     4.3    14.6    +      -       -      +
     52A  ARG*     5.1     5.6    -      -       -      +
    331A  ARG*     4.4    12.1    -      -       +      -
    332A  VAL*     1.3    74.8    -      -       -      +
    334A  GLY*     1.3    56.2    +      -       -      +
    356A  LEU*     3.2    22.7    +      -       +      +
    357A  ALA      3.8     3.4    -      -       -      +
    358A  GLU*     3.6    37.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     3.6    16.6    -      -       -      -
    285A  ARG*     5.7     0.4    -      -       -      -
    301A  GLN*     5.8     0.6    +      -       -      -
    332A  VAL*     3.3    10.8    +      -       -      +
    333A  ILE*     1.3    79.4    -      -       -      +
    335A  PHE*     1.3    66.6    +      -       -      +
    356A  LEU      3.0    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     3.6     8.0    -      -       -      +
    285A  ARG*     2.5    66.7    +      -       +      +
    287A  LEU*     3.9    22.2    -      -       +      -
    299A  ILE*     4.1    19.7    -      -       +      -
    301A  GLN*     3.4    43.5    -      -       +      -
    315A  ILE*     3.6    26.7    -      -       +      -
    332A  VAL*     4.5     0.9    -      -       +      -
    334A  GLY*     1.3    78.3    -      -       -      +
    336A  THR*     1.3    63.3    +      -       -      +
    337A  VAL*     4.8     2.2    -      -       +      -
    353A  LEU*     3.8    17.5    -      -       +      -
    354A  VAL      3.2    13.7    -      -       -      +
    355A  VAL*     3.8     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     4.6     8.1    -      -       +      -
     40A  TYR*     4.5    25.9    -      -       +      +
     47A  LEU*     5.2     1.1    -      -       +      -
    285A  ARG*     4.7     7.3    +      -       -      +
    287A  LEU*     5.8     1.1    -      -       -      -
    335A  PHE*     1.3    77.8    -      -       -      +
    337A  VAL*     1.3    75.0    +      -       -      +
    338A  LEU*     4.0    15.3    -      -       +      -
    353A  LEU*     3.3     7.2    -      -       -      +
    354A  VAL*     2.8    53.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  TYR*     5.5     1.6    -      -       -      -
    287A  LEU*     3.8    22.2    -      -       +      +
    289A  LEU*     3.6    26.7    -      -       +      -
    299A  ILE*     3.6    24.5    -      -       +      -
    335A  PHE*     4.8     2.5    -      -       +      -
    336A  THR*     1.3    86.0    +      -       -      +
    338A  LEU*     1.3    64.8    +      -       -      +
    339A  THR*     3.5     9.6    +      -       +      +
    350A  PRO*     3.6    18.4    -      -       +      -
    352A  ALA      3.2    14.8    -      -       -      +
    353A  LEU*     3.8    13.5    -      -       +      -
    366A  LEU*     3.8     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  TYR*     3.4    45.8    -      -       +      +
    336A  THR*     4.0     9.6    -      -       +      -
    337A  VAL*     1.3    73.8    -      -       -      +
    339A  THR*     1.3    59.8    +      -       -      +
    350A  PRO*     3.3     3.5    -      -       -      +
    351A  TYR*     3.0    43.8    +      -       +      +
    352A  ALA*     2.8    21.4    +      -       +      +
    354A  VAL*     3.7    24.9    -      -       +      -
    421A  PRO*     3.6    39.0    -      -       +      -
    422A  ILE*     4.5    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  TYR*     5.9     0.2    -      -       -      -
     42A  PRO*     5.9     5.2    -      -       -      +
    240A  ARG*     5.6     0.7    +      -       -      -
    289A  LEU*     4.4    12.3    -      -       +      -
    337A  VAL      3.5    11.4    +      -       -      +
    338A  LEU*     1.3    77.9    -      -       -      +
    340A  GLU*     1.3    59.5    +      -       -      +
    341A  ALA*     3.0    22.4    +      -       -      +
    348A  ASP*     3.4    33.4    +      -       +      +
    349A  ASP      3.7     4.5    -      -       -      -
    350A  PRO*     4.0    16.6    -      -       +      -
    351A  TYR*     3.6     8.9    +      -       -      -
----------------------------------------------------------
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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