Contacts of the strand formed by residues 156 - 161 (chain D) in PDB entry 3NY5


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 ILE 156 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199C  ARG*     6.2     1.6    -      -       -      +
    151D  HIS*     3.6    21.9    +      -       +      +
    154D  LYS*     3.9    15.7    -      -       +      +
    155D  PRO*     1.3    79.7    -      -       -      +
    157D  VAL*     1.3    66.1    +      -       -      +
    158D  ARG*     4.1    24.0    -      -       +      +
    168D  VAL*     3.5    31.2    -      -       +      -
    169D  VAL      3.2    11.9    -      -       -      +
    170D  PRO*     4.3     5.8    -      -       +      -
    171D  ALA*     4.0     1.8    -      -       -      +
    218D  THR*     3.8     0.5    -      -       -      -
    219D  GLY*     3.1    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156D  ILE*     1.3    79.3    -      -       -      +
    158D  ARG*     1.3    67.8    +      -       -      +
    159D  VAL*     3.8     6.9    +      -       +      +
    168D  VAL*     3.4     4.9    -      -       -      -
    169D  VAL*     2.9    38.7    +      -       +      +
    171D  ALA*     3.9     7.4    -      -       +      -
    214D  ILE*     3.8    23.3    -      -       +      +
    217D  LEU*     3.4    31.0    -      -       +      +
    219D  GLY*     4.8     0.4    -      -       -      +
    220D  GLU      3.6    14.6    -      -       -      +
    222D  LEU*     3.7    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  TRP*     3.7    31.2    -      -       +      -
    156D  ILE*     4.1    17.3    -      -       +      -
    157D  VAL*     1.3    75.1    -      -       -      +
    159D  VAL*     1.3    59.5    +      -       -      +
    160D  PHE*     4.2     1.8    -      -       +      -
    167D  THR      3.9     4.5    -      -       -      -
    168D  VAL*     4.6     6.1    -      -       +      -
    219D  GLY*     3.0    26.6    +      -       -      -
    220D  GLU      3.3    10.3    +      -       -      +
    221D  GLU*     3.3    41.6    +      -       +      +
    222D  LEU      2.8    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 159 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  TRP*     3.9     1.0    -      -       -      -
    157D  VAL*     3.9    21.5    -      -       +      +
    158D  ARG*     1.3    77.6    -      -       -      +
    160D  PHE*     1.3    65.2    +      -       -      +
    161D  LEU*     3.6    19.6    +      -       +      +
    166D  ARG*     3.3     6.3    -      -       -      +
    167D  THR*     2.8    44.9    +      -       +      +
    169D  VAL*     4.3     9.9    -      -       +      -
    181D  LEU*     3.5    37.5    -      -       +      -
    222D  LEU*     3.5    12.6    -      -       +      +
    224D  VAL*     3.7    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 160 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  THR      5.3     2.7    -      -       -      -
    216C  TRP*     3.7    22.7    -      +       -      -
    158D  ARG*     5.0     1.1    -      -       +      -
    159D  VAL*     1.3    75.6    -      -       -      +
    161D  LEU*     1.3    60.1    +      -       -      +
    164D  LYS      6.4     0.7    -      -       -      -
    165D  GLN      3.8     6.3    -      -       -      +
    166D  ARG*     3.9    33.4    -      -       +      -
    221D  GLU*     3.6    38.8    -      -       +      -
    222D  LEU      2.8    18.5    +      -       -      +
    223D  HIS*     3.5    35.6    -      +       +      -
    224D  VAL*     2.8    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 161 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159D  VAL*     3.6    28.3    -      -       +      +
    160D  PHE*     1.3    78.7    -      -       -      +
    162D  PRO*     1.3    81.5    -      -       +      +
    163D  ASN      3.7     0.3    +      -       -      -
    164D  LYS*     3.8     4.2    +      -       -      -
    165D  GLN*     2.6    31.8    +      -       +      +
    166D  ARG      4.0     6.3    -      -       -      -
    167D  THR*     3.7    22.9    -      -       +      -
    181D  LEU*     4.8     4.0    -      -       +      -
    184D  ALA*     4.2     5.2    -      -       +      +
    185D  LEU*     4.3    11.7    -      -       +      -
    188D  ARG*     3.6    40.6    -      -       -      +
    224D  VAL*     3.9    18.6    -      -       +      -
----------------------------------------------------------
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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