Contacts of the strand formed by residues 156 - 161 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  HIS      4.9     5.7    -      -       -      +
    154A  LYS*     3.3    19.5    +      -       +      +
    155A  PRO*     1.3    78.4    -      -       -      +
    157A  VAL*     1.3    65.3    +      -       -      +
    158A  ARG*     4.1    23.3    -      -       +      +
    168A  VAL*     3.5    31.4    -      -       +      -
    169A  VAL      3.3     8.3    -      -       -      +
    170A  PRO*     4.5     5.8    -      -       +      -
    171A  ALA*     4.0     1.8    -      -       -      +
    218A  THR*     3.7     2.6    -      -       -      +
    219A  GLY*     3.0    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  ILE*     1.3    82.1    -      -       -      +
    158A  ARG*     1.3    66.7    +      -       -      +
    159A  VAL*     3.9     4.6    +      -       +      -
    168A  VAL*     3.4     4.0    -      -       -      -
    169A  VAL*     2.8    42.5    +      -       +      +
    171A  ALA*     4.0     9.0    -      -       +      -
    214A  ILE*     3.7    23.8    -      -       +      -
    217A  LEU*     3.5    25.8    -      -       +      +
    220A  GLU      3.6    16.2    -      -       -      +
    222A  LEU*     3.6    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  ILE*     4.1    17.8    -      -       +      +
    157A  VAL*     1.3    73.3    -      -       -      +
    159A  VAL*     1.3    61.7    +      -       -      +
    160A  PHE*     4.2    12.6    -      -       +      -
    167A  THR      3.8     5.2    -      -       -      +
    168A  VAL*     4.6    11.0    -      -       +      +
    219A  GLY      3.8    17.8    +      -       -      -
    220A  GLU*     3.3    10.4    +      -       -      +
    221A  GLU*     2.9    49.1    +      -       +      +
    222A  LEU      2.9    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  VAL*     4.0    21.3    -      -       +      +
    158A  ARG*     1.3    80.7    -      -       -      +
    160A  PHE*     1.3    68.4    +      -       -      +
    161A  LEU*     3.8    18.7    +      -       +      +
    166A  ARG*     3.3     5.8    -      -       -      +
    167A  THR*     2.7    46.8    +      -       +      +
    169A  VAL*     4.2     9.0    -      -       +      -
    181A  LEU*     3.7    42.6    -      -       +      -
    222A  LEU*     3.6    13.5    -      -       +      +
    224A  VAL*     4.0     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  ARG*     4.8    13.9    -      -       +      -
    159A  VAL*     1.3    78.2    -      -       -      +
    161A  LEU*     1.3    62.0    +      -       -      +
    165A  GLN      3.7     4.5    -      -       -      +
    166A  ARG*     4.1    37.2    -      -       +      -
    221A  GLU*     3.5    37.7    -      -       +      -
    222A  LEU      2.9    13.8    +      -       -      +
    223A  HIS*     3.5    36.4    -      +       -      +
    224A  VAL*     2.9    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  VAL*     3.8    26.9    -      -       +      +
    160A  PHE*     1.3    77.3    -      -       -      +
    162A  PRO*     1.3    79.7    -      -       +      +
    163A  ASN      3.6     0.3    +      -       -      -
    164A  LYS*     3.6     3.5    +      -       -      -
    165A  GLN*     2.7    30.5    +      -       +      +
    166A  ARG      4.0     6.5    -      -       -      -
    167A  THR*     3.9    20.6    -      -       +      -
    181A  LEU*     4.9     2.0    -      -       +      -
    184A  ALA*     4.4     3.1    -      -       +      +
    185A  LEU*     3.9    26.0    -      -       +      -
    188A  ARG*     3.4    45.3    -      -       -      +
    224A  VAL*     4.1    10.3    -      -       +      -
----------------------------------------------------------
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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