Contacts of the strand formed by residues 159 - 163 (chain A) in PDB entry 1V1A


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 ARG 159 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ARG*     3.1    24.3    +      -       -      +
    128A  PHE*     3.2    37.6    -      -       +      +
    129A  LEU      2.6    32.9    +      -       -      -
    157A  GLY      5.1     3.6    -      -       -      +
    158A  VAL*     1.3    72.7    -      -       -      +
    160A  VAL*     1.3    55.8    +      -       -      +
    161A  SER      4.0     0.2    -      -       -      -
    188A  ASP*     3.5    34.9    +      -       +      +
    189A  LEU*     4.9     7.8    -      -       -      +
    214A  PRO*     5.4     5.5    -      -       -      +
    215A  GLU*     3.4    25.7    +      -       -      +
    261A  ALA*     5.9     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PHE*     5.6     0.4    -      -       -      -
    129A  LEU*     3.6     9.0    -      -       +      +
    131A  LEU*     5.6     3.8    -      -       +      -
    150A  MET*     3.4    53.4    -      -       +      +
    153A  ALA*     4.2     7.6    -      -       +      -
    154A  LYS*     4.6     2.9    -      -       +      +
    158A  VAL      4.1     8.1    -      -       -      +
    159A  ARG*     1.3    74.7    -      -       -      +
    161A  SER*     1.3    64.6    +      -       -      +
    162A  LEU*     5.1     1.6    -      -       +      +
    186A  GLY      3.3    24.5    -      -       -      +
    187A  VAL*     3.8    12.5    -      -       +      +
    188A  ASP*     3.1    29.6    +      -       -      +
    189A  LEU*     3.6     5.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PHE*     4.6     5.8    -      -       -      -
    129A  LEU      2.8    12.7    +      -       -      +
    130A  HIS*     3.3    17.6    +      -       -      -
    131A  LEU*     2.8    28.6    +      -       -      +
    159A  ARG      3.9     1.6    +      -       -      -
    160A  VAL*     1.3    73.0    -      -       -      +
    162A  LEU*     1.3    62.6    +      -       -      +
    189A  LEU*     3.7    13.1    -      -       -      +
    191A  PHE*     3.1    30.7    -      -       -      -
    258A  LEU*     4.0    20.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  HIS*     4.6     0.2    -      -       -      -
    131A  LEU*     3.5    12.6    -      -       +      -
    132A  SER      3.7    35.9    -      -       -      +
    133A  GLY*     3.8     4.7    -      -       -      +
    136A  PRO*     5.9     0.4    -      -       +      -
    150A  MET*     5.2     7.0    -      -       +      -
    160A  VAL*     4.0     2.6    +      -       +      -
    161A  SER*     1.3    76.7    +      -       -      +
    163A  ASP*     1.3    64.0    +      -       -      +
    164A  VAL*     4.6     1.8    -      -       -      +
    179A  PHE*     4.8    12.6    -      -       +      -
    180A  LEU*     4.9    12.6    -      -       +      -
    183A  ALA*     4.6    15.3    -      -       +      -
    184A  LEU*     5.9     0.9    -      -       +      -
    187A  VAL*     3.9    33.2    -      -       +      -
    189A  LEU      3.1     7.5    +      -       -      -
    190A  LEU*     3.5    20.8    -      -       +      +
    191A  PHE*     3.1    25.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  HIS*     4.0    19.5    +      -       +      +
    131A  LEU      3.3     7.9    +      -       -      +
    132A  SER*     3.3     5.0    +      -       -      -
    133A  GLY      2.7    20.0    +      -       -      -
    162A  LEU*     1.3    74.8    -      -       -      +
    164A  VAL*     1.3    66.8    +      -       -      +
    165A  ASN*     2.9    40.2    +      -       -      +
    191A  PHE*     3.8    22.8    -      -       +      +
    196A  GLU*     4.6     1.0    -      -       -      +
    219A  LYS*     3.6    23.5    +      -       -      +
    250A  GLY      4.3     7.4    -      -       -      +
    251A  ASP*     4.1     6.6    -      -       -      +
    254A  ALA*     4.5     5.1    -      -       +      +
----------------------------------------------------------
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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