Contacts of the strand formed by residues 159 - 167 (chain I) in PDB entry 6A3V


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 GLY 159 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191G  GLU*     3.4    23.5    +      -       -      -
    158I  SER*     1.3    78.8    -      -       -      +
    160I  SER*     1.3    62.0    +      -       -      -
    184I  ASP*     3.6     4.2    -      -       -      +
    185I  LEU*     2.8    38.1    +      -       -      +
    219I  GLU      3.3    10.5    -      -       -      -
    220I  ALA*     4.0     2.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 160 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192G  ALA      5.0     5.0    +      -       -      -
    193G  ARG*     3.5    25.8    +      -       -      -
    159I  GLY*     1.3    74.2    +      -       -      -
    161I  VAL*     1.3    62.7    +      -       -      +
    162I  SER*     4.9     3.8    -      -       -      -
    182I  THR*     4.1    17.1    -      -       -      +
    183I  VAL      3.5     5.6    -      -       -      -
    217I  HIS      5.0     0.2    -      -       -      -
    218I  THR*     3.1     6.1    +      -       -      -
    219I  GLU*     2.7    47.9    +      -       -      +
    220I  ALA*     4.9     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 161 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102I  LEU*     4.0    10.1    -      -       +      -
    147I  LEU*     3.8    25.9    -      -       +      +
    149I  LEU*     3.7    30.1    -      -       +      -
    160I  SER*     1.3    76.3    -      -       -      +
    162I  SER*     1.3    62.5    +      -       -      +
    182I  THR*     3.7     0.9    -      -       -      -
    183I  VAL      3.0    32.9    +      -       -      +
    185I  LEU*     3.8    16.8    -      -       +      -
    216I  LEU*     3.8    29.8    -      -       +      -
    217I  HIS      4.0     2.5    -      -       -      -
    218I  THR*     3.5    15.3    -      -       -      +
    228I  LEU*     4.8     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 162 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160I  SER*     4.9     4.2    -      -       -      -
    161I  VAL*     1.3    75.4    +      -       -      +
    163I  LEU*     1.3    62.3    +      -       -      +
    164I  ALA*     5.6     1.1    -      -       -      -
    181I  LEU      3.2    10.3    -      -       -      -
    182I  THR*     3.9    17.5    +      -       -      +
    215I  HIS      3.9     0.5    -      -       -      +
    216I  LEU*     3.4     9.5    -      -       -      +
    217I  HIS*     2.8    53.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 163 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107I  LEU*     3.7    27.8    -      -       +      -
    109I  TRP*     6.0     2.2    -      -       +      -
    145I  PHE*     3.6    31.9    -      -       +      -
    146I  GLN      4.0    11.0    -      -       -      +
    147I  LEU*     3.7    39.9    -      -       +      -
    161I  VAL      4.1     1.0    +      -       -      -
    162I  SER*     1.3    77.1    -      -       -      +
    164I  ALA*     1.3    61.6    +      -       -      +
    180I  ALA*     3.2     3.8    -      -       -      +
    181I  LEU*     2.7    46.0    +      -       +      +
    214I  VAL*     3.8    15.0    -      -       +      -
    215I  HIS      4.0     0.4    -      -       -      +
    216I  LEU*     4.2    14.6    -      -       +      -
    233I  THR*     4.5     5.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 164 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145I  PHE*     4.0     4.7    -      -       -      -
    162I  SER*     5.6     1.1    -      -       -      -
    163I  LEU*     1.3    77.0    -      -       -      +
    165I  LEU*     1.3    59.2    +      -       -      +
    166I  HIS*     3.6    27.6    +      -       +      +
    177I  ALA*     4.7     6.5    -      -       +      -
    179I  LEU      3.3     7.0    -      -       -      +
    180I  ALA*     5.0     3.8    -      -       +      -
    214I  VAL*     3.3     5.5    -      -       -      +
    215I  HIS*     3.0    38.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 165 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143I  VAL*     4.0    11.4    -      -       +      -
    145I  PHE*     3.5    33.4    -      -       +      -
    164I  ALA*     1.3    70.9    -      -       -      +
    166I  HIS*     1.3    61.8    -      -       -      +
    167I  LEU*     4.0    26.7    -      -       +      -
    177I  ALA*     4.0     1.3    -      -       -      -
    178I  ALA*     3.1    37.0    +      -       +      +
    179I  LEU*     2.6    21.9    +      -       +      +
    204I  LEU*     4.5     6.5    -      -       +      -
    212I  LEU*     4.0    18.6    -      -       +      -
    213I  GLY      3.3    12.6    -      -       -      +
    214I  VAL*     4.2     6.5    -      -       +      -
    235I  LEU*     3.8    18.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 166 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164I  ALA*     3.6    26.6    +      -       +      +
    165I  LEU*     1.3    74.5    -      -       -      +
    167I  LEU*     1.3    65.2    +      -       -      +
    168I  GLN*     3.6    13.9    +      -       -      +
    177I  ALA*     3.9    29.5    -      -       +      +
    178I  ALA      5.0     1.3    -      -       -      +
    212I  LEU*     4.0     1.9    -      -       -      -
    213I  GLY*     3.1    31.5    +      -       -      +
    215I  HIS*     3.3    32.8    +      +       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 167 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60H  ARG*     5.7     3.1    -      -       -      +
    165I  LEU*     4.0    12.3    +      -       +      -
    166I  HIS*     1.3    72.1    -      -       -      +
    168I  GLN*     1.3    66.9    +      -       -      +
    169I  PRO      3.5     7.8    -      -       -      +
    178I  ALA*     4.5    19.4    -      -       +      +
    204I  LEU*     5.7     2.2    -      -       +      -
    205I  HIS      4.6     7.9    -      -       -      +
    206I  LEU*     3.9    17.5    -      -       +      -
    210I  GLN*     3.6    27.6    -      -       +      +
    211I  ARG      3.6     1.3    -      -       -      +
    212I  LEU*     3.7    36.1    -      -       +      -
----------------------------------------------------------
 Back to top of page


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