Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 1VQ4


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 161 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26700    G      3.9     8.5    -      -       -      +
   26710    U      3.2    40.1    +      -       -      +
     23B  THR*     4.3     2.8    +      -       -      +
     25B  ARG*     3.0    17.0    +      -       -      -
    109B  LEU*     4.7     2.9    -      -       +      -
    112B  THR*     4.3    17.9    -      -       +      +
    113B  LEU*     4.4    16.4    -      -       +      -
    143B  ILE*     3.7    24.2    -      -       +      -
    144B  THR      3.1    10.5    -      -       -      +
    145B  HIS*     3.9    14.1    -      -       +      +
    159B  PRO      3.8     8.9    +      -       -      +
    160B  ASP*     1.3    74.3    -      -       -      +
    162B  MET*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26710    U      3.9     2.2    -      -       -      -
     23B  THR*     3.4    10.5    -      -       +      -
     25B  ARG*     3.3    17.0    -      -       -      +
     42B  ALA*     4.1     9.9    -      -       +      -
     79B  MET*     5.0     6.3    -      -       -      +
    143B  ILE*     4.9     0.2    -      -       -      -
    144B  THR*     2.6    43.1    +      -       -      +
    146B  THR*     4.9     4.0    -      -       -      -
    160B  ASP      4.0    13.7    -      -       -      +
    161B  VAL*     1.3    78.0    -      -       -      +
    163B  GLU*     1.3    60.1    +      -       -      +
    164B  THR*     3.7     3.3    +      -       -      +
    308B  LEU*     3.2    42.2    -      -       +      -
    310B  ARG*     3.1    50.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26710    U      2.7    18.0    +      -       -      +
   26720    C      2.8    25.5    +      -       -      +
     29B  TRP*     3.8     9.8    -      -       -      -
     85B  ARG*     2.6    40.0    +      -       -      -
     87B  TYR*     2.4    28.1    +      -       -      -
    141B  ARG*     3.1    36.5    +      -       +      +
    142B  LEU      3.5    10.8    -      -       -      +
    143B  ILE*     3.7    10.2    -      -       +      +
    162B  MET*     1.3    70.7    -      -       -      +
    164B  THR*     1.3    61.6    +      -       -      +
    165B  ARG      4.3     0.2    -      -       -      -
    310B  ARG*     3.4    18.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  TRP*     3.8     7.9    -      -       +      -
     38B  VAL*     3.5    21.2    -      -       +      +
     39B  GLN      3.6     7.2    -      -       -      +
     40B  GLY*     3.5    38.5    -      -       -      +
     41B  PHE*     5.0     0.5    +      -       -      -
     79B  MET*     5.5     3.2    -      -       -      +
    141B  ARG*     3.8     3.1    -      -       -      -
    142B  LEU*     2.8    42.6    +      -       -      +
    144B  THR*     4.7     8.7    +      -       -      +
    162B  MET*     3.7     6.3    +      -       -      +
    163B  GLU*     1.3    71.3    -      -       -      +
    165B  ARG*     1.3    63.2    +      -       -      +
    166B  VAL*     4.3     1.0    -      -       -      +
    310B  ARG*     3.1    19.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  TRP*     3.5    50.0    -      -       +      -
     30B  PRO      3.9     7.9    +      -       -      -
     32B  ASP*     2.6    37.6    +      -       -      -
     38B  VAL*     3.7     1.2    -      -       -      -
     39B  GLN*     2.6    71.5    +      -       -      +
    139B  ASP*     3.0    43.6    +      -       -      +
    140B  LEU      3.9     4.5    -      -       -      +
    141B  ARG*     3.5    12.8    -      -       +      +
    164B  THR*     1.3    77.3    -      -       -      +
    166B  VAL*     1.3    62.7    +      -       -      +
    167B  GLY*     3.6     4.4    -      -       -      -
    174B  ARG*     4.2     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  GLY*     3.5    25.8    -      -       -      +
     38B  VAL*     4.1     7.6    -      -       +      +
    140B  LEU*     3.0    24.8    +      -       +      +
    141B  ARG*     4.5     0.7    -      -       -      -
    142B  LEU*     3.6    40.6    -      -       +      -
    164B  THR      4.3     1.8    -      -       -      +
    165B  ARG*     1.3    87.1    +      -       -      +
    167B  GLY*     1.3    62.2    +      -       -      +
    174B  ARG*     3.2    33.9    +      -       +      +
    177B  HIS*     4.3    13.2    -      -       +      -
    178B  ALA*     4.9     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  SER      5.4     0.2    -      -       -      -
     32B  ASP*     3.4    17.5    -      -       -      -
     35B  GLN      3.8     0.7    -      -       -      +
     36B  PRO*     3.4     1.2    -      -       -      +
     37B  GLY      2.9    32.1    +      -       -      +
     39B  GLN*     3.8    14.6    +      -       -      -
    165B  ARG*     3.6     6.5    -      -       -      -
    166B  VAL*     1.3    77.2    -      -       -      +
    168B  GLY*     1.3    62.5    +      -       -      -
    174B  ARG*     3.6     6.1    -      -       -      -
----------------------------------------------------------
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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