Contacts of the strand formed by residues 133 - 140 (chain B) in PDB entry 3V4V


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 133 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131B  TYR      3.6     4.9    -      -       -      +
    132B  PRO*     1.3    82.2    -      -       -      +
    134B  ASP*     1.3    81.6    +      -       -      +
    135B  LEU*     4.1     7.2    -      -       +      +
    163B  LEU*     5.1     8.1    -      -       +      -
    167B  THR*     4.3     7.6    +      -       +      -
    169B  SER      3.5     5.9    +      -       -      -
    170B  VAL*     3.4    31.0    -      -       +      +
    171B  ARG      3.5     5.9    +      -       -      -
    259B  ARG*     3.3     7.5    +      -       -      +
    261B  VAL*     3.6     0.8    -      -       -      +
    262B  SER*     3.6    10.3    -      -       -      +
    264B  LEU*     4.4    17.3    -      -       +      -
    367B  TYR*     3.2    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL*     1.3    73.3    -      -       -      +
    135B  LEU*     1.3    60.2    +      -       -      +
    171B  ARG*     3.5    12.9    +      -       -      +
    216B  LEU*     3.3    26.7    -      -       +      +
    257B  GLY      3.7     1.6    -      -       -      +
    258B  TRP*     3.5    11.8    -      -       +      -
    259B  ARG*     2.6    71.3    +      -       -      +
    261B  VAL*     3.8     4.3    -      -       +      +
    262B  SER      3.2     9.8    +      -       -      +
    263B  ARG*     4.8     1.6    -      -       +      -
    264B  LEU*     2.9    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL*     4.0    10.4    -      -       +      -
    134B  ASP*     1.3    71.4    -      -       -      +
    136B  TYR*     1.3    66.7    +      -       -      +
    137B  TYR*     4.0     3.5    +      -       +      +
    159B  LEU*     3.7    29.8    -      -       +      -
    163B  LEU*     4.3    16.4    -      -       +      -
    170B  VAL*     5.8     0.2    -      -       +      -
    171B  ARG      3.2     8.1    +      -       -      +
    172B  ILE*     3.2    15.9    -      -       +      +
    173B  GLY      2.9    24.6    +      -       -      +
    216B  LEU*     3.2     3.2    -      -       -      +
    264B  LEU*     3.5    28.7    -      -       +      -
    266B  VAL*     3.5    26.2    -      -       +      +
    363B  ILE*     4.1    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  ASP      4.0     0.2    +      -       -      -
    135B  LEU*     1.3    74.2    -      -       -      +
    137B  TYR*     1.3    64.2    +      -       -      +
    138B  LEU*     3.4    26.0    +      -       +      -
    173B  GLY*     3.8    13.7    -      -       -      -
    174B  PHE      3.1    21.3    +      -       -      -
    175B  GLY*     3.3    12.0    -      -       -      -
    210B  PHE*     3.9     3.3    -      +       -      -
    212B  HIS*     2.6    46.0    +      +       -      +
    214B  LEU      4.2     0.7    -      -       -      -
    216B  LEU*     4.2     4.7    -      -       +      -
    249B  ALA*     4.6     5.2    -      -       +      -
    256B  ILE*     3.6    32.4    -      -       +      +
    258B  TRP*     3.6    23.6    -      +       +      -
    264B  LEU      3.3     8.2    +      -       -      +
    265B  LEU*     3.5    19.7    -      -       +      +
    266B  VAL      2.9    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  LEU*     4.0     5.8    +      -       +      +
    136B  TYR*     1.3    70.5    -      -       -      +
    138B  LEU*     1.3    58.8    +      -       -      +
    139B  MET*     3.4    34.1    -      -       +      +
    152B  VAL*     3.7    28.0    -      -       +      +
    159B  LEU*     5.7     6.3    -      -       +      -
    173B  GLY      3.0    15.4    +      -       -      +
    174B  PHE*     3.4    29.3    -      +       +      -
    175B  GLY      2.9    26.2    +      -       -      +
    223B  PHE*     5.0     8.3    -      +       +      -
    266B  VAL*     3.7    22.7    -      -       +      -
    268B  THR*     3.2    34.2    +      -       +      +
    356B  SER*     4.7     5.7    +      -       -      -
    359B  VAL*     4.1    19.5    -      -       +      +
    363B  ILE*     4.7     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136B  TYR*     3.4    13.1    +      -       +      -
    137B  TYR*     1.3    71.2    -      -       -      +
    139B  MET*     1.3    59.8    +      -       -      +
    175B  GLY      3.3    23.1    -      -       -      +
    176B  SER      4.1     0.4    -      -       -      +
    177B  PHE*     4.0    14.6    -      -       +      -
    210B  PHE*     3.6    24.5    -      -       +      -
    245B  ALA*     3.7    23.1    -      -       +      +
    246B  ILE*     3.8    29.8    -      -       +      +
    249B  ALA*     4.8     4.3    -      -       +      -
    265B  LEU*     3.8    20.6    -      -       +      -
    266B  VAL      2.8    13.3    +      -       -      +
    267B  PHE*     3.6     6.6    -      -       +      -
    268B  THR*     3.1    25.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  TYR*     3.4    26.2    +      -       +      +
    138B  LEU*     1.3    71.8    -      -       -      +
    140B  ASP*     1.3    72.4    +      -       -      +
    141B  LEU*     3.5     7.0    +      -       +      +
    145B  MET*     4.0    11.7    -      -       +      +
    148B  ASP*     3.6    33.2    -      -       +      +
    149B  LEU*     3.7    38.8    -      -       +      +
    152B  VAL*     4.2    11.7    -      -       +      -
    174B  PHE*     3.8    18.2    -      -       +      -
    175B  GLY      2.7    10.3    +      -       -      -
    176B  SER*     3.2     5.9    -      -       -      -
    177B  PHE*     3.1    28.6    +      -       -      -
    268B  THR*     3.4    13.2    -      -       -      +
    356B  SER*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  MET*     1.3    72.2    -      -       -      +
    141B  LEU*     1.3    64.8    +      -       -      +
    142B  SER*     2.3    28.3    +      -       -      -
    145B  MET*     3.1    42.1    -      -       +      +
    177B  PHE*     3.1    35.5    -      -       +      +
    240B  GLU*     3.1    25.5    -      -       -      +
    268B  THR      3.2    23.3    +      -       -      +
    269B  SER*     4.0     8.7    -      -       -      +
    270B  ASP*     4.1     4.9    -      -       -      +
----------------------------------------------------------
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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