Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 2VM8


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 ASP 134 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  THR      3.9     9.1    +      -       -      +
    103A  MET*     3.4    10.5    -      -       +      -
    104A  ILE      3.4    18.0    +      -       -      -
    133A  CYS*     1.3    80.1    -      -       -      +
    135A  TYR*     1.3    61.5    +      -       -      +
    398A  LYS*     2.9    27.5    +      -       -      +
    408A  ASP*     4.4     2.0    -      -       -      +
    448A  SER*     4.6     3.2    +      -       -      +
    449A  GLN*     3.9    13.9    +      -       -      +
    466A  GLY*     3.9     0.2    -      -       -      -
    467A  ARG*     3.0    56.9    +      -       -      +
    469A  ILE*     3.8    17.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE*     4.9     0.4    -      +       -      -
    103A  MET*     3.9     5.6    -      -       -      +
    104A  ILE*     3.1    31.2    -      -       +      +
    124A  ARG*     2.7    23.9    +      -       -      -
    127A  ALA*     3.7    30.3    -      -       +      -
    128A  ASP*     2.6    26.8    +      -       -      -
    131A  SER*     4.2    14.8    -      -       -      +
    133A  CYS      4.0     3.6    -      -       -      +
    134A  ASP*     1.3    78.2    -      -       -      +
    136A  SER*     1.3    67.2    +      -       -      +
    137A  LEU*     3.8    25.1    -      -       +      -
    466A  GLY      4.4     3.4    -      -       -      -
    467A  ARG      2.9    25.7    +      -       -      +
    468A  TYR*     3.4    28.1    -      +       -      -
    469A  ILE*     2.6    33.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  MET*     3.6    17.2    -      -       -      +
    104A  ILE      3.0     5.5    +      -       -      +
    105A  ILE*     3.1    15.1    -      -       -      -
    106A  ASP      2.8    28.4    +      -       -      -
    135A  TYR*     1.3    78.8    -      -       -      +
    137A  LEU*     1.3    65.5    +      -       -      +
    468A  TYR*     4.0     9.7    +      -       -      -
    469A  ILE      2.6    24.1    +      -       -      -
    471A  ARG*     3.2    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE*     4.7     2.5    -      -       +      -
    105A  ILE*     4.2     0.9    -      -       -      -
    106A  ASP*     3.3    32.5    -      -       +      +
    108A  VAL*     4.0    23.1    -      -       +      -
    120A  PHE*     4.1    10.3    -      -       +      -
    123A  TRP*     4.0    26.0    -      -       +      +
    124A  ARG*     3.6    37.0    -      -       +      +
    135A  TYR*     3.8    17.0    -      -       +      -
    136A  SER*     1.3    83.2    +      -       -      +
    138A  HIS*     1.3    61.9    +      -       -      +
    139A  VAL*     4.0     0.5    +      -       -      +
    161A  VAL*     4.2    12.5    -      -       -      +
    468A  TYR*     4.0     8.3    +      -       +      -
    471A  ARG*     2.8    21.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL      2.9    23.3    +      -       -      -
    105A  ILE*     3.0    29.5    -      -       +      +
    106A  ASP      2.7    14.1    +      -       -      +
    107A  HIS*     3.2    42.7    -      +       +      +
    108A  VAL*     2.8    27.7    +      -       -      +
    137A  LEU*     1.3    76.5    -      -       -      +
    139A  VAL*     1.3    61.7    +      -       -      +
    140A  ASP*     4.8     0.4    -      -       -      +
    163A  SER*     2.7    32.8    +      -       -      +
    196A  GLN*     3.8    17.5    +      -       -      +
    392A  PHE*     3.8    28.3    -      +       -      -
    471A  ARG*     4.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     3.8    29.8    -      -       +      +
    110A  PRO*     4.5     3.6    -      -       +      -
    116A  LEU*     4.6    13.7    -      -       +      +
    120A  PHE*     4.2    17.5    -      -       +      -
    137A  LEU      4.6     0.7    -      -       -      +
    138A  HIS*     1.3    76.4    -      -       -      +
    140A  ASP*     1.3    76.6    +      -       -      +
    141A  ILE*     5.3     0.2    -      -       +      -
    155A  LEU*     4.5    17.7    -      -       +      -
    161A  VAL*     4.4    13.9    -      -       +      -
    163A  SER      3.1     9.5    +      -       -      -
    164A  PHE*     3.0    28.0    -      -       +      +
    165A  LEU      3.0    20.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  ARG*     2.8    24.5    +      -       -      -
    107A  HIS*     2.8    26.2    +      -       -      +
    108A  VAL      2.9    18.3    +      -       -      +
    109A  VAL*     4.0    11.5    -      -       +      +
    110A  PRO*     3.1    25.7    -      -       -      +
    116A  LEU*     4.6     0.3    -      -       -      +
    139A  VAL*     1.3    80.4    -      -       -      +
    141A  ILE*     1.3    60.1    +      -       -      +
    142A  SER*     6.5     0.2    -      -       -      -
    165A  LEU*     3.6    18.4    -      -       -      +
    167A  TYR*     2.5    36.0    +      -       +      +
----------------------------------------------------------
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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