Contacts of the strand formed by residues 31 - 38 (chain C) in PDB entry 2V10


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 GLN 31 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  GLY*     3.5     4.2    -      -       -      -
     26C  ILE      3.0    27.3    +      -       -      +
     29C  PRO      4.1    10.7    +      -       -      +
     30C  PRO*     1.4    72.2    -      -       -      +
     32C  THR*     1.3    65.4    +      -       -      +
     33C  PHE*     3.4    24.3    +      -       +      -
     62C  LYS*     5.0     5.6    -      -       -      +
     63C  LEU      3.8     4.0    -      -       -      +
     64C  PHE*     3.2    21.3    -      -       +      -
     65C  ASP*     2.9    48.7    +      -       -      +
     68C  ASP*     4.1    20.6    +      -       -      +
     69C  SER*     4.3     4.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  GLU*     4.3    27.1    -      -       +      +
     24C  ILE      3.8     8.4    +      -       -      +
     25C  GLY*     4.4     5.2    -      -       -      -
     30C  PRO*     4.1     9.0    +      -       -      +
     31C  GLN*     1.3    76.2    +      -       -      +
     33C  PHE*     1.3    63.0    +      -       -      +
     34C  LYS*     5.9     0.2    -      -       -      +
     62C  LYS*     3.3    29.3    -      -       -      +
    125C  ASP*     4.7     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 33 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  GLU*     3.5     4.0    -      -       -      +
     24C  ILE*     2.9    36.1    +      -       +      +
     26C  ILE*     3.6    30.3    -      -       +      -
     31C  GLN*     3.4    33.7    -      -       +      -
     32C  THR*     1.3    81.7    -      -       -      +
     34C  LYS*     1.3    61.9    -      -       -      +
     35C  VAL*     4.4     7.0    -      -       +      -
     46C  VAL*     4.3    24.7    -      -       +      -
     62C  LYS*     3.5    46.0    -      -       +      -
     63C  LEU      3.7     7.0    -      -       -      -
     64C  PHE*     3.5    28.5    -      +       +      -
    125C  ASP*     3.8    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 34 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  TYR*     3.5    38.1    -      -       +      -
     22C  GLY      3.4     5.8    -      -       -      -
     23C  GLU*     3.6    21.4    +      -       -      +
     33C  PHE*     1.3    69.1    -      -       -      +
     35C  VAL*     1.3    71.1    +      -       -      +
    123C  GLU*     3.7    22.9    -      -       -      +
    124C  PHE*     4.2     1.3    -      -       -      -
    125C  ASP*     3.0    40.1    +      -       -      +
    126C  GLY      3.3     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 35 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  TYR*     3.0     8.8    -      -       -      +
     22C  GLY      2.6    48.2    +      -       -      +
     24C  ILE*     4.0    33.0    -      -       +      -
     33C  PHE*     4.2     7.2    -      -       +      +
     34C  LYS*     1.3    90.4    -      -       -      +
     36C  VAL*     1.4    61.8    -      -       -      +
     37C  PHE*     3.6    29.6    -      -       +      -
     46C  VAL*     4.8     4.7    -      -       +      -
    124C  PHE*     4.4     1.3    -      -       -      -
    126C  GLY*     3.6    22.7    -      -       -      +
    127C  VAL      4.4     2.0    -      -       -      +
    128C  VAL*     4.2     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 36 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  TYR      3.9     9.6    -      -       -      +
     21C  TYR*     4.7     0.7    -      -       +      -
     35C  VAL*     1.4    70.7    -      -       -      +
     37C  PHE*     1.3    64.2    +      -       -      +
     38C  ASP*     3.3     4.2    +      -       +      +
    124C  PHE*     3.2    51.8    -      -       +      -
    126C  GLY      3.5     3.2    +      -       -      -
    127C  VAL*     3.8    11.5    -      -       +      +
    128C  VAL*     3.1    23.9    +      -       -      +
    162C  TYR*     5.2     0.2    -      -       -      +
    227C  THR      4.5     0.4    -      -       -      +
    228C  GLY*     3.7    18.8    -      -       -      +
   1341C  C61      3.5    41.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 37 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  VAL*     4.2    21.5    -      -       +      -
     12C  LEU*     3.9    13.2    -      -       +      -
     20C  TYR      4.6     2.6    +      -       -      -
     21C  TYR      5.1     0.2    -      -       -      -
     22C  GLY*     3.7    26.5    -      -       -      -
     24C  ILE*     3.8    18.8    -      -       +      -
     35C  VAL*     3.6    21.1    -      -       +      -
     36C  VAL*     1.3    72.9    -      -       -      +
     38C  ASP*     1.3    51.1    +      -       -      +
     99C  VAL*     4.4    10.3    -      -       +      -
    128C  VAL*     3.4    34.1    -      -       +      -
    130C  MET*     4.1    13.9    -      -       +      -
    160C  PHE*     3.4    15.1    -      -       +      -
    162C  TYR*     4.2     2.0    +      -       -      -
    176C  ILE*     3.5    32.8    -      -       +      -
    227C  THR*     2.4    28.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 38 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  VAL*     3.3     4.6    +      -       +      +
     37C  PHE*     1.3    73.0    -      -       -      +
     39C  THR*     1.3    61.8    +      -       -      +
     40C  GLY      2.9    17.1    +      -       -      -
     41C  SER*     2.4    31.7    +      -       -      +
     83C  TYR*     4.4     0.3    -      -       -      -
    127C  VAL*     4.7     8.8    -      -       +      +
    128C  VAL      3.0    14.3    +      -       -      +
    129C  GLY*     3.4     3.8    -      -       -      -
    130C  MET*     2.8    21.7    +      -       -      -
    226C  ASP*     3.0     8.5    -      -       -      +
    227C  THR*     3.3     2.5    -      -       -      -
    228C  GLY*     3.3    14.5    -      -       -      +
   1341C  C61      3.0    33.6    +      -       -      +
----------------------------------------------------------
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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