Contacts of the strand formed by residues 1967 - 1972 (chain A) in PDB entry 2V5P


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 GLN1967 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1827A  VAL*     3.6    12.7    -      -       -      +
   1828A  THR      5.3     2.4    +      -       -      +
   1829A  ARG*     6.5     0.2    -      -       -      -
   1965A  ARG*     4.2    24.7    -      -       +      +
   1966A  PRO*     1.3    89.2    -      -       -      +
   1968A  VAL*     1.3    64.9    +      -       -      +
   1969A  PHE      3.2     0.2    +      -       -      -
   1979A  PHE*     3.4     7.8    -      -       -      -
   1980A  GLU*     2.8    43.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1968 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1827A  VAL*     3.7    12.9    -      -       +      +
   1829A  ARG*     3.0    60.9    +      -       +      +
   1834A  TYR*     4.2    11.0    -      -       +      -
   1967A  GLN*     1.3    74.0    +      -       -      +
   1969A  PHE*     1.3    60.7    +      -       -      +
   1970A  SER      4.3     4.5    -      -       -      +
   1971A  GLU*     3.8    30.7    -      -       +      -
   1977A  VAL*     4.4    10.3    -      -       +      -
   1979A  PHE*     3.6    24.2    -      -       +      -
   1980A  GLU*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE1969 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1829A  ARG*     4.2     7.8    +      -       -      -
   1954A  ILE*     4.5    13.0    -      -       +      -
   1967A  GLN      3.2     1.6    +      -       -      -
   1968A  VAL*     1.3    74.4    -      -       -      +
   1970A  SER*     1.3    78.7    -      -       -      +
   1978A  THR*     2.9    27.5    +      -       +      +
   1979A  PHE      4.3     0.7    -      -       -      -
   1980A  GLU*     4.0    40.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER1970 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1829A  ARG*     5.3     1.1    -      -       -      +
   1968A  VAL*     3.8     1.9    -      -       -      +
   1969A  PHE*     1.3    92.4    -      -       -      +
   1971A  GLU*     1.3    63.8    +      -       -      +
   1972A  VAL*     4.0    12.7    +      -       -      +
   1976A  ASP*     3.8     2.1    +      -       -      +
   1977A  VAL*     3.4     4.3    -      -       -      +
   1978A  THR*     2.9    52.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU1971 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1829A  ARG*     4.1    21.4    +      -       -      +
   1832A  ARG*     2.8    43.2    +      -       -      +
   1834A  TYR*     2.6    35.9    +      -       -      +
   1968A  VAL*     3.8    23.7    -      -       +      +
   1970A  SER*     1.3    72.5    -      -       -      +
   1972A  VAL*     1.3    63.0    +      -       -      +
   1973A  ARG      4.0     2.0    +      -       -      -
   1974A  GLY*     4.9     4.7    -      -       -      +
   1976A  ASP      3.6     4.7    -      -       -      +
   1977A  VAL*     4.0     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1972 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1970A  SER*     4.9    12.1    -      -       -      +
   1971A  GLU*     1.3    76.2    -      -       -      +
   1973A  ARG*     1.3    86.0    +      -       +      +
   1974A  GLY      2.7    15.9    +      -       -      +
   1975A  CYS*     2.8    16.7    +      -       +      +
   1976A  ASP*     2.8    35.0    +      -       +      +
----------------------------------------------------------
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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