Contacts of the strand formed by residues 259 - 262 (chain V) in PDB entry 3EXG


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 LEU 259 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208V  THR*     3.5    20.4    -      -       +      +
    210V  VAL*     3.8    22.7    -      -       +      -
    249V  ILE*     4.5     1.6    -      -       +      -
    253V  VAL*     3.8    14.8    -      -       +      -
    258V  HIS*     1.3    77.6    -      -       -      +
    260V  VAL*     1.3    85.7    +      -       -      +
    261V  THR*     4.5     5.2    -      -       +      -
    275V  ILE*     4.5    15.7    -      -       +      +
    276V  CYS*     5.5     0.2    -      -       -      -
    279V  ILE*     3.6    32.1    -      -       +      -
    288V  LEU*     4.2     9.8    -      -       +      +
    291V  PRO      4.2     2.2    +      -       -      +
    292V  ALA*     3.3    25.8    -      -       +      +
    293V  VAL      3.2    20.4    +      -       -      -
    326V  THR*     4.7     3.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 260 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207V  ILE*     3.7    22.2    -      -       +      -
    208V  THR      2.8    11.3    +      -       -      +
    209V  VAL*     3.3     7.8    -      -       +      +
    210V  VAL      2.9    23.2    +      -       -      -
    259V  LEU*     1.3    80.2    -      -       -      +
    261V  THR*     1.3    74.0    +      -       -      +
    262V  VAL*     4.5     8.1    -      -       +      -
    293V  VAL*     3.4    30.3    -      -       +      +
    295V  VAL*     4.3    13.0    -      -       +      -
    319V  ILE*     5.5     1.3    -      -       +      -
    322V  ALA*     4.6     4.9    -      -       +      +
    323V  ILE*     4.5    17.3    -      -       +      -
    326V  THR*     4.1     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 261 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210V  VAL*     3.4    11.2    -      -       +      -
    259V  LEU*     4.5     9.2    -      -       +      -
    260V  VAL*     1.3    77.7    -      -       -      +
    262V  VAL*     1.3    63.7    +      -       -      +
    263V  GLU*     4.1     1.3    -      -       -      -
    272V  GLY*     3.8    12.2    -      -       -      +
    275V  ILE*     3.8    41.7    -      -       +      -
    276V  CYS*     4.9     4.7    -      -       -      -
    292V  ALA*     6.3     0.4    -      -       +      -
    293V  VAL      3.0     7.4    +      -       -      +
    294V  ARG*     3.4    27.4    -      -       -      +
    295V  VAL*     2.8    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 262 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209V  VAL*     4.1     9.0    -      -       +      -
    210V  VAL      2.7     9.9    +      -       -      -
    211V  SER*     2.7    37.9    +      -       -      +
    212V  HIS*     3.9     1.4    +      -       -      -
    215V  PRO*     4.0    19.7    -      -       +      +
    219V  CYS*     3.7    21.1    -      -       -      -
    238V  MET*     5.3     0.4    -      -       -      +
    260V  VAL*     4.5     3.8    -      -       +      -
    261V  THR*     1.3    80.1    -      -       -      +
    263V  GLU*     1.3    62.3    +      -       -      +
    295V  VAL*     3.3    19.7    -      -       +      +
    314V  PRO*     4.3     5.8    -      -       +      -
    319V  ILE*     3.8    38.4    -      -       +      -
----------------------------------------------------------
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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