Contacts of the strand formed by residues 259 - 262 (chain R) 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 R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207R  ILE*     4.6     1.1    -      -       -      -
    208R  THR*     3.3    19.5    -      -       +      +
    210R  VAL*     3.8    25.8    -      -       +      -
    249R  ILE*     4.3     2.2    -      -       +      -
    253R  VAL*     4.0    13.0    -      -       +      -
    258R  HIS*     1.3    79.0    -      -       -      +
    260R  VAL*     1.3    83.2    +      -       -      +
    261R  THR*     4.5     5.8    -      -       +      +
    275R  ILE*     4.2    15.0    -      -       +      +
    276R  CYS*     5.7     0.7    -      -       -      -
    279R  ILE*     3.4    33.7    -      -       +      -
    288R  LEU*     4.4     6.7    -      -       +      +
    290R  ALA      5.3     0.8    +      -       -      -
    291R  PRO      4.3     1.6    -      -       -      +
    292R  ALA*     3.2    43.5    -      -       +      +
    293R  VAL*     3.2     3.6    +      -       -      +
    326R  THR*     4.6     3.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 260 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207R  ILE*     4.0    16.4    -      -       +      -
    208R  THR      2.7    12.4    +      -       -      +
    209R  VAL*     3.1     9.8    -      -       +      +
    210R  VAL      2.8    29.8    +      -       -      -
    259R  LEU*     1.3    79.5    -      -       -      +
    261R  THR*     1.3    61.1    +      -       -      +
    262R  VAL*     4.3     7.2    -      -       +      -
    293R  VAL*     3.5    25.4    -      -       +      +
    295R  VAL*     3.9    26.7    -      -       +      -
    319R  ILE*     5.3     1.3    -      -       +      +
    322R  ALA*     4.4     7.6    -      -       +      +
    323R  ILE*     4.4    15.5    -      -       +      +
    326R  THR*     3.8    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 261 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210R  VAL*     3.4     9.4    -      -       +      +
    259R  LEU*     4.6     9.4    -      -       +      -
    260R  VAL*     1.3    72.1    -      -       -      +
    262R  VAL*     1.3    59.2    +      -       -      +
    263R  GLU*     5.0     2.5    +      -       -      +
    272R  GLY*     3.3    23.3    -      -       -      -
    275R  ILE*     4.0    37.5    -      -       +      -
    276R  CYS*     4.2    19.5    -      -       -      -
    293R  VAL      3.1     7.0    +      -       -      +
    294R  ARG*     3.7    11.3    -      -       -      +
    295R  VAL*     2.7    37.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 262 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209R  VAL*     4.1    12.3    -      -       +      -
    210R  VAL      2.9     7.1    +      -       -      -
    211R  SER*     2.7    46.9    +      -       -      +
    212R  HIS*     4.0     1.9    +      -       -      -
    215R  PRO*     3.9    16.8    -      -       +      -
    219R  CYS*     3.8    23.1    -      -       -      -
    238R  MET*     5.1     0.5    -      -       -      +
    260R  VAL*     4.3     4.7    -      -       +      -
    261R  THR*     1.3    76.9    -      -       -      +
    263R  GLU*     1.3    61.9    +      -       -      +
    295R  VAL*     3.3    16.6    -      -       +      +
    314R  PRO*     4.8     7.0    -      -       +      -
    319R  ILE*     4.1    25.4    -      -       +      -
----------------------------------------------------------
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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