Contacts of the strand formed by residues 332 - 336 (chain A) in PDB entry 3I8E


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 332 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  GLU      4.6     0.8    +      -       -      -
    308A  THR*     3.2    22.6    -      -       -      +
    309A  SER*     2.9    45.3    +      -       -      +
    323A  PHE*     3.6     5.5    -      -       -      -
    324A  VAL*     2.8    41.2    +      -       +      +
    330A  ASP      4.3     0.7    -      -       -      +
    331A  SER*     1.3    79.2    -      -       -      +
    333A  LEU*     1.3    58.4    +      -       -      +
    334A  VAL*     3.8    18.9    -      -       +      +
    349A  ALA*     4.6     9.2    -      -       -      +
    351A  GLU      3.2    15.5    -      -       -      +
    352A  THR*     4.0    13.6    +      -       -      +
    353A  PHE*     3.5    11.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLU*     4.9     4.0    -      -       -      +
     48A  GLY*     4.0    26.7    -      -       -      -
     49A  LEU*     3.9    22.9    -      -       +      +
    317A  LEU*     3.9    11.2    -      -       +      -
    321A  VAL*     3.9    17.0    -      -       +      -
    322A  VAL      3.6     1.1    -      -       -      +
    323A  PHE*     3.7    39.0    -      -       +      -
    332A  GLN*     1.3    72.4    -      -       -      +
    334A  VAL*     1.3    65.0    +      -       -      +
    349A  ALA*     4.0     0.3    -      -       -      -
    350A  MET*     3.0    34.1    +      -       +      -
    351A  GLU*     2.8    25.8    +      -       +      +
    353A  PHE*     3.6    10.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  LEU*     4.9     4.3    -      -       +      -
    307A  GLU      5.2     0.4    -      -       -      +
    308A  THR*     4.8     8.1    -      -       +      -
    320A  GLY      3.3     2.1    -      -       -      +
    321A  VAL      3.4     0.9    -      -       -      -
    322A  VAL*     2.5    57.2    +      -       +      +
    324A  VAL*     4.5     5.6    -      -       +      -
    332A  GLN*     3.8    31.4    -      -       +      +
    333A  LEU*     1.3    81.0    -      -       -      +
    335A  LYS*     1.3    64.4    +      -       -      +
    336A  LEU*     4.9     0.9    -      -       +      -
    347A  VAL*     3.6    32.1    -      -       +      -
    348A  VAL      3.8     1.6    -      -       -      +
    349A  ALA*     4.0    15.0    -      -       +      -
    350A  MET*     4.1     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  ASN*     3.3    27.9    +      -       -      +
    320A  GLY*     3.7     5.4    -      -       -      -
    321A  VAL*     4.0     3.4    -      -       +      +
    334A  VAL*     1.3    73.9    -      -       -      +
    336A  LEU*     1.3    73.3    +      -       -      +
    337A  ASN*     3.4    28.2    +      -       -      +
    346A  TYR      3.5     1.4    -      -       -      +
    347A  VAL*     3.5     5.9    -      -       -      -
    348A  VAL*     2.9    45.5    +      -       +      +
    350A  MET*     3.9    21.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  VAL*     5.8     2.2    -      -       +      -
    272A  LEU*     4.1    10.3    -      -       +      -
    280A  LEU*     3.7    25.4    -      -       +      -
    282A  MET*     3.9    28.5    -      -       +      -
    305A  LEU*     3.8    17.7    -      -       +      -
    316A  TYR*     5.3     6.1    -      -       +      -
    320A  GLY*     3.0    33.0    +      -       -      +
    322A  VAL*     4.1    14.1    -      -       +      -
    334A  VAL*     4.9     2.2    -      -       +      -
    335A  LYS*     1.3    77.1    -      -       -      +
    337A  ASN*     1.3    67.4    +      -       -      +
    338A  VAL*     5.6     0.7    -      -       -      +
    346A  TYR*     3.6     3.6    -      -       +      +
    347A  VAL*     3.8    15.9    -      -       +      -
----------------------------------------------------------
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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