Contacts of the strand formed by residues 263 - 265 (chain F) in PDB entry 4IGM


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 TYR 263 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219F  LYS*     5.1    16.9    +      -       +      +
    220F  VAL      2.7    20.5    +      -       -      +
    221F  CYS*     3.1     8.7    -      -       +      -
    222F  PHE*     2.9    24.4    +      -       -      -
    261F  SER      6.0     0.2    -      -       -      -
    262F  PHE*     1.3    79.6    -      -       -      +
    264F  THR*     1.3    68.8    +      -       -      +
    284F  ASP      3.5    18.9    +      -       -      -
    285F  LYS*     3.1    46.7    -      -       +      +
    287F  ILE*     3.7    27.8    -      -       +      -
    323F  ASN      3.7    15.7    -      -       -      -
    326F  ALA*     3.9    18.6    -      -       +      +
    327F  PHE*     3.9    24.3    +      +       +      -
----------------------------------------------------------
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Residues in contact with THR 264 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203F  ILE*     5.1     0.4    -      -       +      -
    221F  CYS*     3.6     6.1    -      -       -      -
    222F  PHE*     3.3    13.0    -      -       +      +
    225F  GLY      3.9    14.1    -      -       -      +
    226F  GLY*     3.9    21.1    -      -       -      +
    262F  PHE*     4.1    20.9    -      -       +      -
    263F  TYR*     1.3    79.5    -      -       -      +
    265F  ASP*     1.3    62.6    +      -       -      +
    277F  LEU*     3.4    22.7    -      -       -      +
    281F  ILE*     3.9    18.1    -      -       +      +
    285F  LYS      3.1     3.7    +      -       -      +
    286F  VAL*     3.4     4.9    -      -       -      +
    287F  ILE*     2.9    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 265 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  ILE*     3.9    21.1    -      -       +      -
      6F  HIS*     3.0    26.4    +      -       -      -
    172F  PHE*     4.1     4.5    -      -       +      -
    221F  CYS*     3.7     2.1    -      -       -      -
    222F  PHE      2.9    10.7    +      -       -      +
    223F  ALA*     3.3     5.3    -      -       -      -
    224F  HIS*     2.9    32.8    +      -       -      -
    225F  GLY*     2.9    24.1    +      -       -      -
    264F  THR*     1.3    75.0    -      -       -      +
    266F  ALA*     1.3    57.4    +      -       -      +
    267F  LEU*     3.0    16.2    +      -       -      +
    277F  LEU*     3.7     2.8    -      -       -      +
    286F  VAL*     4.5     0.4    -      -       -      -
    287F  ILE      3.0    11.2    -      -       -      +
    289F  GLY*     4.5     4.7    -      -       -      -
----------------------------------------------------------
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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