Contacts of the strand formed by residues 872 - 875 (chain A) in PDB entry 3I7L


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 SER 872 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    723A  LYS*     6.1     2.7    -      -       -      -
    815A  SER*     3.5    12.8    -      -       -      -
    870A  VAL*     3.2     2.7    -      -       -      +
    871A  TYR*     1.3    83.3    -      -       -      +
    873A  MET*     1.3    65.6    +      -       -      +
    882A  ALA*     3.5     0.5    -      -       -      +
    883A  SER*     2.9    38.0    +      -       -      +
    912A  LEU      3.4    18.4    +      -       -      -
    913A  TYR*     4.7     1.3    -      -       -      -
    914A  LEU*     3.6    24.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 873 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    815A  SER*     3.5    23.3    -      -       -      +
    816A  LEU      4.9     5.2    -      -       -      +
    817A  VAL*     4.2    23.8    -      -       +      +
    830A  ILE*     4.0    28.5    -      -       -      +
    832A  GLY*     3.6    14.4    -      -       -      -
    848A  ILE*     4.0    10.5    -      -       +      -
    870A  VAL*     3.0    37.2    -      -       +      -
    872A  SER*     1.3    78.1    -      -       -      +
    874A  VAL*     1.3    60.4    +      -       -      +
    880A  LEU*     4.2    15.9    -      -       +      -
    881A  LEU      3.1    17.5    -      -       -      +
    882A  ALA*     3.5     5.6    -      -       +      +
    914A  LEU*     4.2     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 874 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    817A  VAL*     4.9     3.1    -      -       -      -
    873A  MET*     1.3    75.0    -      -       -      +
    875A  GLU*     1.3    78.6    +      -       +      +
    880A  LEU*     4.0     5.3    -      -       -      +
    881A  LEU*     3.0    44.7    +      -       +      +
    914A  LEU*     4.1    26.5    -      -       +      +
    915A  LYS*     4.8     4.5    -      -       +      +
    916A  THR*     3.7    30.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 875 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    817A  VAL*     4.3    11.4    -      -       +      +
    819A  CYS*     3.8    35.0    -      -       +      -
    820A  LYS      4.4     7.8    -      -       -      +
    821A  LEU*     4.7     0.7    -      -       +      -
    874A  VAL*     1.3    92.0    -      -       +      +
    876A  PHE*     1.3    76.4    +      -       -      +
    878A  GLY*     3.1    25.8    +      -       -      -
    879A  LYS      4.0    10.8    -      -       -      +
    880A  LEU*     4.9     3.8    -      -       -      -
    916A  THR*     4.3     6.4    +      -       -      +
----------------------------------------------------------
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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