Contacts of the strand formed by residues 264 - 267 (chain A) in PDB entry 1CP3


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 CYS 264 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  ARG*     3.7    20.4    -      -       -      +
    195A  TYR      3.5     1.7    -      -       -      +
    196A  ALA*     5.0     0.2    -      -       -      -
    197A  TYR*     3.1    33.5    +      -       -      +
    199A  THR      3.5    20.0    -      -       -      +
    200A  ALA*     4.1     0.2    -      -       -      -
    201A  PRO*     4.2     4.9    -      -       -      -
    240A  ASN*     4.4     0.2    +      -       -      -
    263A  PRO*     1.3    80.5    -      -       -      +
    265A  ILE*     1.3    60.5    +      -       -      +
    266A  VAL*     4.1     8.3    -      -       -      -
    266B  VAL*     3.8    16.4    -      -       -      -
    267B  SER      3.6     4.3    -      -       -      -
    268B  MET*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  LEU*     4.1     9.4    -      -       +      -
    195A  TYR      3.7     3.8    -      -       -      +
    196A  ALA*     4.8     2.7    -      -       -      +
    233A  MET*     3.3    41.5    -      -       +      +
    236A  LEU*     3.6    44.6    -      -       +      -
    237A  THR*     4.3     6.7    -      -       -      +
    240A  ASN*     3.9    24.7    -      -       -      +
    263A  PRO*     6.1     0.2    -      -       +      -
    264A  CYS*     1.3    73.5    -      -       -      +
    266A  VAL*     1.3    65.0    +      -       -      +
    267A  SER      4.0     0.9    -      -       -      +
    265B  ILE      3.4     1.0    -      -       -      +
    266B  VAL*     3.2     4.3    -      -       -      -
    267B  SER*     2.7    50.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  ARG*     5.5     1.3    -      -       -      +
    194A  LEU*     3.4     3.3    -      -       -      -
    195A  TYR*     2.8    54.6    +      -       +      +
    197A  TYR*     3.7    27.1    -      -       +      -
    264A  CYS*     4.1    10.1    -      -       -      -
    265A  ILE*     1.3    78.6    -      -       -      +
    267A  SER*     1.3    60.1    -      -       -      +
    268A  MET*     4.2     9.2    -      -       +      -
    201B  PRO*     5.6     3.4    -      -       +      -
    264B  CYS*     3.3    33.7    -      -       -      -
    265B  ILE      3.1     3.8    -      -       -      +
    266B  VAL*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  PHE      3.9     2.2    -      -       -      -
    194A  LEU*     4.1     4.2    -      -       -      +
    233A  MET*     4.1    27.3    -      -       -      +
    265A  ILE      4.0     0.4    -      -       -      -
    266A  VAL*     1.3    73.2    -      -       -      +
    268A  MET*     1.3    61.3    +      -       -      +
    269A  LEU*     3.2    29.7    +      -       -      +
    237B  THR*     5.1     2.9    +      -       -      -
    240B  ASN*     3.6     9.8    +      -       -      -
    264B  CYS*     3.7     2.3    -      -       -      -
    265B  ILE*     2.7    52.2    +      -       -      +
----------------------------------------------------------
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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