Contacts of the strand formed by residues 319 - 323 (chain A) in PDB entry 1CIP


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 ILE 319 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  PHE*     3.7    29.4    -      -       +      -
    254A  CYS*     3.8    22.2    -      -       -      -
    264A  ILE*     3.6    11.4    -      -       +      +
    266A  LEU*     3.8    20.4    -      -       +      -
    308A  GLU*     4.1    26.5    -      -       +      +
    311A  ASN*     3.8    24.4    -      -       +      +
    317A  LYS*     4.2     0.4    +      -       +      -
    318A  GLU*     1.3    87.9    -      -       -      +
    320A  TYR*     1.3    63.5    +      -       -      +
    321A  THR*     3.5    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  SER*     4.7    13.0    -      -       -      -
    264A  ILE      2.9    24.6    +      -       -      +
    265A  ILE*     3.4    22.0    -      -       +      +
    266A  LEU      2.9    21.0    +      -       -      -
    318A  GLU*     3.5    53.7    +      -       +      +
    319A  ILE*     1.3    70.4    -      -       -      +
    321A  THR*     1.3    61.6    +      -       -      +
    322A  HIS*     3.8    11.8    -      -       +      +
    339A  VAL*     6.2     0.4    -      -       +      -
    342A  VAL*     3.9    36.3    -      -       +      -
    346A  ASN*     2.8    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  LEU*     3.3    17.8    -      -       +      +
    268A  LEU*     3.8    31.2    -      -       +      -
    304A  GLN*     3.9    20.6    +      -       +      +
    308A  GLU*     2.7    25.7    +      -       -      +
    319A  ILE*     3.5    18.3    +      -       -      +
    320A  TYR*     1.3    71.2    -      -       -      +
    322A  HIS*     1.3    73.5    +      -       -      +
    323A  PHE*     4.4     6.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  ILE*     4.5     0.2    -      -       +      -
    266A  LEU      2.9     6.9    +      -       -      +
    267A  PHE*     3.4    13.0    -      +       +      -
    268A  LEU*     2.8    24.9    +      -       -      +
    320A  TYR*     3.8    19.8    -      -       +      +
    321A  THR*     1.3    83.4    +      -       -      +
    323A  PHE*     1.3    65.8    +      -       -      +
    324A  THR*     3.9     1.5    +      -       +      +
    335A  VAL*     3.7    33.9    -      -       +      +
    338A  ALA*     3.9    27.9    -      -       +      +
    339A  VAL*     3.9    24.0    +      -       +      +
    342A  VAL*     5.6     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  LEU*     3.9    15.3    -      -       +      -
    268A  LEU*     3.3    41.7    -      -       +      +
    271A  LYS*     3.9    20.2    +      -       +      +
    296A  TYR*     4.2    13.2    -      +       -      +
    300A  ALA*     3.7    35.4    -      -       +      -
    301A  ALA*     4.7     1.1    -      -       -      -
    304A  GLN*     3.4    30.7    -      -       -      -
    321A  THR*     4.4     5.6    -      -       +      -
    322A  HIS*     1.3    77.5    -      -       -      +
    324A  THR*     1.3    61.9    +      -       -      +
    331A  ASN*     4.0     9.7    +      -       -      +
    335A  VAL*     4.3     5.0    -      -       -      +
----------------------------------------------------------
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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