Contacts of the strand formed by residues 33 - 39 (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 GLU 33 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ARG*     1.3    84.8    +      -       +      +
     34A  VAL*     1.3    68.2    -      -       -      +
     35A  LYS*     4.3     1.8    -      -       +      +
    195A  HIS*     3.4    18.6    +      -       -      +
    197A  LYS*     2.9    42.1    +      -       +      +
    219A  THR*     4.4     5.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ARG      4.4     1.1    -      -       -      +
     33A  GLU*     1.3    81.2    -      -       -      +
     35A  LYS*     1.3    59.7    +      -       -      +
     36A  LEU*     3.9    17.6    +      -       +      -
    194A  LEU*     3.7    39.0    -      -       +      -
    195A  HIS      3.1     9.2    +      -       -      +
    196A  PHE*     3.4    30.1    -      -       +      +
    197A  LYS*     2.8    29.9    +      -       -      +
    219A  THR*     3.7    17.9    -      -       +      -
    343A  ILE*     4.3    11.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLU*     5.3     2.4    -      -       +      +
     34A  VAL*     1.3    71.4    -      -       -      +
     36A  LEU*     1.3    65.8    +      -       -      +
     37A  LEU*     5.2     2.7    -      -       -      -
    197A  LYS*     3.3     7.9    -      -       +      +
    199A  PHE*     3.6    44.6    -      -       +      -
    213A  HIS      5.5     0.4    +      -       -      -
    214A  CYS*     3.2    28.1    +      -       -      +
    216A  GLU*     2.8    30.6    +      -       -      +
    217A  GLY*     3.4    20.9    -      -       -      +
    218A  VAL*     3.8     8.8    -      -       -      +
    219A  THR*     2.8    34.1    +      -       -      +
    220A  ALA      3.2     8.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  VAL*     4.0     5.6    -      -       +      +
     35A  LYS*     1.3    79.4    -      -       -      +
     37A  LEU*     1.3    56.3    +      -       -      +
     38A  LEU*     4.2     0.9    -      -       +      -
    189A  PHE*     4.9     0.7    -      -       +      -
    196A  PHE*     3.4    34.5    -      -       +      -
    197A  LYS      2.9    10.5    +      -       -      +
    198A  MET*     3.4    33.3    -      -       +      +
    199A  PHE*     2.8    34.8    +      -       -      +
    220A  ALA*     3.3    31.2    -      -       +      +
    222A  ILE*     4.6    14.8    -      -       +      -
    336A  PHE*     4.1    12.8    -      -       +      -
    343A  ILE*     3.7    17.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LYS*     5.2     2.2    -      -       -      -
     36A  LEU*     1.3    74.6    -      -       -      +
     38A  LEU*     1.3    66.0    +      -       -      +
     39A  LEU*     3.9    36.8    -      -       +      -
    199A  PHE*     3.6    19.5    -      -       +      +
    201A  VAL*     4.7     4.5    -      -       +      -
    214A  CYS*     3.6    44.9    -      -       +      +
    215A  PHE*     4.2    12.8    -      -       +      -
    218A  VAL*     4.0    23.8    -      -       +      +
    220A  ALA      3.0     7.5    +      -       -      -
    221A  ILE*     3.3    12.6    -      -       +      +
    222A  ILE*     2.8    26.5    +      -       -      +
    259A  PHE*     5.1     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     6.2     0.9    -      -       +      -
     37A  LEU*     1.3    73.4    -      -       -      +
     39A  LEU*     1.3    70.8    +      -       -      +
     46A  LYS*     3.4    28.5    -      -       +      +
     49A  ILE*     4.2    15.7    -      -       +      -
     50A  VAL*     3.2    36.1    -      -       +      +
    198A  MET*     4.1    20.6    -      -       +      -
    199A  PHE      2.9    11.0    +      -       -      +
    200A  ASP*     4.2     8.5    -      -       +      +
    201A  VAL*     3.7    16.8    +      -       -      +
    222A  ILE*     3.3    35.0    -      -       +      +
    224A  CYS*     4.2    12.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     3.8    30.7    +      -       +      -
     38A  LEU*     1.3    83.3    -      -       -      +
     40A  GLY*     1.3    53.7    +      -       -      +
     46A  LYS*     3.4    12.0    -      -       -      +
    201A  VAL*     3.8    13.2    -      -       +      -
    211A  TRP*     3.8    33.4    -      -       +      -
    215A  PHE*     4.6     3.8    -      -       +      -
    221A  ILE*     4.2    14.1    -      -       +      -
    222A  ILE      3.0     6.6    +      -       -      +
    223A  PHE*     3.3    15.4    -      -       +      -
    224A  CYS*     2.7    31.7    +      -       -      +
    253A  ILE*     3.6    41.5    -      -       +      -
----------------------------------------------------------
 Back to top of page


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