Contacts of the strand formed by residues 126 - 129 (chain B) 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 ILE 126 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  GLY*     3.1     2.9    -      -       -      -
    123B  GLU*     2.8    62.8    +      -       +      +
    124B  GLU      4.1     9.2    -      -       -      +
    125B  GLY*     1.3    82.1    -      -       -      +
    127B  ILE*     1.3    71.0    +      -       -      +
    128B  PHE*     4.0     4.5    -      -       +      -
    133B  PRO*     3.6    29.8    -      -       +      +
    134B  VAL      3.6    17.3    -      -       -      +
    135B  ASP*     4.2     8.3    -      -       +      -
    136B  LEU*     4.3     3.9    -      -       -      +
    162B  ALA*     5.0     0.2    -      -       -      +
    163B  CYS      4.5     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ILE*     4.4    10.1    -      -       +      -
    118B  LEU*     4.3    22.7    -      -       +      +
    120B  SER*     4.7     9.0    -      -       -      -
    121B  HIS      3.3     6.7    -      -       -      +
    126B  ILE*     1.3    79.8    -      -       -      +
    128B  PHE*     1.3    65.3    +      -       -      +
    134B  VAL*     2.8    41.2    +      -       +      +
    136B  LEU*     3.9    25.1    -      -       +      -
    139B  ILE*     3.6    25.1    -      -       +      -
    160B  ILE*     4.2    17.9    -      -       +      -
    161B  GLN      5.2     0.4    -      -       -      +
    162B  ALA*     3.9    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  ASN*     3.1     9.5    +      -       -      -
     55B  PHE*     3.9    15.5    -      +       +      -
     59B  THR*     5.1    12.1    -      -       +      -
     61B  MET*     4.8    21.5    -      -       +      -
     96B  ILE*     4.7     0.5    -      -       -      +
    120B  SER*     2.7    23.9    +      -       -      +
    121B  HIS*     2.9    30.2    +      -       +      +
    122B  GLY*     3.7     8.5    -      -       -      -
    123B  GLU*     3.2    40.6    -      -       +      -
    126B  ILE*     4.0     5.2    -      -       +      -
    127B  ILE*     1.3    77.9    -      -       -      +
    129B  GLY*     1.3    67.3    +      -       -      +
    132B  GLY*     3.7     7.4    -      -       -      -
    133B  PRO*     3.6    34.5    -      -       +      -
    134B  VAL*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  ASN*     3.4    10.5    -      -       -      -
     55B  PHE*     3.6     5.3    -      -       -      -
     59B  THR*     5.4     0.2    -      -       -      +
     91B  LEU      3.4     5.8    -      -       -      -
     93B  ARG*     3.5    13.7    -      -       -      -
     96B  ILE*     3.9     9.4    -      -       -      -
    127B  ILE      3.8     1.4    +      -       -      -
    128B  PHE*     1.3    87.2    -      -       -      +
    130B  THR*     1.3    65.9    +      -       -      +
    131B  ASN      3.3     2.9    -      -       -      -
    132B  GLY      2.6    20.3    +      -       -      -
    134B  VAL*     4.3     1.4    -      -       -      +
----------------------------------------------------------
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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