Contacts of the strand formed by residues 45 - 51 (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 GLY 45 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  GLU*     3.2     6.1    -      -       -      +
     44A  MET*     1.3    81.3    -      -       -      +
     46A  LEU*     1.3    65.0    +      -       -      -
     82A  LYS      4.7     0.4    +      -       -      -
     83A  TYR*     3.3    10.7    -      -       -      -
     84A  GLU*     2.9    26.6    +      -       -      +
    111A  ARG*     3.8    18.2    -      -       -      -
    113A  SER      3.4    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLY*     1.3    72.6    -      -       -      -
     47A  CYS*     1.3    59.9    +      -       -      +
     48A  ILE*     4.0    14.6    -      -       +      -
     83A  TYR*     3.9     2.2    -      -       -      -
     84A  GLU*     3.4    33.9    -      -       +      +
     86A  ARG*     3.5    23.3    -      -       -      +
    103A  VAL*     4.4     6.1    -      -       +      -
    106A  GLU*     3.4    25.1    -      -       -      +
    108A  HIS*     4.1    15.5    -      -       +      -
    111A  ARG*     3.2    32.5    -      -       -      +
    113A  SER      3.8     4.4    +      -       -      -
    114A  PHE*     3.6    13.5    -      -       +      -
    115A  VAL*     2.8    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     1.3    75.8    -      -       -      +
     48A  ILE*     1.3    59.2    +      -       -      +
     49A  ILE*     3.8    23.0    +      -       -      -
     78A  PHE*     3.9    27.8    -      -       +      -
     83A  TYR*     3.8    26.0    -      -       +      -
     84A  GLU      3.0     6.8    +      -       -      -
     85A  VAL*     3.4     9.8    -      -       +      +
     86A  ARG      3.1    24.3    +      -       -      +
    115A  VAL*     3.3    22.0    -      -       +      -
    117A  VAL*     4.6     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     4.3    12.8    -      -       +      -
     47A  CYS*     1.3    73.2    -      -       -      +
     49A  ILE*     1.3    62.1    +      -       -      +
     50A  ILE*     4.1    13.9    -      -       +      -
     86A  ARG*     3.6    35.9    -      -       +      +
     88A  LYS*     4.9     3.4    -      -       +      -
     99A  LEU*     4.4    12.3    -      -       +      -
    100A  MET*     4.1    18.4    -      -       +      -
    103A  VAL*     4.2    20.9    -      -       +      -
    114A  PHE*     3.8    26.2    -      -       +      -
    115A  VAL      2.9     7.3    +      -       -      +
    116A  CYS*     3.2     8.5    -      -       -      -
    117A  VAL*     2.8    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  CYS*     4.0    15.3    -      -       -      +
     48A  ILE*     1.3    76.8    -      -       -      +
     50A  ILE*     1.3    63.5    +      -       -      +
     51A  ASN*     4.6     4.0    -      -       +      +
     71A  ALA*     4.1     6.5    -      -       -      +
     74A  LEU*     3.7    30.7    -      -       +      -
     75A  ARG*     3.8    12.1    -      -       -      +
     85A  VAL*     3.8    12.1    -      -       +      -
     86A  ARG      3.0    10.4    +      -       -      +
     87A  ASN*     3.5    28.6    -      -       -      +
     88A  LYS*     2.8    30.0    +      -       -      +
    117A  VAL*     3.6    15.5    -      -       +      -
    119A  LEU*     4.1    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ILE*     4.4     6.3    -      -       +      -
     49A  ILE*     1.3    73.2    -      -       -      +
     51A  ASN*     1.3    59.6    +      -       -      +
     52A  ASN*     4.0    19.1    -      -       -      +
     88A  LYS*     3.6     4.0    -      -       +      -
     91A  LEU*     4.6     9.6    -      -       +      -
     96A  ILE*     4.2    36.1    -      -       +      -
     99A  LEU*     4.3    18.6    -      -       +      -
    100A  MET*     4.1    24.9    -      -       +      -
    116A  CYS*     4.6     1.8    -      -       -      -
    117A  VAL      2.9     9.0    +      -       -      +
    118A  LEU*     3.5    33.0    -      -       +      -
    119A  LEU*     2.8    31.1    +      -       -      +
    120A  SER*     6.3     0.9    -      -       -      -
    127A  ILE*     5.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ILE*     4.6     4.3    -      -       +      -
     50A  ILE*     1.3    72.0    -      -       -      +
     52A  ASN*     1.3    62.4    +      -       -      +
     53A  LYS*     3.8     3.3    +      -       -      +
     67A  THR*     2.5    45.7    +      -       -      +
     68A  ASP*     3.6    18.5    -      -       -      +
     71A  ALA*     3.7    19.1    -      -       +      +
     87A  ASN*     5.8     0.4    -      -       -      +
     88A  LYS      2.8    10.2    +      -       -      +
     89A  ASN*     2.9    30.3    +      -       -      +
     90A  ASP*     2.9    22.3    +      -       -      +
    119A  LEU*     3.5    16.3    -      -       +      +
----------------------------------------------------------
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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