Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 1CF5


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 VAL 79 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  ARG*     3.3     5.6    -      -       -      +
     76A  THR*     2.9    31.0    +      -       +      +
     77A  ARG*     5.8     4.5    -      -       +      +
     78A  ASP*     1.3    88.1    -      -       -      +
     80A  SER*     1.3    64.4    +      -       -      +
     81A  TYR*     3.6    26.9    -      -       +      +
     99A  ARG*     3.3    29.6    -      -       +      +
    101A  ILE*     3.3    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TYR      3.4     6.3    -      -       -      -
     75A  ARG*     3.9     2.7    -      -       -      -
     79A  VAL*     1.3    76.3    -      -       -      +
     81A  TYR*     1.3    55.3    +      -       -      +
     82A  PHE*     2.8    28.8    +      -       -      -
     95A  PHE*     3.0    24.1    -      -       -      +
     98A  THR*     3.0    25.9    +      -       -      -
     99A  ARG      3.0     3.6    +      -       -      -
    100A  LYS*     3.4     2.4    -      -       -      -
    101A  ILE*     2.7    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ALA*     3.2     3.6    -      -       -      +
     74A  TYR*     2.8    57.6    +      +       +      -
     76A  THR*     3.1    34.9    -      -       +      +
     77A  ARG*     5.2     2.9    +      -       -      -
     79A  VAL*     3.6    25.1    -      -       +      +
     80A  SER*     1.3    73.7    -      -       -      +
     82A  PHE*     1.3    60.1    +      -       -      +
    101A  ILE*     3.1    35.8    -      -       +      +
    103A  LEU*     3.5    38.4    -      -       +      +
    140A  TYR*     3.4    38.4    -      +       +      +
----------------------------------------------------------
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Residues in contact with PHE 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL      3.8     2.5    -      -       -      -
     73A  ALA*     3.4    25.4    -      -       +      -
     80A  SER*     2.8    30.5    -      -       -      -
     81A  TYR*     1.3    72.6    -      -       -      +
     83A  PHE*     1.3    60.4    +      -       -      +
     86A  SER*     3.9    12.1    -      -       -      +
     90A  ALA*     3.9    26.5    -      -       +      -
     91A  TYR*     3.5    48.2    -      +       +      +
     94A  LEU*     4.2    20.4    -      -       +      -
     95A  PHE*     4.0     9.0    -      +       -      -
    100A  LYS*     3.8    20.0    -      -       +      -
    101A  ILE      2.8    16.2    +      -       -      +
    102A  THR*     3.4     0.7    -      -       -      -
    103A  LEU*     2.7    36.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  VAL*     3.5    39.7    -      -       +      -
     72A  VAL*     3.1    29.7    +      -       -      +
     73A  ALA*     4.8     2.7    -      -       -      -
     74A  TYR*     6.5     0.2    -      +       -      -
     82A  PHE*     1.3    73.5    -      -       -      +
     84A  LYS*     1.3    66.9    +      -       -      +
     85A  GLU      3.0     2.1    +      -       -      -
     86A  SER*     2.7    26.2    +      -       -      +
     91A  TYR*     4.1     5.2    +      -       -      -
    102A  THR*     4.4     0.7    -      -       -      -
    103A  LEU*     4.5     5.8    -      -       +      -
    105A  TYR*     3.5    14.1    -      +       -      -
    106A  THR      3.5     4.7    -      -       -      -
    107A  GLY*     3.1    42.2    -      -       -      +
    112A  LEU*     3.8    22.2    -      -       +      -
    149A  LEU*     3.8    34.5    -      -       +      -
    153A  ILE*     5.6     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  PHE*     1.3    68.2    -      -       -      +
     85A  GLU*     1.3    98.8    +      -       +      +
    102A  THR*     3.9    13.7    -      -       +      -
    103A  LEU      3.3    20.2    +      -       -      +
    104A  PRO*     3.9    19.1    -      -       +      +
    105A  TYR*     3.1    13.1    +      -       -      +
    106A  THR*     3.1    41.9    -      -       -      +
    107A  GLY      4.6     0.2    +      -       -      -
    111A  ASN*     4.7     2.8    +      -       -      -
----------------------------------------------------------
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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