Contacts of the strand formed by residues 78 - 87 (chain C) in PDB entry 1F4J


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 78 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  ALA      3.4     1.2    +      -       -      -
     77C  LYS*     1.3    79.2    -      -       -      +
     79C  ALA*     1.3    60.4    +      -       -      -
    112C  ARG*     3.3    20.0    -      -       -      +
    113C  PHE      3.2    11.0    -      -       -      -
    114C  SER*     4.3     0.9    -      -       -      -
    124C  ASP*     6.0     0.2    -      -       -      -
    209C  HIS*     5.5     0.7    -      -       -      -
    262C  ILE*     3.6    19.3    -      -       -      +
    325C  TYR*     2.6    28.1    +      -       -      -
    329C  VAL*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  GLY*     1.3    75.8    -      -       -      +
     80C  GLY*     1.3    60.2    +      -       -      +
    112C  ARG*     3.2     3.1    -      -       -      +
    113C  PHE*     2.8    36.8    +      -       -      +
    209C  HIS*     3.7    31.2    -      -       +      +
    262C  ILE*     3.8    26.5    -      -       +      -
    265C  LEU*     4.2     9.4    -      -       +      -
    325C  TYR*     4.5     3.6    -      -       -      -
    329C  VAL*     4.2     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  ALA*     1.3    75.4    -      -       -      +
     81C  ALA*     1.3    63.5    -      -       -      +
     82C  PHE*     4.8     1.1    -      -       -      -
    111C  VAL      3.3     9.9    -      -       -      -
    112C  ARG*     4.4     0.9    -      -       -      -
    265C  LEU*     3.9     7.5    -      -       -      +
    321C  ASN*     4.4     2.8    +      -       -      -
    322C  PRO*     3.3    23.1    -      -       -      +
    325C  TYR*     4.6     2.2    -      -       -      -
    329C  VAL*     3.8    27.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80C  GLY*     1.3    76.3    -      -       -      +
     82C  PHE*     1.3    74.7    +      -       -      +
    111C  VAL*     2.8    32.7    +      -       +      +
    113C  PHE*     5.4     0.6    -      -       +      -
    265C  LEU*     3.9     9.2    -      -       +      -
    269C  ILE*     3.6    29.2    -      -       +      -
    318C  LEU*     3.9    23.3    -      -       +      -
    320C  ARG      3.6     5.4    -      -       -      -
    322C  PRO*     4.4     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80C  GLY*     4.8     0.7    -      -       -      -
     81C  ALA*     1.3    84.4    -      -       -      +
     83C  GLY*     1.3    59.9    +      -       -      +
    109C  ILE      3.4     8.1    -      -       -      +
    110C  ALA*     3.6    30.1    -      -       +      -
    111C  VAL      5.7     0.9    -      -       -      -
    137C  TYR*     4.7     3.8    -      +       -      -
    318C  LEU*     3.6     8.6    -      -       -      -
    319C  ASN*     3.0     7.2    +      -       -      -
    320C  ARG*     2.8    79.8    +      -       -      +
    321C  ASN      4.3     0.2    -      -       -      -
    322C  PRO*     3.7    18.8    -      -       +      -
    328C  GLU*     3.4    52.5    -      -       +      -
    329C  VAL*     5.1     1.3    -      -       +      -
    332C  ILE*     4.9     2.7    -      -       +      -
    375C  VAL*     4.3    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82C  PHE*     1.3    77.0    -      -       -      +
     84C  TYR*     1.3    63.7    +      -       -      +
    108C  PRO*     3.3     8.0    -      -       -      +
    109C  ILE*     2.7    34.2    +      -       -      +
    317C  VAL      3.1    11.7    -      -       -      -
    319C  ASN*     3.4    15.7    -      -       -      -
    320C  ARG*     4.8     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83C  GLY*     1.3    76.0    -      -       -      +
     85C  PHE*     1.3    69.9    +      -       -      +
     86C  GLU*     3.6    28.1    +      -       +      -
    106C  LYS*     3.9    33.8    +      -       +      -
    107C  THR      3.3    17.5    -      -       -      +
    108C  PRO*     4.3     1.6    -      -       +      -
    109C  ILE*     3.5    10.2    -      -       -      +
    315C  LYS*     3.9     0.8    -      -       +      +
    316C  LEU*     3.6     0.2    -      -       -      -
    317C  VAL*     2.9    73.5    +      -       +      +
    319C  ASN*     3.7    20.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  TYR*     1.3    74.8    -      -       -      +
     86C  GLU*     1.3    64.4    +      -       -      +
     87C  VAL*     3.7    17.9    -      -       +      -
     99C  VAL*     3.5    44.4    -      -       +      -
    100C  PHE*     3.9    22.9    -      +       -      -
    105C  LYS      4.9     0.2    -      -       -      -
    106C  LYS*     3.1     4.2    -      -       -      -
    107C  THR*     2.7    45.2    +      -       -      +
    109C  ILE*     3.8    13.5    -      -       +      -
    136C  PHE*     3.8    15.3    -      +       +      -
    279C  PHE*     4.1    16.4    -      +       +      -
    313C  VAL*     4.5     2.9    -      -       +      -
    314C  GLY*     3.9     9.9    -      -       -      -
    315C  LYS      3.2    31.2    -      -       -      -
    316C  LEU*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  TYR*     3.6    21.1    +      -       +      -
     85C  PHE*     1.3    78.7    -      -       -      +
     87C  VAL*     1.3    71.2    +      -       -      +
     88C  THR*     3.8     8.2    -      -       +      +
    104C  GLY*     4.0    17.4    -      -       -      +
    105C  LYS      3.4     2.5    -      -       -      -
    106C  LYS*     3.3    33.4    -      -       +      -
    314C  GLY*     3.2     3.5    -      -       -      -
    315C  LYS*     2.9    40.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  PHE*     3.7    11.0    -      -       +      -
     86C  GLU*     1.3    76.7    -      -       -      +
     88C  THR*     1.3    59.1    +      -       -      +
     89C  HIS      3.2    26.9    -      -       -      +
     90C  ASP*     5.3     0.2    -      -       -      -
     99C  VAL      3.3    26.0    -      -       -      +
    100C  PHE*     3.9    16.6    -      -       +      +
    102C  HIS      3.4    28.0    -      -       -      +
    103C  ILE*     3.8     8.6    -      -       -      +
    104C  GLY*     2.8    26.7    +      -       -      +
    105C  LYS*     3.0    16.3    +      -       +      +
    313C  VAL*     3.9     8.5    -      -       +      +
    314C  GLY*     4.2     1.1    -      -       -      -
----------------------------------------------------------
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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