Contacts of the strand formed by residues 80 - 87 (chain C) in PDB entry 4IHB


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 PHE 80 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  VAL*     3.7    31.4    -      -       +      -
     69C  VAL      4.3     2.0    -      -       -      -
     70C  LYS*     4.3    13.2    -      -       -      +
     78C  ASN*     3.5     5.1    -      -       -      +
     79C  ARG*     1.3    76.7    -      -       -      +
     81C  LEU*     1.3    67.9    +      -       -      +
     82C  GLY*     3.6    19.7    -      -       -      -
     83C  GLU*     3.4    42.0    -      -       +      -
    106C  LEU      3.9     1.3    -      -       -      -
    107C  ASP*     3.7     4.9    -      -       +      -
    108C  THR*     3.5    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  VAL*     3.6    30.1    -      -       +      -
     13C  HIS      4.3     8.0    -      -       -      +
     14C  THR*     3.6    38.4    -      -       +      -
     15C  PRO*     4.8     3.6    -      -       +      -
     20C  SER*     4.7     0.7    -      -       -      -
     22C  ALA*     4.7     2.5    -      -       +      -
     69C  VAL*     3.0    20.3    +      -       +      +
     70C  LYS      3.9     5.6    -      -       -      +
     71C  ASP*     3.6    25.6    -      -       +      +
     78C  ASN      3.9    12.8    -      -       -      +
     79C  ARG      3.9     0.4    -      -       -      +
     80C  PHE*     1.3    89.5    -      -       -      +
     82C  GLY*     1.3    60.9    +      -       -      +
    105C  LEU*     5.9     0.7    -      -       -      -
    107C  ASP*     4.9     1.0    -      -       -      +
    113C  THR*     3.6    22.2    +      -       -      +
    115C  ALA*     5.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  VAL*     3.5     2.4    -      -       -      +
     69C  VAL*     2.8    29.3    +      -       -      +
     80C  PHE*     3.6     9.9    -      -       -      -
     81C  LEU*     1.3    81.4    -      -       -      +
     83C  GLU*     1.3    62.1    +      -       -      +
    105C  LEU*     4.2    20.0    -      -       -      -
    106C  LEU      3.2    15.0    -      -       -      -
    113C  THR*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  HIS*     2.5    35.4    +      -       -      +
     67C  VAL      3.2    12.1    -      -       -      +
     68C  VAL*     3.7    10.0    -      -       +      +
     80C  PHE*     3.4    25.1    -      -       +      -
     82C  GLY*     1.3    75.6    -      -       -      +
     84C  ALA*     1.3    62.9    +      -       -      +
     85C  LYS*     5.3     5.0    -      -       +      +
    104C  PRO      4.3     0.2    -      -       -      +
    105C  LEU*     3.7     5.7    -      -       -      +
    106C  LEU*     2.8    42.7    +      -       +      +
    107C  ASP      4.2     0.2    -      -       -      +
    108C  THR*     4.9     1.9    -      -       -      -
    110C  LYS*     2.8    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  LEU      3.8     1.0    -      -       -      +
     66C  HIS*     3.8     3.5    -      -       -      -
     67C  VAL*     2.8    40.1    +      -       +      +
     83C  GLU*     1.3    75.4    -      -       -      +
     85C  LYS*     1.3    65.3    +      -       -      +
     86C  VAL*     4.0     6.0    -      -       +      +
    103C  ALA*     4.1    24.9    -      -       +      -
    104C  PRO      4.4     4.9    -      -       -      +
    105C  LEU*     4.0    15.7    -      -       +      +
    106C  LEU*     6.0     0.4    -      -       -      -
    117C  LEU*     5.1     4.3    -      -       +      -
    119C  LEU*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  GLU*     4.1    35.4    +      -       +      +
     65C  LEU      3.6     4.0    -      -       -      +
     66C  HIS*     3.9    38.9    +      -       +      +
     83C  GLU*     5.3     3.4    -      -       +      +
     84C  ALA*     1.3    76.0    -      -       -      +
     86C  VAL*     1.3    62.2    +      -       -      +
     87C  PRO*     3.2    12.7    -      -       -      +
    110C  LYS*     6.2     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  GLU*     3.4     3.5    -      -       -      +
     65C  LEU*     2.8    50.8    +      -       +      +
     67C  VAL*     5.1     2.9    -      -       +      -
     84C  ALA*     4.9     9.2    -      -       +      +
     85C  LYS*     1.3    73.7    -      -       -      +
     87C  PRO*     1.3    67.4    -      -       -      +
     88C  LEU*     3.4     8.0    +      -       +      +
    101C  PHE*     3.5    45.3    -      -       +      -
    103C  ALA*     5.7     2.9    -      -       +      -
    119C  LEU*     4.2    30.1    -      -       +      -
    121C  VAL*     4.6     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61C  GLN*     2.8    18.8    -      -       +      +
     64C  GLU*     3.6    18.8    -      -       +      +
     85C  LYS      3.2    12.1    -      -       -      +
     86C  VAL*     1.3    91.0    -      -       +      +
     88C  LEU*     1.3    58.9    +      -       -      +
     89C  ARG*     4.0    19.5    -      -       -      +
     90C  GLU*     3.2    46.8    -      -       -      +
     91C  VAL*     4.1     1.0    +      -       -      +
    101C  PHE*     5.1     2.7    -      -       +      -
----------------------------------------------------------
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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