Contacts of the strand formed by residues 64 - 72 (chain B) 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 GLU 64 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  GLN*     3.2    21.5    -      -       -      +
     27B  VAL      4.2     0.9    -      -       -      +
     28B  PHE*     4.1     1.6    -      -       -      -
     62B  GLY      3.7    12.1    -      -       -      +
     63B  SER*     1.3    81.9    -      -       -      +
     65B  LEU*     1.3    61.0    +      -       -      +
     66B  HIS*     3.8     3.2    +      -       +      +
     85B  LYS*     3.8    35.7    +      -       +      +
     86B  VAL      3.4    15.0    -      -       -      +
     87B  PRO*     4.1    13.5    -      -       +      +
     88B  LEU*     4.0     6.5    -      -       -      -
     89B  ARG*     5.7     1.0    +      -       -      -
    202B  FMT      2.7    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  LEU*     4.9     1.3    -      -       +      -
      4B  VAL*     4.0    22.2    -      -       +      -
     26B  ALA*     4.4     2.2    -      -       +      -
     27B  VAL      3.6    24.2    -      -       -      +
     28B  PHE*     3.8    18.4    -      -       +      -
     52B  TRP*     4.1    19.1    -      -       +      -
     64B  GLU*     1.3    72.8    -      -       -      +
     66B  HIS*     1.3    59.2    +      -       -      +
     67B  VAL*     3.9    14.2    +      -       +      -
     84B  ALA      3.8     0.9    -      -       -      +
     85B  LYS*     3.4     3.4    -      -       -      -
     86B  VAL*     3.0    45.7    +      -       +      +
     88B  LEU*     3.9    15.6    -      -       +      +
    119B  LEU*     3.6    30.7    -      -       +      -
    121B  VAL*     4.5     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  SER      3.8     0.5    -      -       -      +
     26B  ALA*     3.3     3.3    -      -       -      +
     27B  VAL*     2.8    55.6    +      -       +      +
     64B  GLU*     3.8     2.4    +      -       +      +
     65B  LEU*     1.3    73.6    -      -       -      +
     67B  VAL*     1.3    64.3    +      -       -      +
     68B  VAL*     3.5    19.7    -      -       +      +
     83B  GLU*     2.9    36.1    +      -       -      +
     84B  ALA      3.4    18.4    -      -       -      -
     85B  LYS*     3.7    33.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ILE*     4.9     3.6    -      -       +      -
     24B  CYS*     4.2     6.1    -      -       -      -
     25B  SER      3.3     4.0    -      -       -      +
     26B  ALA*     4.1    13.0    -      -       +      -
     65B  LEU*     4.1    25.4    -      -       +      +
     66B  HIS*     1.3    78.3    -      -       -      +
     68B  VAL*     1.3    63.2    +      -       -      +
     69B  VAL*     5.7     0.2    -      -       -      -
     83B  GLU*     3.2     5.5    -      -       -      +
     84B  ALA*     2.9    53.7    +      -       +      +
     86B  VAL*     5.1     8.3    -      -       +      -
    103B  ALA*     5.9     0.2    -      -       +      -
    105B  LEU*     4.9     2.5    -      -       +      +
    117B  LEU*     3.6    33.7    -      -       +      -
    119B  LEU*     4.7     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  TYR      3.8     0.3    -      -       -      +
     24B  CYS*     3.4     2.3    -      -       -      -
     25B  SER*     2.7    48.4    +      -       -      +
     27B  VAL*     6.4     1.3    -      -       +      -
     66B  HIS*     3.5    31.0    -      -       +      +
     67B  VAL*     1.3    77.4    -      -       -      +
     69B  VAL*     1.3    64.6    -      -       -      +
     70B  LYS*     3.9    32.2    +      -       +      +
     80B  PHE*     3.6    31.0    -      -       +      -
     82B  GLY      3.5     6.3    -      -       -      +
     83B  GLU*     4.2     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ALA*     4.9     1.1    -      -       +      -
     12B  VAL*     4.2    17.5    -      -       +      -
     22B  ALA*     4.1    21.1    -      -       +      -
     23B  TYR      3.4    10.1    -      -       -      +
     24B  CYS*     4.4    14.4    -      -       -      -
     46B  TRP*     4.4    10.3    -      -       +      -
     67B  VAL      5.7     0.2    -      -       -      -
     68B  VAL*     1.3    74.5    -      -       -      +
     70B  LYS*     1.3    62.6    +      -       -      +
     81B  LEU*     2.9    31.2    +      -       +      +
     82B  GLY      2.8    17.8    +      -       -      +
    105B  LEU*     3.6    34.8    -      -       +      -
    117B  LEU*     4.5    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ALA*     3.3     4.9    -      -       -      -
     23B  TYR*     2.9    71.2    +      -       +      +
     25B  SER*     4.4    11.7    +      -       -      -
     32B  LYS*     5.9     3.2    -      -       -      +
     68B  VAL*     3.9    27.7    +      -       +      +
     69B  VAL*     1.3    79.1    -      -       -      +
     71B  ASP*     1.3    62.2    +      -       -      +
     78B  ASN*     3.6    25.1    -      -       +      +
     79B  ARG      3.4     8.1    -      -       -      +
     80B  PHE*     3.9    15.7    -      -       -      +
     81B  LEU*     3.8     5.2    -      -       -      -
     77E  ARG*     5.4     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  THR*     3.3    25.7    +      -       +      +
     17B  THR*     5.0     2.1    +      -       -      +
     19B  ILE      5.2     0.2    -      -       -      +
     20B  SER*     4.7     1.0    -      -       -      -
     21B  ASP*     2.9    27.5    +      -       -      +
     23B  TYR*     4.6     1.8    -      -       -      -
     70B  LYS*     1.3    72.7    -      -       -      +
     72B  HIS*     1.3    75.5    +      -       -      +
     73B  GLU*     3.3    25.6    +      -       -      +
     78B  ASN*     3.5     5.2    -      -       -      +
     79B  ARG*     2.7    42.8    +      -       +      +
     81B  LEU*     3.6    24.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ASP*     3.0    30.0    +      -       +      +
     23B  TYR*     4.3     4.5    -      -       +      -
     37B  VAL*     3.6    35.6    -      -       +      +
     39B  LYS*     6.0     3.1    -      -       +      -
     70B  LYS      4.0     0.6    +      -       -      -
     71B  ASP*     1.3    85.8    +      -       -      +
     73B  GLU*     1.3    66.2    +      -       -      +
     74B  THR*     3.1    44.6    +      -       +      +
     75B  MET*     5.1     4.4    -      -       +      +
     78B  ASN*     3.6    21.2    +      -       -      -
----------------------------------------------------------
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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