Contacts of the strand formed by residues 736 - 743 (chain B) in PDB entry 6IEH


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 LEU 736 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641B  GLU      4.9     1.2    -      -       -      +
    644B  ILE*     5.6     1.5    -      -       +      +
    645B  HIS*     2.8    41.7    +      -       +      +
    650B  CYS*     4.8     4.0    -      -       -      -
    654B  LEU*     4.2    22.0    -      -       +      -
    660B  VAL*     3.8    29.4    -      -       +      -
    661B  LYS      3.2    13.7    -      -       -      +
    662B  VAL*     4.3     7.4    -      -       +      +
    674B  VAL*     5.9     0.2    -      -       +      -
    696B  VAL*     4.4    18.2    -      -       +      -
    698B  VAL*     5.7     1.3    -      -       +      -
    731B  VAL*     5.6     2.0    -      -       +      +
    732B  LEU      4.6     1.5    +      -       -      +
    733B  VAL*     3.2    23.6    -      -       +      +
    734B  HIS      3.2     0.6    -      -       -      -
    735B  LEU*     1.3    76.0    -      -       -      +
    737B  SER*     1.3    62.9    +      -       -      +
    738B  ALA      4.6     0.7    -      -       -      +
    739B  ILE*     4.5    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 737 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641B  GLU*     3.7    45.8    -      -       -      +
    644B  ILE*     5.7     6.1    -      -       -      +
    645B  HIS*     5.5     0.7    -      -       -      -
    661B  LYS*     2.9    23.1    +      -       -      +
    662B  VAL      4.1     0.3    -      -       -      -
    663B  LYS*     3.5    32.2    -      -       -      +
    735B  LEU      3.5     1.2    +      -       -      -
    736B  LEU*     1.3    74.2    -      -       -      +
    738B  ALA*     1.3    61.2    +      -       -      +
    739B  ILE*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 738 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644B  ILE*     5.8     2.2    -      -       -      -
    660B  VAL*     3.1    10.0    -      -       -      +
    661B  LYS*     2.8    58.7    +      -       +      -
    671B  TRP*     4.2     8.7    -      -       +      -
    736B  LEU      3.5     0.8    -      -       -      -
    737B  SER*     1.3    81.3    -      -       -      +
    739B  ILE*     1.3    65.2    +      -       -      +
    776B  LEU*     4.7    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 739 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644B  ILE*     3.5    41.9    -      -       +      +
    650B  CYS*     3.9    19.7    -      -       +      +
    653B  PHE*     4.6     6.7    -      -       +      +
    654B  LEU*     5.6     4.5    -      -       +      -
    658B  ARG*     4.0    17.7    -      -       -      -
    659B  LEU      4.0     4.0    -      -       -      +
    660B  VAL*     4.1    14.8    -      -       +      -
    671B  TRP*     5.0     0.7    -      -       -      -
    736B  LEU*     4.5    12.3    -      -       +      -
    738B  ALA*     1.3    80.3    -      -       -      +
    740B  SER*     1.3    63.3    +      -       -      +
    776B  LEU*     3.5    22.5    -      -       -      +
    777B  LEU*     3.6    27.8    +      -       +      +
    783B  MET*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 740 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    658B  ARG*     3.5    24.8    +      -       -      +
    659B  LEU*     3.2    22.8    +      -       -      -
    671B  TRP*     4.2     3.4    -      -       -      -
    739B  ILE*     1.3    75.8    -      -       -      +
    741B  SER*     1.3    61.9    +      -       -      +
    742B  VAL      3.9     5.4    -      -       -      -
    774B  ILE*     3.0    24.7    -      -       -      -
    775B  PRO      2.8    22.4    -      -       -      -
    776B  LEU*     3.9     0.9    -      -       -      +
    777B  LEU*     3.8     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 741 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  THR*     4.2    16.2    -      -       -      -
    166A  ASP      3.1    28.0    +      -       -      +
    167A  LYS*     3.7    23.8    +      -       -      -
    658B  ARG*     3.4     2.6    +      -       -      -
    740B  SER*     1.3    72.6    -      -       -      +
    742B  VAL*     1.3    65.5    +      -       -      +
    775B  PRO*     3.1    26.5    +      -       -      +
    776B  LEU      4.3     5.0    +      -       -      -
    777B  LEU*     3.6    22.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 742 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  PHE*     3.8    32.3    -      -       +      -
    164A  ARG      3.4    12.8    -      -       -      +
    165A  THR*     4.3     4.3    -      -       +      +
    657B  GLY      4.4     0.2    -      -       -      -
    658B  ARG*     3.6     5.5    -      -       -      +
    659B  LEU*     3.2    53.6    +      -       +      +
    740B  SER      3.2     0.9    -      -       -      +
    741B  SER*     1.3    77.5    -      -       -      +
    743B  ARG*     1.3    64.4    +      -       -      +
    744B  LEU*     4.6     0.4    -      -       +      -
    766B  VAL*     4.2     9.0    -      -       +      -
    770B  PHE*     5.1     4.5    -      -       +      -
    774B  ILE*     4.2     5.4    -      -       +      -
    775B  PRO*     3.6    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 743 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  PHE*     3.7     0.3    -      -       -      -
    164A  ARG*     2.7    73.1    +      -       +      +
    166A  ASP*     3.5    43.3    +      -       +      +
    181A  ARG*     3.9    17.0    +      -       -      +
    182A  GLY*     5.7     2.2    -      -       -      -
    183A  ASP      6.0     0.6    -      -       -      +
    655B  GLN*     3.7    18.7    -      -       -      +
    656B  PRO*     2.5    35.6    +      -       -      +
    657B  GLY      3.1     5.8    -      -       -      -
    658B  ARG*     3.5    28.0    -      -       -      +
    741B  SER      3.4     0.2    +      -       -      -
    742B  VAL*     1.3    78.0    -      -       -      +
    744B  LEU*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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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