Contacts of the strand formed by residues 110 - 117 (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 CYS 110 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  THR*     2.5    39.7    +      -       -      +
    107B  VAL      5.3     0.2    -      -       -      +
    108B  GLU      3.9    12.3    -      -       -      +
    109B  GLY*     1.3    77.2    +      -       -      +
    111B  THR*     1.3    67.2    +      -       -      +
    112B  HIS*     5.7     0.2    -      -       -      -
    142B  ALA*     4.4     8.3    -      -       +      -
    143B  PHE*     3.8    34.5    -      -       +      +
    146B  GLU*     4.4     8.3    -      -       -      -
    307B  ILE*     4.9     4.0    -      -       -      -
    308B  TYR      3.6     8.1    -      -       -      -
    309B  THR*     4.1     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  VAL      5.4     0.4    -      -       -      +
    106B  THR*     4.0     0.2    -      -       -      -
    109B  GLY      5.4     0.5    -      -       -      -
    110B  CYS*     1.3    78.4    +      -       -      +
    112B  HIS*     1.3    62.2    +      -       -      +
    113B  GLU*     4.0    25.6    -      -       +      +
    306B  VAL      4.5     0.7    -      -       -      +
    307B  ILE*     3.4     5.5    -      -       -      +
    308B  TYR*     2.9    49.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  SER*     4.0     0.5    -      -       -      -
    104B  VAL*     2.7    72.8    +      -       +      +
    106B  THR*     3.7    12.9    +      -       +      -
    110B  CYS*     5.7     0.2    -      -       -      -
    111B  THR*     1.3    75.8    -      -       -      +
    113B  GLU*     1.3    69.4    +      -       -      +
    125B  LEU*     4.2    23.1    -      -       +      -
    146B  GLU*     3.2    25.0    +      -       +      +
    149B  GLN*     5.3     1.1    -      -       -      -
    150B  CYS*     4.3     4.9    -      -       -      -
    305B  HIS*     3.5    20.4    +      -       -      -
    306B  VAL      3.7     3.1    -      -       -      -
    307B  ILE*     3.7    25.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  VAL*     4.3     7.6    -      -       +      -
    102B  GLN      3.4    11.4    -      -       -      +
    103B  SER*     4.5    14.9    -      -       -      -
    104B  VAL*     4.1     0.4    -      -       -      -
    111B  THR*     4.0    20.2    -      -       +      +
    112B  HIS*     1.3    83.4    -      -       -      +
    114B  VAL*     1.3    61.6    +      -       -      +
    290B  ARG*     3.0    49.0    +      -       -      +
    305B  HIS*     3.5     2.6    -      -       -      -
    306B  VAL*     3.0    43.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  VAL*     3.6     3.9    -      -       -      -
    102B  GLN*     3.0    31.4    +      -       +      +
    104B  VAL*     4.4     4.4    -      -       +      +
    112B  HIS*     4.8     2.0    -      -       -      +
    113B  GLU*     1.3    74.7    -      -       -      +
    115B  ALA*     1.3    71.3    +      -       -      +
    116B  LEU*     3.7    15.3    +      -       +      +
    122B  TYR*     3.7    36.8    -      -       +      -
    303B  PRO*     4.2     5.4    -      -       +      -
    304B  CYS      3.8     4.5    -      -       -      +
    305B  HIS*     3.0    42.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  VAL*     4.3     3.8    -      -       +      -
    100B  LYS      3.5     8.5    -      -       -      +
    101B  VAL*     4.3     6.5    -      -       +      +
    113B  GLU      4.3     0.2    -      -       -      -
    114B  VAL*     1.3    73.7    -      -       -      +
    116B  LEU*     1.3    59.4    +      -       -      +
    290B  ARG*     5.4     0.9    -      -       +      +
    293B  ALA*     3.9    27.1    -      -       +      +
    294B  GLU*     4.1    22.0    -      -       +      +
    297B  CYS*     4.0     4.7    -      -       +      +
    303B  PRO*     3.4     3.8    -      -       -      +
    304B  CYS      3.1    30.5    +      -       -      +
    306B  VAL*     5.7     1.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  VAL*     3.7     2.9    -      -       -      +
    100B  LYS*     3.0    55.5    +      -       +      +
    102B  GLN*     4.6     5.6    -      -       +      -
    114B  VAL*     4.1    28.0    -      -       +      +
    115B  ALA*     1.3    77.0    -      -       -      +
    117B  PRO*     1.3    79.3    -      -       +      +
    120B  GLU*     4.7     4.0    -      -       +      +
    121B  ASP      4.9     3.6    -      -       -      +
    122B  TYR*     3.9    41.1    -      -       +      +
    123B  LEU      5.2     1.6    -      -       -      +
    155B  GLN*     5.6     1.8    -      -       -      +
    297B  CYS*     3.4     6.1    -      -       -      -
    303B  PRO*     4.2    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  ARG      4.2     5.2    -      -       -      +
     99B  VAL*     4.7     0.4    -      -       +      -
    100B  LYS*     4.1     0.3    -      -       -      -
    116B  LEU*     1.3    91.3    -      -       +      +
    118B  ALA*     1.3    63.8    +      -       -      +
    119B  GLU*     3.1    21.0    +      -       +      +
    120B  GLU*     3.1    28.1    +      -       +      +
    297B  CYS*     3.3    13.2    -      -       -      -
    301B  LYS*     3.9    13.0    -      -       +      +
    302B  GLN*     3.8    33.0    -      -       -      +
    303B  PRO*     4.3     5.2    -      -       +      -
----------------------------------------------------------
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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