Contacts of the strand formed by residues 18 - 23 (chain A) in PDB entry 3H8E


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 18 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ALA*     3.9    33.9    -      -       +      +
     11A  ALA*     4.9     2.5    -      -       -      +
     15A  THR*     3.8     5.5    -      -       +      +
     17A  THR*     1.3    74.0    -      -       -      +
     19A  VAL*     1.4    58.3    -      -       -      +
     20A  ILE*     4.3     8.3    -      -       +      -
     35A  VAL*     3.9    33.4    -      -       +      -
     68A  LEU*     5.0     3.1    -      -       +      -
     70A  ALA*     3.7    20.6    -      -       +      -
     72A  ARG      2.9     7.9    +      -       -      +
     73A  VAL*     3.2    17.1    -      -       +      +
     74A  LEU      2.8    30.3    +      -       -      +
    109A  VAL*     3.6    28.0    -      -       +      +
    111A  ALA*     4.2     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  THR*     4.3    10.5    -      -       +      +
     18A  LEU*     1.4    76.1    -      -       -      +
     20A  ILE*     1.3    66.1    +      -       -      +
     74A  LEU*     3.3    27.4    -      -       +      +
     76A  VAL*     3.9    22.9    -      -       +      -
     96A  VAL*     4.0    33.0    -      -       +      -
    100A  LEU*     4.4     6.5    -      -       +      -
    108A  ALA*     5.0     0.4    -      -       +      -
    109A  VAL      2.8    20.2    +      -       -      +
    110A  LEU*     4.3    11.7    -      -       +      -
    111A  ALA*     2.8    31.2    +      -       -      +
    112A  LEU*     4.3     8.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     4.3     7.9    -      -       +      -
     19A  VAL*     1.3    79.3    -      -       -      +
     21A  PRO*     1.3    69.8    -      -       +      +
     22A  VAL*     5.3     0.9    -      -       +      -
     31A  VAL*     4.7     4.9    -      -       +      -
     32A  ALA*     4.0    23.6    -      -       +      +
     35A  VAL*     4.2    26.9    -      -       +      -
     43A  ILE*     4.2    22.7    -      -       +      -
     73A  VAL*     4.1     8.7    -      -       +      -
     74A  LEU      3.0     2.6    +      -       -      -
     75A  LEU*     3.4    30.8    -      -       +      -
     76A  VAL*     2.9    27.8    +      -       -      +
    111A  ALA*     3.9    20.2    -      -       +      +
    112A  LEU*     4.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ILE*     1.3    89.0    -      -       +      +
     22A  VAL*     1.3    66.2    +      -       -      +
     27A  LYS      4.9     0.7    -      -       -      +
     28A  LEU*     4.2     1.6    -      -       -      +
     29A  GLY      5.2     1.6    +      -       -      -
     31A  VAL*     5.5     1.3    -      -       +      -
     32A  ALA*     3.5    25.2    -      -       +      +
     76A  VAL*     3.2    13.0    -      -       +      +
     78A  SER*     4.2    10.5    -      -       -      +
     92A  LEU*     5.8     0.2    -      -       +      -
    111A  ALA      3.3    17.7    -      -       -      +
    112A  LEU*     3.8    11.9    -      -       +      -
    114A  ASP*     4.9    12.8    -      -       +      -
    115A  VAL*     3.8    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ILE*     5.3     1.6    -      -       +      -
     21A  PRO*     1.3    81.5    -      -       -      +
     23A  GLY*     1.4    74.5    +      -       -      +
     26A  ARG*     4.0    12.8    -      -       -      -
     27A  LYS      3.9     3.4    -      -       -      -
     28A  LEU*     3.8    17.0    -      -       +      -
     47A  LEU*     3.9    32.3    -      -       +      -
     52A  LEU*     4.1    15.3    -      -       +      +
     54A  GLY*     3.8     1.4    -      -       -      +
     75A  LEU*     3.9    33.4    -      -       +      -
     76A  VAL      2.8     9.6    +      -       -      +
     77A  GLY*     3.2     7.6    -      -       -      -
     78A  SER*     2.9    22.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     1.4    82.6    -      -       -      +
     24A  GLU*     1.3    71.6    +      -       -      +
     26A  ARG      3.3    10.9    +      -       -      -
     27A  LYS*     2.9    21.7    +      -       -      -
     52A  LEU      5.6     0.2    -      -       -      +
     53A  ALA      4.2     0.3    -      -       -      +
     54A  GLY*     3.8     7.5    -      -       -      -
     78A  SER*     3.5    14.6    +      -       -      -
     79A  GLY      3.5     7.6    -      -       -      -
----------------------------------------------------------
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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