Contacts of the strand formed by residues 254 - 260 (chain A) in PDB entry 3H44


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 MET 254 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  GLY      4.4     0.9    -      -       -      +
     73A  ILE*     3.4    19.3    -      -       +      -
     74A  LYS*     3.2    24.6    +      -       -      +
     90A  LEU*     3.8    27.4    -      -       +      -
     91A  ASP      3.3     2.2    -      -       -      -
     92A  VAL*     4.0     8.5    -      -       +      -
    169A  PHE*     4.0    18.8    -      -       +      +
    249A  TYR*     3.6    53.4    -      -       +      +
    250A  SER      3.8     8.5    -      -       -      +
    251A  SER*     3.6    19.5    -      -       -      +
    252A  ASN      3.3     3.7    +      -       -      +
    253A  LEU*     1.3    81.9    -      -       -      +
    255A  ALA*     1.3    61.2    +      -       -      +
    278A  VAL*     4.1    13.7    -      -       +      -
    442A  HIS*     3.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LYS*     3.3    10.1    -      -       +      +
     89A  ALA      3.8     0.3    -      -       -      +
     90A  LEU*     3.2     7.4    -      -       -      +
     91A  ASP      2.8    32.0    +      -       -      +
    254A  MET*     1.3    75.1    -      -       -      +
    256A  VAL*     1.3    62.6    +      -       -      +
    438A  ALA*     3.3    28.1    -      -       -      +
    441A  LEU*     3.6    22.9    -      -       +      -
    442A  HIS*     3.6    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ILE*     3.5    23.3    -      -       +      -
     74A  LYS      2.9     9.4    +      -       -      +
     75A  VAL*     3.1    14.5    -      -       +      +
     76A  LEU      2.9    24.8    +      -       -      +
     88A  ALA*     5.3     1.1    -      -       +      -
     89A  ALA      3.3    11.9    -      -       -      +
     90A  LEU*     3.8    20.2    -      -       +      -
    165A  PHE*     5.7     0.9    -      -       +      -
    255A  ALA*     1.3    76.5    -      -       -      +
    257A  VAL*     1.3    68.1    +      -       -      +
    258A  VAL*     3.9    22.9    -      -       +      -
    271A  VAL*     5.0     4.0    -      -       +      -
    275A  PHE*     4.4    30.7    -      -       +      -
    441A  LEU*     3.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  LEU*     3.2    17.7    -      -       +      +
     78A  ILE*     3.8    29.2    -      -       +      -
     88A  ALA*     3.1     6.1    -      -       -      -
     89A  ALA      3.0    30.5    +      -       -      +
    256A  VAL*     1.3    77.4    -      -       -      +
    258A  VAL*     1.3    67.6    +      -       -      +
    259A  LEU      4.3     0.2    -      -       -      -
    434A  THR*     3.6    25.9    -      -       +      +
    437A  ILE*     3.9    13.9    -      -       +      -
    438A  ALA*     3.4    33.0    -      -       -      +
    441A  LEU*     4.1     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  VAL*     5.5     0.2    -      -       -      +
     76A  LEU      3.0     8.3    +      -       -      -
     77A  LEU*     3.5    14.8    -      -       +      +
     78A  ILE      2.7    33.4    +      -       -      +
     87A  SER      3.6     6.3    -      -       -      +
     88A  ALA*     3.7    13.7    -      -       +      -
    158A  LEU*     4.0    30.5    -      -       +      -
    162A  LEU*     4.3    13.0    -      -       +      -
    256A  VAL*     3.9    11.4    -      -       +      -
    257A  VAL*     1.3    80.8    -      -       -      +
    259A  LEU*     1.3    58.1    +      -       -      +
    267A  LEU*     4.0    15.0    -      -       +      +
    270A  LEU*     4.8     2.5    -      -       +      -
    271A  VAL*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ARG*     4.8    10.5    -      -       -      +
     78A  ILE*     3.1    43.1    -      -       +      +
     80A  ASP*     4.7     6.1    -      -       +      +
     83A  THR*     4.0    24.9    -      -       +      +
     85A  LYS      4.0     4.3    -      -       -      +
     86A  SER*     3.2     5.5    -      -       -      -
     87A  SER      2.9    36.9    +      -       -      +
    158A  LEU*     4.3     2.9    -      -       -      +
    257A  VAL      4.3     0.2    -      -       -      -
    258A  VAL*     1.3    78.4    -      -       -      +
    260A  GLY*     1.3    61.2    +      -       -      +
    430A  PRO*     3.8    31.2    -      -       +      -
    433A  TYR*     4.3    13.2    -      -       +      -
    434A  THR*     4.0    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ILE      3.1     5.5    +      -       -      -
     79A  SER*     3.5     5.7    -      -       -      -
     80A  ASP      2.9    20.3    +      -       -      -
     83A  THR*     4.0    10.5    -      -       -      -
     86A  SER*     3.1    16.2    -      -       -      -
    158A  LEU*     4.9     1.1    -      -       -      -
    258A  VAL      4.4     0.2    +      -       -      -
    259A  LEU*     1.3    75.3    -      -       -      +
    261A  ARG*     1.3    64.9    +      -       -      -
    262A  GLU*     3.1    11.9    +      -       -      +
    267A  LEU*     4.4     6.3    -      -       -      +
----------------------------------------------------------
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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