Contacts of the strand formed by residues 53 - 58 (chain B) in PDB entry 3E5X


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 53 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  PHE*     3.6    31.9    -      -       +      -
     52B  SER*     1.3    72.1    -      -       -      +
     54B  ILE*     1.3    60.0    +      -       -      +
     55B  PHE      3.9     0.7    -      -       -      -
     83B  LEU*     3.8    33.2    -      -       +      -
     84B  ILE      3.2     9.9    -      -       -      +
     85B  GLY*     4.3     5.8    -      -       -      -
     87B  LEU*     3.9    15.2    -      -       +      +
    105B  CYS      3.7     1.4    -      -       -      +
    106B  TRP*     3.4     3.3    -      -       -      -
    107B  PHE*     2.7    46.0    +      -       +      +
    112B  LEU*     3.7    23.6    -      -       +      -
    126B  ILE*     3.8    19.3    -      -       +      -
    130B  TYR*     3.4    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  VAL*     4.5     3.1    -      -       +      -
     44B  ILE*     4.2    19.7    -      -       +      -
     50B  ILE*     4.0    15.9    -      -       +      -
     52B  SER      3.9     4.5    -      -       -      +
     53B  MET*     1.3    75.2    -      -       -      +
     55B  PHE*     1.3    62.3    +      -       -      +
     56B  LEU*     3.9     1.7    +      -       +      +
     61B  ILE*     5.2     0.4    -      -       +      -
     82B  SER      3.9     0.5    -      -       -      +
     83B  LEU*     3.4     3.7    -      -       -      -
     84B  ILE*     2.7    65.1    +      -       +      +
    104B  THR*     3.8    32.5    -      -       +      -
    105B  CYS      3.7     1.8    -      -       -      -
    106B  TRP*     3.6    52.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ILE      3.3    26.7    -      -       -      -
     25B  LEU*     3.7    23.6    -      -       +      -
     26B  ARG*     3.8    29.8    -      -       +      -
     29B  THR*     4.0    11.0    -      -       +      -
     53B  MET      3.9     0.8    -      -       -      -
     54B  ILE*     1.3    76.4    -      -       -      +
     56B  LEU*     1.3    62.4    +      -       -      +
     57B  VAL*     3.5    24.5    +      -       +      -
     81B  ASN*     3.5    39.0    -      -       -      -
     82B  SER      3.4    13.7    -      -       -      -
     83B  LEU*     3.9     9.2    -      -       +      -
    104B  THR*     3.1     5.7    -      -       -      -
    105B  CYS*     2.8    44.5    +      -       +      +
    107B  PHE*     3.8    13.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE*     3.9     2.2    +      -       +      +
     55B  PHE*     1.3    73.9    -      -       -      +
     57B  VAL*     1.3    59.2    +      -       -      +
     58B  GLU      3.4    33.9    -      -       -      +
     59B  GLY*     3.6    10.1    -      -       -      +
     60B  LYS*     4.3     0.4    -      -       -      -
     61B  ILE*     3.8    34.3    -      -       +      +
     78B  ALA*     3.1    46.4    -      -       +      +
     79B  GLY*     3.5    16.4    -      -       -      +
     81B  ASN*     2.7    34.3    +      -       -      -
     82B  SER*     2.9    16.0    +      -       -      +
     84B  ILE*     6.0     2.5    -      -       +      -
    102B  THR*     4.0     5.8    -      -       +      -
    103B  ARG      3.9     2.2    -      -       -      -
    104B  THR*     4.5     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  ARG*     2.5    50.1    +      -       +      +
     29B  THR*     4.1    16.4    -      -       +      -
     34B  ILE*     4.7     4.0    -      -       +      -
     55B  PHE*     3.8    25.4    -      -       +      -
     56B  LEU*     1.3    73.0    -      -       -      +
     58B  GLU*     1.3    67.9    +      -       +      +
     80B  GLY*     3.9     3.7    -      -       -      -
    103B  ARG*     2.8    36.1    +      -       +      +
    104B  THR      4.2     5.8    -      -       -      +
    105B  CYS*     4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  ARG*     5.0     1.8    -      -       -      +
     56B  LEU*     3.4     9.1    -      -       -      +
     57B  VAL*     1.3    85.8    -      -       +      +
     59B  GLY*     1.3    59.6    +      -       -      +
     80B  GLY*     4.4     5.6    -      -       -      -
    101B  PRO      5.4     0.9    -      -       -      +
    102B  THR*     3.2     2.3    -      -       -      -
    103B  ARG*     2.8    34.9    +      -       +      +
    505B  3C4      3.7    30.7    -      -       -      +
----------------------------------------------------------
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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