Contacts of the strand formed by residues 149 - 155 (chain B) in PDB entry 2J3T


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 VAL 149 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  GLN*     4.0    14.8    -      -       -      +
     97B  ASP      3.6     4.9    -      -       -      +
     98B  ASN*     3.2    46.9    -      -       +      +
    143B  SER      4.5     0.3    -      -       -      +
    144B  VAL*     4.2     7.7    -      -       -      +
    145B  ALA*     4.3     7.6    +      -       -      +
    146B  ALA      3.1    19.1    +      -       -      +
    148B  PRO*     1.3    78.9    -      -       +      +
    150B  CYS*     1.3    59.6    +      -       -      +
    151B  LYS*     5.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  GLN*     3.7     3.3    -      -       -      +
     97B  ASP*     3.1    29.6    +      -       -      +
    100B  PHE*     3.8    29.2    -      -       -      -
    103B  LEU*     4.2     3.6    -      -       +      -
    120B  LEU*     4.2     8.3    -      -       +      -
    142B  ALA*     6.0     0.2    -      -       -      -
    143B  SER      3.4     5.4    -      -       -      +
    144B  VAL*     3.2    30.7    -      -       +      -
    148B  PRO      3.2     5.1    +      -       -      -
    149B  VAL*     1.3    74.1    -      -       -      +
    151B  LYS*     1.3    60.9    +      -       -      +
    152B  PHE*     3.6    31.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  VAL*     4.5    23.5    -      -       +      +
     95B  LEU      3.5     7.4    -      -       -      +
     96B  GLN*     3.0    35.9    +      -       +      +
    141B  THR      4.0     0.2    -      -       -      +
    142B  ALA*     3.7     1.0    -      -       -      -
    143B  SER*     3.0    47.6    +      -       -      +
    149B  VAL      5.6     0.9    -      -       -      +
    150B  CYS*     1.3    76.2    -      -       -      +
    152B  PHE*     1.3    63.7    -      -       -      +
    153B  GLN*     3.9     2.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 152 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  TRP*     3.8    24.5    -      +       -      -
     82B  MET*     4.9     2.9    -      -       +      -
     94B  VAL*     3.6     2.2    -      -       -      -
     95B  LEU*     2.6    55.7    +      -       +      +
     97B  ASP*     4.9     2.9    -      -       +      -
    100B  PHE*     3.9    24.0    -      +       -      -
    120B  LEU*     4.5     5.2    -      -       +      -
    123B  THR*     3.8    22.2    -      -       +      -
    124B  CYS*     4.0    12.8    -      -       -      -
    127B  LEU*     3.9    26.5    -      -       +      -
    140B  VAL*     4.5     2.2    -      -       +      -
    141B  THR      3.3     5.2    -      -       -      +
    142B  ALA*     4.0    24.2    -      -       +      -
    150B  CYS*     3.6    32.3    -      -       -      -
    151B  LYS*     1.3    72.1    -      -       -      +
    153B  GLN*     1.3    60.6    +      -       -      +
    154B  VAL*     5.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  THR*     4.0    24.4    -      -       +      +
     93B  TYR      3.3    10.8    -      -       -      +
     94B  VAL*     4.5    14.6    -      -       +      +
    139B  VAL      3.3     2.6    -      -       -      +
    140B  VAL*     3.0     6.5    -      -       -      -
    141B  THR*     2.6    56.1    +      -       -      +
    151B  LYS      3.9     2.3    +      -       -      +
    152B  PHE*     1.3    71.3    -      -       -      +
    154B  VAL*     1.3    63.5    +      -       -      +
    155B  VAL*     4.1    13.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  LEU*     4.6    10.1    -      -       +      -
     69B  LEU*     5.5     1.3    -      -       +      -
     91B  GLY      3.3     3.6    -      -       -      +
     92B  THR*     3.3     1.9    -      -       -      -
     93B  TYR*     2.6    47.5    +      -       +      +
     95B  LEU*     3.8    28.7    -      -       +      -
    127B  LEU*     5.0     4.3    -      -       +      -
    131B  LEU*     3.4    31.4    -      -       +      -
    138B  SER*     4.0     5.2    -      -       -      +
    139B  VAL      3.6     2.0    -      -       -      -
    140B  VAL*     3.9    19.5    -      -       +      -
    152B  PHE      4.7     0.9    -      -       -      +
    153B  GLN*     1.3    75.0    -      -       -      +
    155B  VAL*     1.3    61.1    +      -       -      +
    156B  ILE*     3.9    16.6    -      -       +      -
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Residues in contact with VAL 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  GLN      6.1     0.2    -      -       -      +
     91B  GLY      3.8     2.0    -      -       -      -
     92B  THR*     3.6    29.4    -      -       +      +
    138B  SER*     3.3     3.9    -      -       -      -
    139B  VAL*     2.9    47.5    +      -       +      +
    141B  THR*     5.8     0.4    -      -       -      +
    153B  GLN*     4.1    17.3    -      -       +      +
    154B  VAL*     1.3    74.9    -      -       -      +
    156B  ILE*     1.3    68.2    +      -       -      +
    157B  PRO*     3.3    11.5    -      -       +      +
----------------------------------------------------------
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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