Contacts of the strand formed by residues 139 - 146 (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 139 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  ARG*     4.5     3.4    -      -       -      +
    138B  SER*     1.3    83.1    -      -       -      +
    140B  VAL*     1.3    63.1    +      -       -      +
    141B  THR*     3.9    20.0    +      -       +      -
    153B  GLN      3.3     3.5    -      -       -      +
    155B  VAL*     2.9    45.4    +      -       +      +
    157B  PRO*     6.0     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  GLU*     5.4     4.2    -      -       -      +
    124B  CYS*     3.5    41.4    -      -       +      +
    127B  LEU*     4.0    18.8    -      -       +      -
    128B  ARG*     3.9    36.4    -      -       +      +
    131B  LEU*     4.3     0.9    -      -       +      -
    138B  SER*     4.1     8.5    -      -       -      +
    139B  VAL*     1.3    77.3    -      -       -      +
    141B  THR*     1.3    72.5    +      -       -      +
    152B  PHE*     4.5     2.9    -      -       +      -
    153B  GLN      3.0     8.3    -      -       -      +
    154B  VAL*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  CYS*     3.8     3.1    -      -       -      -
    139B  VAL*     3.9    17.2    +      -       +      -
    140B  VAL*     1.3    79.5    -      -       -      +
    142B  ALA*     1.3    63.8    +      -       -      +
    151B  LYS      4.0     0.2    -      -       -      +
    152B  PHE*     3.3     5.4    -      -       -      +
    153B  GLN*     2.6    64.6    +      -       -      +
    155B  VAL*     5.8     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  LEU*     3.5    33.2    -      -       +      +
    124B  CYS*     3.3    24.6    -      -       -      -
    141B  THR*     1.3    77.0    -      -       -      +
    143B  SER*     1.3    64.0    +      -       -      +
    150B  CYS*     6.0     0.4    -      -       -      -
    151B  LYS      3.7     4.5    -      -       -      +
    152B  PHE*     4.0    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  LEU*     4.5     0.6    -      -       -      +
    142B  ALA*     1.3    78.5    -      -       -      +
    144B  VAL*     1.3    66.1    +      -       -      +
    145B  ALA      4.2     0.8    +      -       -      -
    149B  VAL      4.5     0.3    -      -       -      +
    150B  CYS*     3.4     3.0    -      -       -      +
    151B  LYS*     3.0    51.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  LEU*     3.9    11.2    -      -       +      -
    113B  LEU*     3.6    22.4    -      -       +      +
    116B  ALA*     4.5     8.7    -      -       +      -
    117B  PRO*     5.4     7.0    -      -       +      +
    120B  LEU*     3.4    25.3    -      -       +      +
    143B  SER*     1.3    75.6    +      -       -      +
    145B  ALA*     1.3    62.8    +      -       -      +
    146B  ALA      3.7    14.4    -      -       -      +
    147B  LEU*     3.8    23.6    -      -       +      +
    149B  VAL      4.2     5.6    -      -       -      +
    150B  CYS*     3.2    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110B  LEU*     5.5     1.0    -      -       -      +
    113B  LEU*     3.2    24.2    -      -       -      +
    143B  SER      4.2     1.2    +      -       -      -
    144B  VAL*     1.3    74.1    -      -       -      +
    146B  ALA*     1.3    64.5    +      -       +      +
    149B  VAL      4.3     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  GLY*     3.5    22.0    -      -       -      +
    110B  LEU*     5.4     3.1    -      -       +      -
    113B  LEU*     4.1     2.7    -      -       -      -
    144B  VAL*     3.6     3.3    -      -       -      -
    145B  ALA*     1.3    84.7    -      -       +      +
    147B  LEU*     1.3    68.6    +      -       -      +
    149B  VAL*     3.1    23.9    +      -       -      +
----------------------------------------------------------
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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