Contacts of the strand formed by residues 135 - 140 (chain T) in PDB entry 1V2J


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 GLN 135 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133T  GLY      3.4     8.7    +      -       -      +
    134T  THR*     1.3    77.3    -      -       -      +
    136T  CYS*     1.3    65.4    +      -       -      +
    159T  LYS*     4.1    12.8    -      -       +      +
    160T  ALA      3.7    15.8    +      -       -      +
    161T  PRO*     3.5    20.0    -      -       -      +
    184T  TYR*     3.9    17.3    -      -       -      -
    201T  CYS*     3.7    12.3    -      -       -      +
    202T  SER      4.7     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 136 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134T  THR      3.7     3.1    -      -       -      -
    135T  GLN*     1.3    77.2    -      -       -      +
    137T  LEU*     1.3    60.3    +      -       -      +
    138T  ILE*     4.1     2.9    -      -       +      -
    158T  LEU      3.6     0.5    -      -       -      +
    159T  LYS*     3.2     7.8    -      -       -      +
    160T  ALA*     2.6    43.3    +      -       -      +
    162T  ILE*     3.7    27.1    -      -       -      -
    199T  VAL*     3.8    17.3    -      -       +      -
    200T  VAL      3.3     5.4    -      -       -      +
    201T  CYS*     2.0    46.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 137 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20T  TYR*     3.6    24.0    -      -       -      +
     26T  THR      5.8     0.9    -      -       -      +
     27T  VAL*     4.5    11.2    -      -       +      -
     29T  TYR*     4.1    20.6    +      -       -      +
    136T  CYS*     1.3    74.0    -      -       -      +
    138T  ILE*     1.3    63.6    +      -       -      +
    139T  SER*     4.4     2.2    +      -       -      -
    157T  CYS*     4.0    26.5    -      -       +      -
    158T  LEU      3.5    13.7    -      -       -      +
    159T  LYS*     4.4     6.3    -      -       +      -
    198T  PRO*     3.6     2.6    -      -       -      +
    199T  VAL*     3.5     2.6    -      -       -      -
    200T  VAL*     2.7    39.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 138 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16T  ILE*     4.1    14.9    -      -       +      +
    136T  CYS*     4.7     3.1    -      -       +      +
    137T  LEU*     1.3    78.5    -      -       -      +
    139T  SER*     1.3    66.2    +      -       -      +
    157T  CYS*     3.5     1.2    -      -       -      -
    158T  LEU*     2.8    50.5    +      -       +      +
    160T  ALA*     3.8    28.0    -      -       +      +
    183T  ALA*     4.9     5.8    -      -       +      -
    184T  GLY*     6.1     0.2    -      -       -      -
    190T  SER*     4.3     6.1    -      -       -      -
    198T  PRO      3.5    11.4    -      -       -      +
    199T  VAL*     4.1    17.0    -      -       +      -
    213T  VAL*     4.0    22.4    -      -       +      -
    228T  TYR*     3.5    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 139 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16T  ILE*     4.1     8.7    -      -       -      +
     22T  CYS*     4.3     3.1    -      -       -      -
     27T  VAL*     3.7    14.8    -      -       -      +
     29T  TYR*     5.1     0.7    +      -       -      -
     30T  GLN*     2.7    33.1    +      -       -      +
    137T  LEU*     5.2     3.1    +      -       -      +
    138T  ILE*     1.3    80.9    -      -       -      +
    140T  GLY*     1.3    58.9    +      -       -      +
    155T  LEU*     4.4     5.4    -      -       -      -
    156T  LYS      3.2    14.6    -      -       -      -
    157T  CYS*     4.0    15.7    -      -       -      -
    194T  ASP*     4.4     4.7    -      -       -      +
    197T  GLY*     4.6     5.9    -      -       -      -
    198T  PRO*     3.7    16.7    +      -       -      +
    213T  VAL*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16T  ILE*     3.9     3.0    -      -       -      +
     30T  GLN*     4.3     7.2    -      -       -      -
    139T  SER*     1.3    76.6    -      -       -      +
    141T  TRP*     1.3    59.2    +      -       -      -
    142T  GLY      3.4     0.6    +      -       -      -
    155T  LEU*     3.6    16.2    -      -       -      +
    156T  LYS*     3.0    35.9    +      -       -      +
    194T  ASP*     3.3    19.4    -      -       -      +
----------------------------------------------------------
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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