Contacts of the strand formed by residues 105 - 110 (chain B) in PDB entry 5J2Q


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 SER 105 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  LYS*     4.1     0.3    -      -       -      +
    104B  LYS*     1.3    80.1    -      -       -      +
    106B  VAL*     1.3    65.5    +      -       -      +
    190B  GLY*     3.3     2.1    -      -       -      -
    191B  SER      3.1    27.7    +      -       -      +
    193B  LEU      5.1     4.8    +      -       -      -
    195B  ILE*     5.0    10.6    -      -       -      +
    198B  HIS*     3.4    34.6    -      -       -      +
    233B  GLU*     5.2     4.9    -      -       -      -
    234B  LEU      3.3     7.4    -      -       -      -
    235B  HIS*     3.3    22.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  LEU*     4.0    15.5    -      -       +      -
    103B  LYS*     4.1     7.2    -      -       +      -
    105B  SER*     1.3    80.7    -      -       -      +
    107B  THR*     1.3    67.7    +      -       -      +
    108B  VAL*     4.1     0.9    +      -       +      -
    188B  TYR*     4.3    22.2    -      -       +      -
    189B  VAL      3.2    17.5    -      -       -      +
    190B  GLY*     3.6    13.0    -      -       -      -
    198B  HIS*     4.4     0.2    -      -       -      -
    233B  GLU*     3.8     1.8    -      -       -      -
    234B  LEU*     2.7    58.5    +      -       +      +
    236B  PRO*     3.6    24.5    -      -       +      -
    381B  VAL*     5.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  VAL*     1.3    73.0    -      -       -      +
    108B  VAL*     1.3    65.8    +      -       -      +
    109B  LEU*     3.7    13.1    +      -       +      -
    187B  LEU      3.5     3.8    -      -       -      +
    188B  TYR*     3.8     1.4    -      -       -      -
    189B  VAL*     2.9    31.7    +      -       -      +
    198B  HIS*     2.9    24.6    +      -       -      -
    202B  ILE*     3.6    36.8    -      -       +      +
    233B  GLU*     4.1    18.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  VAL      4.1     1.3    +      -       -      +
    107B  THR*     1.3    77.4    -      -       -      +
    109B  LEU*     1.3    65.3    +      -       -      +
    110B  ASP      4.2     0.7    +      -       -      -
    186B  ASP*     4.0    30.7    -      -       +      +
    187B  LEU      3.8     3.1    -      -       -      +
    188B  TYR*     3.6    34.8    -      -       +      +
    233B  GLU*     5.6     3.3    -      -       -      +
    234B  LEU*     4.2    26.7    -      -       +      -
    377B  THR*     5.1     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  THR*     4.1    12.1    -      -       +      -
    108B  VAL*     1.3    77.5    -      -       -      +
    110B  ASP*     1.3    61.1    +      -       -      +
    111B  VAL*     3.9     5.6    -      -       +      -
    186B  ASP*     3.3     7.4    -      -       -      +
    187B  LEU*     2.8    49.9    +      -       +      +
    189B  VAL*     4.2     9.6    -      -       +      -
    202B  ILE*     3.9    31.0    -      -       +      +
    205B  LEU*     4.1    29.8    -      -       +      -
    206B  ARG*     3.4    33.9    -      -       +      +
    209B  LEU*     4.9     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  LYS*     5.2     6.7    +      -       -      -
     72B  ARG*     3.1    37.8    +      -       -      -
    108B  VAL      4.2     1.0    +      -       -      +
    109B  LEU*     1.3    73.6    -      -       -      +
    111B  VAL*     1.3    61.0    +      -       -      +
    112B  GLY      3.1    16.3    +      -       -      -
    113B  ASP*     5.2     2.9    +      -       -      +
    185B  ASP*     3.4    13.8    -      -       -      +
    186B  ASP*     4.4     5.4    -      -       -      +
    206B  ARG*     5.4     5.8    +      -       -      +
    409B  THR*     3.9    11.2    -      -       +      +
----------------------------------------------------------
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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