Contacts of the strand formed by residues 135 - 141 (chain B) in PDB entry 1OBZ


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 GLY 135 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLY*     6.4     0.7    -      -       -      -
    232A  LEU      5.5     0.4    -      -       -      -
    233A  LEU*     3.9    15.0    -      -       -      -
    131B  SER*     3.3     8.7    +      -       -      -
    132B  ILE      2.9    31.0    +      -       -      -
    133B  ASP      3.1     2.4    +      -       -      -
    134B  ASN*     1.3    79.6    -      -       -      +
    136B  ILE*     1.3    66.0    +      -       -      +
    137B  PHE*     4.1     2.9    -      -       -      -
    157B  GLN*     4.5     6.3    -      -       -      -
    166B  CYS      5.0     0.7    -      -       -      -
    167B  ALA*     4.9     5.4    -      -       -      -
    169B  TRP      4.7     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  LEU*     3.7    35.7    -      -       +      -
    130B  LYS      3.5     2.5    -      -       -      +
    131B  SER*     3.7    17.3    -      -       -      +
    135B  GLY*     1.3    78.4    -      -       -      +
    137B  PHE*     1.3    61.1    +      -       -      +
    157B  GLN*     3.5     8.5    -      -       -      +
    158B  VAL*     2.7    44.9    +      -       +      +
    166B  CYS*     3.7    39.2    -      -       +      +
    169B  TRP*     3.6    26.7    -      -       +      +
    170B  SER      4.1     2.9    -      -       -      +
    174B  ALA*     4.0    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LEU*     3.9    24.0    -      -       +      -
    129B  LEU*     3.3     7.2    -      -       -      -
    130B  LYS      2.9    30.0    +      -       -      +
    132B  ILE*     3.5    50.0    -      -       +      -
    133B  ASP*     5.5     0.4    -      -       +      -
    135B  GLY      4.1     6.1    -      -       -      -
    136B  ILE*     1.3    74.4    -      -       -      +
    138B  VAL*     1.3    65.8    +      -       -      +
    139B  GLN*     3.4    17.0    +      -       -      +
    155B  GLY*     3.5    21.3    -      -       -      +
    156B  ASP      3.3     7.9    -      -       -      +
    157B  GLN*     3.6    35.9    -      -       +      -
    158B  VAL*     4.7     0.4    -      -       -      +
    194B  PRO*     4.0    13.9    -      -       +      -
    195B  PHE*     5.7     2.9    -      +       -      -
    270B  MET*     4.7     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  LEU*     3.8    15.7    -      -       +      -
    128B  ARG      3.8     4.3    -      -       -      -
    129B  LEU*     3.9    15.5    -      -       +      -
    137B  PHE*     1.3    70.6    -      -       -      +
    139B  GLN*     1.3    68.7    +      -       -      +
    140B  LEU      4.1     2.9    -      -       -      +
    141B  VAL*     3.5    29.2    -      -       +      -
    152B  LEU*     4.5    10.1    -      -       +      -
    153B  ARG*     3.3    24.2    -      -       -      +
    154B  PHE*     3.5     3.6    -      -       -      +
    155B  GLY      2.9    23.4    +      -       -      -
    156B  ASP*     2.8    30.7    +      -       +      +
    158B  VAL*     4.0    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  ARG*     2.8    27.2    +      -       +      +
    129B  LEU      4.0     1.3    -      -       -      +
    130B  LYS*     3.1    47.6    +      -       +      +
    132B  ILE*     3.9     9.7    -      -       -      +
    137B  PHE*     3.4    23.8    +      -       -      +
    138B  VAL*     1.3    92.2    +      -       -      +
    140B  LEU*     1.3    68.3    +      -       -      +
    154B  PHE*     3.3    39.7    -      -       -      -
    155B  GLY*     5.2     0.8    -      -       -      +
    247B  ILE*     4.0     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  GLY      3.8     0.5    -      -       -      +
    127B  LEU*     3.6     4.9    -      -       -      +
    128B  ARG*     3.0    71.7    +      -       +      +
    138B  VAL*     3.8     1.4    -      -       -      +
    139B  GLN*     1.3    83.8    -      -       -      +
    141B  VAL*     1.3    71.9    +      -       -      +
    142B  GLN*     3.4    24.7    -      -       -      +
    154B  PHE*     5.7     1.6    -      -       -      -
    245B  ASN*     6.2     1.3    -      -       -      +
    247B  ILE*     4.2    27.4    -      -       +      +
    248B  GLY*     5.0     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  GLY      3.4     7.2    -      -       -      +
    127B  LEU*     4.1     6.1    -      -       +      -
    138B  VAL*     3.5    29.8    -      -       +      -
    140B  LEU*     1.3    80.8    -      -       -      +
    142B  GLN*     1.3    71.7    +      -       -      +
    143B  ALA      3.6     1.6    +      -       -      -
    147B  ALA*     4.0     5.4    -      -       +      -
    148B  SER*     3.5    36.3    -      -       -      +
    152B  LEU*     3.5    23.6    -      -       +      +
    153B  ARG*     3.8     8.3    -      -       -      -
    154B  PHE      4.3     1.5    -      -       -      +
    245B  ASN*     5.0     9.7    +      -       -      +
----------------------------------------------------------
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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