Contacts of the strand formed by residues 69 - 76 (chain B) in PDB entry 5D0A


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 69 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     5.9     0.2    -      -       -      -
     25B  THR      3.2    13.2    -      -       -      -
     26B  THR*     4.2     1.1    -      -       -      -
     27B  ALA*     3.7     3.8    -      -       -      +
     68B  LYS*     1.3    78.3    -      -       -      +
     70B  ILE*     1.3    71.1    +      -       -      +
    173B  ILE*     3.7     3.6    -      -       -      +
    174B  THR*     2.6    52.3    +      -       -      +
    176B  ILE      2.6    18.4    +      -       -      -
    178B  PHE*     3.4    28.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     3.7     2.9    -      -       -      +
     25B  THR*     2.6    44.6    +      -       +      +
     26B  THR      3.6    12.3    -      -       -      +
     27B  ALA*     4.5     0.7    -      -       -      -
     30B  PHE*     4.1    16.4    -      -       +      -
     60B  PRO*     3.7    34.3    -      -       +      -
     69B  SER*     1.3    80.4    -      -       -      +
     71B  VAL*     1.3    66.6    +      -       -      +
     72B  ALA      3.7     0.7    +      -       -      -
    138B  LEU*     4.3     7.4    -      -       +      -
    143B  VAL*     3.6    31.2    -      -       +      -
    171B  GLU*     3.8    17.9    -      -       +      -
    172B  MET      3.6    11.7    -      -       -      +
    173B  ILE*     4.3    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     4.1    11.4    -      -       +      -
     22B  ILE*     3.6    31.2    -      -       +      -
     23B  GLY      3.4     8.5    -      -       -      +
     24B  PHE*     3.8    23.3    -      -       +      -
     70B  ILE*     1.3    74.3    -      -       -      +
     72B  ALA*     1.3    61.4    +      -       -      +
     73B  ILE*     3.9     7.2    +      -       +      +
    113B  LEU*     5.3     0.6    -      -       +      +
    116B  LEU*     5.3     2.0    -      -       +      -
    171B  GLU*     3.2     6.9    -      -       -      -
    172B  MET*     2.9    53.4    +      -       +      +
    174B  THR*     4.5     9.2    -      -       +      -
    178B  PHE*     4.1    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ILE*     3.2     4.9    -      -       -      +
     23B  GLY      2.7    37.5    +      -       -      +
     70B  ILE      3.7     1.8    +      -       -      -
     71B  VAL*     1.3    71.7    -      -       -      +
     73B  ILE*     1.3    62.8    +      -       -      +
    143B  VAL*     4.0    16.8    -      -       +      -
    144B  ALA*     4.3     7.4    -      -       +      -
    147B  ALA*     3.8    18.8    -      -       +      -
    149B  ILE*     3.6    23.1    -      -       +      +
    170B  ALA      3.7     7.0    -      -       -      +
    171B  GLU*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     3.9    31.0    -      -       +      -
     21B  LYS      3.3     4.0    -      -       -      -
     22B  ILE*     4.2    10.3    -      -       +      -
     71B  VAL*     3.9     5.4    +      -       +      +
     72B  ALA*     1.3    79.7    -      -       -      +
     74B  ALA*     1.3    61.6    +      -       -      +
     75B  LEU*     4.5     2.7    -      -       +      -
    109B  LEU*     4.4    11.9    -      -       +      +
    112B  LYS*     4.4    13.5    -      -       +      -
    113B  LEU*     3.5    31.2    -      -       +      +
    116B  LEU*     3.9    22.9    -      -       +      -
    149B  ILE*     4.7     2.6    -      -       -      +
    168B  TYR      3.9     0.2    -      -       -      +
    169B  LEU*     3.5     5.2    -      -       -      +
    170B  ALA*     3.0    52.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 74 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     4.0     0.3    -      -       -      +
     20B  ASP*     3.0    24.7    +      -       -      +
     21B  LYS*     2.8    25.8    +      -       +      +
     73B  ILE*     1.3    76.2    -      -       -      +
     75B  LEU*     1.3    64.8    +      -       -      +
     76B  ALA      4.3     0.4    -      -       -      -
    149B  ILE*     3.9    26.2    -      -       +      -
    160B  THR*     5.4     0.7    -      -       +      -
    163B  TYR*     6.4     0.2    -      -       +      -
    167B  VAL*     4.2    14.1    -      -       +      -
    168B  TYR      3.2    11.0    -      -       -      +
    169B  LEU*     3.9     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  GLY      3.6    13.5    -      -       -      +
     19B  VAL*     3.9    25.1    -      -       +      -
     20B  ASP*     3.2     3.6    -      -       -      +
     73B  ILE*     4.5     6.5    -      -       +      -
     74B  ALA*     1.3    80.4    -      -       -      +
     76B  ALA*     1.3    63.0    +      -       -      +
     77B  TYR      3.7     0.3    +      -       -      -
    108B  VAL*     4.2    15.5    -      -       +      -
    109B  LEU*     4.2    23.8    -      -       +      -
    112B  LYS*     4.5    10.8    -      -       +      -
    167B  VAL*     4.2     3.4    -      -       -      -
    168B  TYR*     2.8    39.6    +      -       -      +
    258B  HIS*     3.5    27.6    -      -       +      +
    261B  MET*     3.9    20.6    -      -       +      -
    505B  PO4      4.3     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ASP*     2.7    16.5    +      -       -      +
     75B  LEU*     1.3    73.5    -      -       -      +
     77B  TYR*     1.3    61.3    +      -       -      +
     78B  PRO*     4.6     0.5    -      -       -      +
    163B  TYR*     3.6    43.7    -      -       +      -
    166B  TYR      3.4     8.5    -      -       -      +
    167B  VAL*     3.9     2.8    -      -       -      +
    255B  PHE*     4.1    17.7    -      -       +      +
    257B  LEU*     4.7     2.6    +      -       +      +
    258B  HIS*     3.2    25.6    -      -       -      -
    261B  MET*     3.6     1.6    -      -       -      +
----------------------------------------------------------
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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