Contacts of the strand formed by residues 165 - 175 (chain B) in PDB entry 4JDA


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 TYR 165 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  GLU*     2.9    33.9    +      -       -      +
     57B  ARG*     4.0    20.6    -      -       +      -
     58B  VAL      3.5    12.1    -      -       -      +
     59B  ASP*     3.7    13.7    -      -       +      +
     60B  ALA      4.0     7.9    -      -       -      +
     61B  PRO*     5.6     0.2    -      -       -      +
    152B  GLU*     3.5     4.7    -      -       -      +
    153B  PHE*     2.6    75.7    +      +       +      +
    155B  VAL*     3.6    29.5    -      -       +      +
    164B  VAL*     1.3    77.0    -      -       -      +
    166B  SER*     1.3    67.5    +      -       -      +
    167B  VAL*     4.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  ARG*     3.6     3.3    -      -       -      -
     58B  VAL*     3.0    31.8    +      -       -      +
     60B  ALA      2.6    24.6    +      -       -      -
     62B  ALA*     3.2    12.3    +      -       -      +
     65B  ILE*     3.2    22.6    -      -       -      +
    150B  VAL*     3.9    13.9    -      -       -      -
    151B  ASN      3.2    14.4    -      -       -      -
    152B  GLU*     4.1     2.3    -      -       -      -
    153B  PHE*     4.6     0.4    -      -       -      -
    165B  TYR*     1.3    80.6    -      -       -      +
    167B  VAL*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  LEU*     4.7    10.1    -      -       +      -
     29B  GLU*     4.2    14.1    -      -       +      +
     33B  LEU*     5.4     4.7    -      -       +      -
     55B  ALA*     4.5     9.4    -      -       +      -
     56B  HIS      3.8     7.4    -      -       -      +
     57B  ARG*     3.7    26.7    -      -       +      +
    149B  SER      3.6     1.9    -      -       -      +
    151B  ASN*     2.8    34.6    +      -       +      +
    153B  PHE*     3.8    26.9    -      -       +      -
    165B  TYR*     4.3     0.9    -      -       +      -
    166B  SER*     1.3    74.3    -      -       -      +
    168B  VAL*     1.3    66.5    +      -       -      +
    169B  LEU*     3.9    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE      3.7     0.9    -      -       -      +
     55B  ALA*     3.4     3.3    -      -       -      -
     56B  HIS*     3.0    37.8    +      -       +      +
     58B  VAL*     4.2    17.3    -      -       +      -
     65B  ILE*     4.2    23.3    -      -       +      -
     69B  VAL*     5.5     0.2    -      -       +      -
    148B  THR*     3.7    26.7    -      -       +      -
    149B  SER      3.4     6.7    -      -       -      +
    150B  VAL*     4.3    12.8    -      -       +      -
    167B  VAL*     1.3    75.8    -      -       -      +
    169B  LEU*     1.3    64.1    +      -       -      +
    197B  LEU*     3.9    25.5    -      -       +      +
    200B  LEU*     4.4     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  LEU*     4.8     7.0    -      -       +      -
     33B  LEU*     5.2     9.6    -      -       +      -
     36B  ILE*     5.8     1.1    -      -       +      -
     37B  ILE*     5.0     9.9    -      -       +      -
     41B  HIS*     3.3    29.5    -      -       +      +
     53B  LEU*     4.0    17.0    -      -       +      -
     54B  ILE      3.4     1.6    -      -       -      -
     55B  ALA*     3.8    26.2    -      -       +      -
    148B  THR*     3.1     6.8    -      -       -      +
    149B  SER*     2.9    40.0    +      -       -      +
    151B  ASN*     4.1    10.5    -      -       -      +
    167B  VAL*     3.9    13.0    -      -       +      -
    168B  VAL*     1.3    72.8    -      -       -      +
    170B  GLU*     1.3    60.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  SER      4.3     0.3    -      -       -      +
     53B  LEU*     4.0     1.1    -      -       -      -
     54B  ILE*     2.7    42.3    +      -       -      +
     78B  TYR*     5.6     5.4    +      -       -      -
     79B  LYS*     5.6     1.2    -      -       -      -
    132B  PHE*     6.2     0.9    -      -       -      -
    144B  TYR*     5.5     0.9    -      -       -      +
    146B  SER*     3.7    14.6    -      -       -      +
    147B  VAL      3.3     2.5    -      -       -      -
    148B  THR*     2.9    33.2    -      -       +      +
    168B  VAL      4.0     0.2    +      -       -      -
    169B  LEU*     1.3    74.2    -      -       -      +
    171B  SER*     1.3    61.5    +      -       -      +
    172B  TYR*     5.3     1.9    -      -       +      -
    193B  VAL*     3.4    36.9    -      -       +      +
    196B  ASN*     4.8     5.2    +      -       -      +
    197B  LEU*     4.0    20.0    -      -       +      +
    301B  A9S      4.1    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  HIS*     2.8    48.8    +      -       -      -
     43B  PHE*     3.4     6.9    -      -       -      -
     52B  SER      3.2    12.6    -      -       -      -
     53B  LEU*     3.6    15.3    -      -       -      -
    146B  SER*     3.2     4.5    +      -       -      -
    147B  VAL*     2.8    35.5    +      -       -      +
    170B  GLU*     1.3    75.8    -      -       -      +
    172B  TYR*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  PHE*     3.3     8.0    -      -       -      -
     50B  CYS*     3.8    22.9    -      -       -      -
     51B  THR*     2.4    35.9    +      -       -      -
     52B  SER*     3.0    36.5    +      -       -      -
     54B  ILE*     5.4     3.4    -      -       +      -
    144B  TYR*     3.5    32.5    -      +       +      +
    145B  ARG      3.2    12.3    -      -       -      +
    146B  SER*     4.3     0.9    -      -       -      -
    170B  GLU*     5.3     2.2    -      -       +      -
    171B  SER*     1.3    77.0    -      -       -      +
    173B  ILE*     1.3    63.1    +      -       -      +
    174B  VAL*     4.1     6.1    -      -       +      -
    186B  ARG*     3.3    23.2    +      -       -      +
    189B  VAL*     3.4    28.9    -      -       +      +
    190B  ASP*     2.7    23.8    +      -       -      -
    193B  VAL*     4.4     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  PHE*     3.6    38.8    -      -       +      -
     44B  PRO*     3.9    23.1    -      -       +      +
     45B  ARG*     5.6     0.9    -      -       -      -
     46B  SER*     4.8     3.4    -      -       -      +
     49B  THR*     4.0    27.8    -      -       +      +
     50B  CYS      3.2    11.4    -      -       -      +
     51B  THR*     4.4     6.3    -      -       +      -
    143B  ASN      4.7     4.3    -      -       -      +
    144B  TYR*     3.3     2.3    -      -       -      -
    145B  ARG*     2.9    44.3    +      -       +      +
    172B  TYR*     1.3    75.8    -      -       -      +
    174B  VAL*     1.3    70.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  THR*     3.2     6.7    -      -       -      -
     50B  CYS*     2.8    48.5    +      -       +      +
    141B  LEU*     3.5    51.1    -      -       +      +
    142B  ASN      3.8     1.3    -      -       -      +
    143B  ASN      4.2     6.5    -      -       -      -
    144B  TYR*     3.8    14.8    -      -       +      -
    172B  TYR*     4.1    14.6    -      -       +      -
    173B  ILE*     1.3    79.6    -      -       -      +
    175B  ASP*     1.3    69.5    +      -       -      +
    185B  THR*     4.2    16.8    -      -       +      -
    189B  VAL*     4.8     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  ASN      3.7     7.4    -      -       -      +
     49B  THR*     3.8    15.9    -      -       -      +
    140B  ARG      4.6     3.8    -      -       -      +
    142B  ASN*     3.2    28.6    +      -       +      +
    143B  ASN*     2.7    33.2    +      -       -      +
    174B  VAL*     1.3    85.2    -      -       -      +
    176B  ILE*     1.3    71.0    +      -       -      +
    177B  PRO*     3.1    10.3    -      -       +      +
    185B  THR*     4.9     0.5    -      -       -      +
----------------------------------------------------------
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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