Contacts of the strand formed by residues 71 - 85 (chain B) in PDB entry 5JTP


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 GLU 71 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  ASN*     3.2    26.2    +      -       -      +
     30B  HIS*     4.8     4.7    -      -       -      +
     31B  VAL*     3.6    29.8    +      -       +      +
     33B  GLN*     4.6     4.6    -      -       -      +
     34B  LYS*     2.9    34.3    +      -       -      +
     67B  SER*     3.2     5.7    -      -       -      -
     68B  LEU      2.9    28.6    +      -       -      +
     70B  GLU*     1.3    80.2    -      -       -      +
     72B  THR*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  PRO*     3.8    21.6    -      -       +      +
     27B  ASN*     3.1    40.2    +      -       -      +
     31B  VAL*     3.4     5.8    -      -       -      +
     65B  THR*     5.9     0.4    -      -       +      -
     66B  ALA      3.6    13.7    -      -       -      +
     67B  SER*     3.9     4.4    -      -       -      -
     70B  GLU      4.4     0.2    +      -       -      -
     71B  GLU*     1.3    74.6    -      -       -      +
     73B  ALA*     1.3    62.3    +      -       -      +
     74B  PHE      3.9     6.1    -      -       -      +
     75B  LEU*     3.8    27.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  ALA*     3.9    12.3    -      -       -      +
     26B  PRO*     4.1     2.8    -      -       -      +
     28B  ALA      4.5     1.0    +      -       -      -
     31B  VAL*     4.0     8.3    -      -       -      +
     38B  PRO*     3.5    33.9    -      -       +      -
     66B  ALA      3.0     9.4    +      -       -      +
     67B  SER*     3.5     1.6    -      -       -      +
     68B  LEU*     3.9    14.8    -      -       +      +
     72B  THR*     1.3    76.2    -      -       -      +
     74B  PHE*     1.3    62.8    +      -       +      +
    123B  PHE*     3.1    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  PHE*     3.6    31.0    -      +       +      -
     24B  GLU      3.7     6.5    -      -       -      -
     25B  ALA*     4.4     0.7    -      -       +      +
     38B  PRO*     3.5    18.6    -      -       +      -
     64B  VAL*     4.1    16.8    -      -       +      -
     66B  ALA*     3.0    53.3    +      -       +      +
     72B  THR*     3.9     1.1    -      -       -      +
     73B  ALA*     1.3    79.6    -      -       -      +
     75B  LEU*     1.3    67.5    +      -       -      +
     76B  CYS*     4.0     8.5    -      -       +      -
    118B  VAL*     3.5    23.6    -      -       +      -
    123B  PHE*     3.7    37.7    -      +       +      -
    124B  PRO      5.1     2.2    -      -       -      -
    126B  LEU*     3.9    25.1    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     22B  SER*     4.2     1.2    +      -       -      +
     23B  PHE*     3.3     3.8    +      -       -      -
     24B  GLU*     2.8    64.5    +      -       +      +
     26B  PRO*     4.6     7.6    -      -       +      -
     63B  THR*     6.2     2.7    -      -       +      -
     64B  VAL      3.5     4.7    -      -       -      +
     65B  THR*     3.7    33.9    -      -       +      +
     72B  THR*     3.8    22.2    -      -       +      +
     74B  PHE*     1.3    82.8    -      -       -      +
     76B  CYS*     1.3    59.9    +      -       -      +
     77B  GLU*     4.2     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  SER      3.5    13.7    -      -       -      -
     23B  PHE*     3.7    12.3    -      -       +      -
     62B  VAL      4.3     0.5    -      -       -      +
     63B  THR*     3.8     0.8    -      -       -      -
     64B  VAL*     2.8    44.8    +      -       +      +
     74B  PHE*     4.0     6.7    -      -       +      -
     75B  LEU*     1.3    73.2    -      -       -      +
     77B  GLU*     1.3    56.4    +      -       -      +
     78B  VAL*     4.5     2.2    +      -       -      -
    114B  ILE*     3.3    49.5    -      -       +      +
    117B  MET*     3.7    16.4    -      -       -      -
    118B  VAL*     4.0    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ASP*     4.2     8.2    -      -       -      +
     21B  ILE      3.6     0.3    -      -       -      -
     22B  SER*     2.8    53.1    +      -       -      +
     61B  ARG*     2.9    44.9    +      -       +      +
     62B  VAL      3.3     7.2    -      -       -      +
     63B  THR*     3.2    35.2    +      -       +      +
     75B  LEU      4.2     1.2    +      -       -      -
     76B  CYS*     1.3    73.7    -      -       -      +
     78B  VAL*     1.3    71.2    +      -       -      +
     79B  GLN*     3.5    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  THR*     3.9     8.1    -      -       +      -
     20B  ASP      3.6     4.9    -      -       -      +
     21B  ILE*     3.5    31.4    -      -       +      -
     60B  LEU      3.9     0.2    -      -       -      +
     61B  ARG*     3.6     1.9    -      -       -      +
     62B  VAL*     2.9    35.3    +      -       +      +
     76B  CYS*     4.4     4.0    -      -       -      -
     77B  GLU*     1.3    79.0    -      -       -      +
     79B  GLN*     1.3    71.7    +      -       -      +
     80B  GLN*     4.0     2.0    -      -       -      +
    110B  ALA*     4.0    16.4    -      -       +      +
    113B  CYS*     3.7    15.7    -      -       +      +
    114B  ILE*     3.5    40.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  THR*     3.6     1.6    -      -       -      +
     19B  LYS*     2.9    31.3    +      -       +      +
     20B  ASP*     2.9    41.3    +      -       +      +
     59B  VAL*     3.7    22.5    -      -       +      +
     60B  LEU      3.1     7.2    -      -       -      +
     61B  ARG*     3.5    33.1    +      -       +      +
     77B  GLU*     3.5    19.8    -      -       -      +
     78B  VAL*     1.3    78.8    -      -       -      +
     80B  GLN*     1.3    60.9    +      -       -      +
     81B  GLY      3.6     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ARG      4.6     0.9    -      -       -      +
     16B  ILE*     3.3    16.7    -      -       +      +
     17B  TYR*     3.1    22.8    +      -       -      -
     18B  THR*     2.9    27.1    +      -       -      +
     59B  VAL*     4.6     0.4    -      -       -      -
     60B  LEU*     2.8    32.4    +      -       +      +
     78B  VAL*     4.0     2.4    -      -       -      +
     79B  GLN*     1.3    70.4    -      -       -      +
     81B  GLY*     1.3    59.9    +      -       -      +
    106B  LEU*     3.3    46.7    -      -       +      +
    109B  TYR*     3.3    32.9    +      -       +      +
    110B  ALA*     3.7    15.4    -      -       +      +
    113B  CYS*     4.6     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  TYR*     2.7    41.5    +      -       -      +
     19B  LYS*     3.8    15.1    -      -       -      +
     57B  GLU*     3.5     9.6    -      -       -      -
     58B  VAL      3.2    10.5    -      -       -      -
     59B  VAL*     4.0     3.6    -      -       -      +
     79B  GLN      3.6     5.3    +      -       -      -
     80B  GLN*     1.3    75.0    -      -       -      +
     82B  GLY*     1.3    58.3    +      -       -      -
    106B  LEU*     3.4     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ARG      3.3    12.3    -      -       -      -
     17B  TYR*     3.8     3.3    -      -       -      -
     57B  GLU*     3.2     6.3    +      -       -      -
     58B  VAL      2.8    36.0    +      -       -      -
     81B  GLY*     1.3    74.1    -      -       -      -
     83B  ILE*     1.3    63.2    +      -       -      -
     84B  PHE*     3.2    13.9    -      -       -      -
    106B  LEU*     3.9    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PRO*     4.1    10.5    -      -       +      -
     32A  PHE*     3.7    31.9    -      -       +      -
     14B  GLN*     3.0    44.2    +      -       +      -
     15B  ARG*     2.8    34.5    +      -       +      +
     17B  TYR*     3.7    12.6    -      -       +      -
     51B  LEU*     3.8    15.3    -      -       +      -
     55B  VAL*     3.5    30.3    -      -       +      -
     56B  TYR      3.8     4.3    -      -       -      +
     57B  GLU*     3.8    13.5    -      -       +      +
     82B  GLY*     1.3    71.8    -      -       -      -
     84B  PHE*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  PHE*     3.6    30.5    -      +       +      -
     12B  GLN      3.8     5.4    -      -       -      -
     13B  ILE*     3.9    27.1    -      -       +      -
     14B  GLN*     4.6     0.7    -      -       -      +
     16B  ILE*     4.9     0.2    -      -       +      -
     55B  VAL*     4.7     0.9    -      -       -      -
     56B  TYR*     2.9    35.1    +      -       -      +
     58B  VAL*     4.0    13.9    -      -       +      -
     82B  GLY*     3.2    32.8    -      -       -      -
     83B  ILE*     1.3    76.3    -      -       -      +
     85B  SER*     1.3    61.7    +      -       -      +
     86B  ILE*     3.6    16.7    +      -       +      +
     98B  LEU*     5.4     0.7    -      -       +      -
    102B  CYS*     3.6    45.3    -      -       +      -
    105B  ILE*     3.9    15.7    -      -       +      -
    106B  LEU*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  THR*     3.7     1.6    -      -       -      +
     11B  PHE*     3.2    22.0    -      -       -      +
     12B  GLN*     3.3    14.8    +      -       -      -
     14B  GLN*     2.9    35.2    +      -       -      +
     54B  ASP*     3.1    15.0    -      -       -      -
     55B  VAL*     3.6    20.2    -      -       -      +
     84B  PHE*     1.3    67.9    -      -       -      +
     86B  ILE*     1.4    59.7    +      -       -      +
     87B  ALA*     5.3     0.9    -      -       -      +
----------------------------------------------------------
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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