Contacts of the strand formed by residues 96 - 105 (chain B) in PDB entry 6UPR


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 GLN 96 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  GLY*     3.3    15.8    -      -       -      +
     43B  PHE      3.3    23.7    +      -       -      +
     89B  ASP*     4.5     9.7    -      -       -      +
     90B  LEU      3.7     7.8    +      -       -      +
     91B  GLN*     2.3    35.4    +      -       -      +
     94B  ASN      4.4     0.2    +      -       -      -
     95B  VAL*     1.3    70.8    -      -       -      +
     97B  LEU*     1.3    67.9    +      -       -      +
     98B  LYS      3.8     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  PHE*     3.6    29.2    -      -       +      +
     45B  PHE*     3.7    26.9    -      -       +      -
     65B  PHE*     4.3    17.5    -      -       +      -
     88B  TYR      3.6     1.2    -      -       -      +
     89B  ASP*     3.5     4.2    -      -       -      -
     90B  LEU*     2.8    48.5    +      -       +      +
     92B  GLU*     4.0    25.1    -      -       +      +
     95B  VAL*     2.9    14.1    +      -       +      +
     96B  GLN*     1.3    75.7    +      -       -      +
     98B  LYS*     1.3    60.8    +      -       -      +
     99B  LEU*     3.5    13.9    -      -       +      +
    285B  MET*     4.2    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  PHE      3.2     9.9    +      -       -      +
     44B  SER*     3.3    15.1    -      -       -      +
     45B  PHE      3.0    22.6    +      -       -      +
     46B  ASN*     4.5     1.0    -      -       -      +
     87B  THR*     3.8    20.6    -      -       +      -
     88B  TYR      3.7     2.5    -      -       -      -
     89B  ASP*     2.7    38.1    +      -       -      +
     96B  GLN      3.8     0.8    +      -       -      -
     97B  LEU*     1.3    70.1    -      -       -      +
     99B  LEU*     1.3    60.8    +      -       -      +
    100B  THR*     3.7     1.6    +      -       -      -
    146B  HIS*     3.4    33.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  PHE*     3.3    23.6    -      -       +      +
     47B  ILE*     3.9    27.1    -      -       +      -
     65B  PHE*     3.5    34.5    -      -       +      -
     69B  PHE*     3.9    14.1    -      -       +      -
     86B  GLN      3.7     0.9    -      -       -      +
     87B  THR*     3.1     1.6    -      -       -      +
     88B  TYR*     2.5    48.1    +      -       +      +
     90B  LEU*     3.9    14.1    -      -       +      -
     97B  LEU*     3.5    11.8    -      -       +      -
     98B  LYS*     1.3    72.6    -      -       -      +
    100B  THR*     1.3    66.3    +      -       -      +
    101B  ILE*     3.9    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  PHE      2.9     7.8    +      -       -      +
     46B  ASN*     3.3    21.7    +      -       +      +
     47B  ILE*     2.9    28.2    +      -       -      +
     85B  PRO*     4.0    15.0    -      -       +      -
     86B  GLN      3.3     9.2    -      -       -      +
     87B  THR*     2.8    27.3    +      -       -      +
     98B  LYS      3.7     0.9    +      -       -      -
     99B  LEU*     1.3    72.6    -      -       -      +
    101B  ILE*     1.3    64.2    +      -       -      +
    102B  VAL*     3.7    22.0    -      -       +      -
    123B  TYR*     4.5     4.5    -      -       -      +
    146B  HIS*     4.5    10.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ILE*     3.6     7.9    -      -       +      +
     49B  CYS*     4.6    10.1    -      -       +      -
     61B  MET*     4.2    36.1    -      -       +      -
     65B  PHE*     4.7     1.3    -      -       +      -
     69B  PHE*     3.7    40.2    -      -       +      -
     84B  ARG      3.6     2.6    -      -       -      +
     85B  PRO*     3.5     1.7    -      -       -      +
     86B  GLN*     2.8    35.7    +      -       +      +
     88B  TYR*     4.2     8.7    -      -       +      -
     99B  LEU*     3.9    24.0    -      -       +      -
    100B  THR*     1.3    74.4    -      -       -      +
    102B  VAL*     1.3    64.9    +      -       -      +
    103B  ASP*     4.1     4.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ILE      2.7    15.5    +      -       -      +
     48B  LEU*     3.5     7.6    -      -       +      +
     49B  CYS*     2.7    34.7    +      -       -      +
     83B  LEU*     3.7    27.6    -      -       +      -
     84B  ARG      3.6    12.1    -      -       -      +
     85B  PRO*     3.9     2.9    -      -       +      -
    100B  THR*     3.7    16.6    -      -       +      +
    101B  ILE*     1.3    77.2    -      -       -      +
    103B  ASP*     1.3    58.1    +      -       -      +
    123B  TYR*     3.6    37.0    -      -       +      +
    150B  ILE*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  CYS*     3.7     8.5    -      -       +      +
     57B  LYS*     2.6    40.5    +      -       -      +
     58B  SER*     5.3     1.9    +      -       -      -
     74B  ALA*     6.2     0.2    -      -       -      +
     82B  ARG      3.3     0.3    -      -       -      +
     83B  LEU*     3.5     3.8    -      -       -      -
     84B  ARG*     2.9    63.3    +      -       -      +
    101B  ILE*     4.1     5.6    +      -       +      +
    102B  VAL*     1.3    73.2    -      -       -      +
    104B  ALA*     1.3    69.7    +      -       -      +
    105B  VAL*     3.2    16.2    +      -       +      +
    401B  GTP      4.2    12.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  LEU*     4.8     0.2    -      -       -      +
     49B  CYS      3.2    15.2    +      -       -      +
     50B  VAL*     4.4     7.9    -      -       +      -
     57B  LYS*     3.4    10.9    +      -       -      -
     81B  VAL*     3.9    17.9    -      -       +      -
     82B  ARG      3.4     5.2    -      -       -      -
     83B  LEU*     4.1     9.7    -      -       +      +
    102B  VAL      4.2     0.2    -      -       -      -
    103B  ASP*     1.3    78.3    +      -       -      +
    105B  VAL*     1.3    63.6    +      -       -      +
    106B  GLY      3.6     0.9    +      -       -      -
    107B  PHE*     3.7    14.7    +      -       +      +
    120B  ILE*     4.1    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  LYS*     5.0     1.1    -      -       -      +
     74B  ALA*     4.0    24.0    -      -       +      -
     78B  GLU*     4.2    19.4    -      -       +      +
     80B  CYS      3.9     1.6    -      -       -      +
     81B  VAL*     3.2     8.3    -      -       -      -
     82B  ARG*     2.5    61.5    +      -       +      +
     84B  ARG*     3.8    29.2    -      -       +      +
    103B  ASP*     3.6    25.8    -      -       -      +
    104B  ALA*     1.3    70.8    -      -       -      +
    106B  GLY*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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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