Contacts of the strand formed by residues 93 - 100 (chain B) in PDB entry 5UHF


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 VAL 93 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  SER*     4.0    16.2    -      -       -      +
     89B  GLU*     4.9     9.0    -      -       +      +
     91B  GLU      3.3    13.9    +      -       -      +
     92B  PRO*     1.3    74.4    -      -       -      +
     94B  THR*     1.3    68.6    +      -       -      +
    113B  PRO*     4.4    15.5    -      -       +      -
    116B  VAL*     4.1    25.8    -      -       +      -
    139B  VAL*     3.7     3.1    -      -       -      +
    140B  VAL*     2.9    53.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  PRO      5.1     0.3    +      -       -      -
     93B  VAL*     1.3    81.8    +      -       -      +
     95B  MET*     1.3    62.0    +      -       -      +
     96B  TYR*     3.9    26.4    -      -       +      +
    113B  PRO*     3.7    13.4    -      -       -      +
    137B  GLU*     3.8    26.6    +      -       +      +
    138B  LEU      3.2    17.1    +      -       -      +
    139B  VAL*     4.3    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  LEU*     5.3     1.3    -      -       -      -
     85B  VAL*     4.3    11.7    -      -       +      -
     93B  VAL*     5.1     0.9    -      -       +      +
     94B  THR*     1.3    73.9    -      -       -      +
     96B  TYR*     1.3    65.0    +      -       -      +
    110B  ILE*     3.6    26.0    -      -       +      -
    111B  VAL      3.3    17.3    -      -       -      +
    112B  PRO*     4.7     3.6    -      -       +      -
    113B  PRO*     3.8    12.8    -      -       +      -
    116B  VAL*     3.6    31.0    -      -       +      -
    118B  VAL*     4.8     6.7    -      -       +      -
    138B  LEU*     2.9    55.9    +      -       +      +
    140B  VAL*     3.7    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  THR*     3.9    23.0    -      -       +      +
     95B  MET*     1.3    79.5    -      -       -      +
     97B  LEU*     1.3    61.0    +      -       -      +
     98B  ARG*     3.6    42.8    -      -       +      +
    110B  ILE*     4.5     1.4    -      -       -      +
    111B  VAL*     3.1    39.5    +      -       +      +
    136B  VAL      3.7     4.9    -      -       -      +
    137B  GLU*     3.7    43.4    +      -       +      -
    138B  LEU*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     80B  LEU*     6.2     1.8    -      -       +      -
     96B  TYR*     1.3    75.3    -      -       -      +
     98B  ARG*     1.3    72.0    +      -       -      +
    105B  VAL*     3.8    24.9    -      -       +      -
    106B  THR      3.9     4.9    -      -       -      +
    109B  ASP*     3.2    44.0    -      -       +      +
    110B  ILE*     3.7    26.5    -      -       +      +
    111B  VAL*     5.3     0.4    -      -       -      -
    125B  ILE*     4.3    11.4    -      -       +      -
    134B  LEU*     4.0     1.6    -      -       -      +
    135B  GLU*     3.9     1.0    -      -       -      -
    136B  VAL*     3.1    39.5    +      -       +      +
    138B  LEU*     5.2     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  TYR*     3.6    45.6    -      -       +      +
     97B  LEU*     1.3    91.0    -      -       -      +
     99B  LYS*     1.3    66.6    +      -       -      +
    109B  ASP*     5.3     2.1    -      -       -      +
    111B  VAL*     5.7     5.5    -      -       -      +
    134B  LEU      3.5     7.2    -      -       -      +
    135B  GLU*     4.1    33.3    +      -       +      +
    136B  VAL      4.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  LEU*     5.3     0.2    -      -       +      -
     98B  ARG*     1.3    77.3    -      -       -      +
    100B  GLN*     1.3    70.4    +      -       -      +
    102B  PRO      5.6     4.2    +      -       -      -
    103B  GLY*     6.2     1.4    -      -       -      -
    104B  GLU      4.9     7.3    +      -       -      +
    105B  VAL*     3.9    31.2    -      -       +      -
    109B  ASP*     3.4    39.5    -      -       +      +
    128B  LEU*     3.2    16.2    -      -       +      +
    134B  LEU*     3.2    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  LYS*     1.3    87.5    +      -       -      +
    101B  GLY*     1.3    73.8    +      -       -      +
    102B  PRO      5.1     0.9    -      -       -      +
    128B  LEU*     4.2     1.8    -      -       -      -
    131B  LYS*     5.1     6.6    -      -       -      +
    132B  GLY      3.3    21.3    -      -       -      +
    133B  LYS*     3.7    38.9    +      -       +      +
    134B  LEU      5.0     0.4    -      -       -      +
----------------------------------------------------------
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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