Contacts of the strand formed by residues 79 - 90 (chain B) in PDB entry 1YHQ


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 MET 79 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  VAL*     6.3     0.2    -      -       +      -
     40B  GLY      4.4     2.0    -      -       -      +
     41B  PHE*     3.1    57.4    -      -       +      -
     42B  ALA*     3.6    27.1    -      -       +      +
     77B  PRO      4.2     2.2    -      -       -      +
     78B  PRO*     1.3    76.3    -      -       -      +
     80B  ARG*     1.3    73.9    +      -       -      +
    144B  THR*     3.6    24.5    -      -       +      -
    145B  HIS      3.5     9.6    -      -       -      +
    146B  THR*     3.9    19.7    -      -       +      +
    147B  VAL*     5.0     0.4    -      -       -      -
    162B  MET*     5.1     4.0    -      -       +      +
    164B  THR*     5.6     2.2    -      -       -      +
    187B  GLU*     3.3     2.8    -      -       -      +
    188B  HIS*     2.9    41.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  PRO      5.2     0.2    -      -       -      +
     79B  MET*     1.3    87.3    -      -       -      +
     81B  ALA*     1.3    59.2    +      -       -      +
     82B  VAL*     3.0    17.5    +      -       +      +
    104B  GLU*     5.6     5.1    +      -       -      +
    105B  PHE*     4.6     3.6    +      -       -      +
    106B  HIS*     4.0    40.1    -      -       -      +
    145B  HIS*     3.1    51.7    +      -       +      +
    147B  VAL*     4.5    12.9    -      -       +      +
    185B  GLY      4.1    17.7    +      -       -      +
    186B  GLY      3.5     4.0    -      -       -      -
    187B  GLU*     4.0    28.7    +      -       +      +
    188B  HIS*     3.9     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  ARG*     1.3    68.4    -      -       -      +
     82B  VAL*     1.3    62.1    +      -       -      +
     83B  ALA      3.5     1.7    +      -       -      -
    142B  LEU*     3.7    38.1    -      -       +      -
    143B  ILE      3.4     8.1    -      -       -      -
    144B  THR*     3.9     5.2    -      -       -      +
    181B  ILE*     4.0    11.0    -      -       +      -
    182B  VAL*     3.8     9.4    -      -       +      +
    185B  GLY      4.2     0.2    -      -       -      -
    186B  GLY*     2.9    36.1    +      -       -      +
    188B  HIS*     3.4    11.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  ARG*     3.0    19.9    +      -       +      +
     81B  ALA*     1.3    73.2    -      -       -      +
     83B  ALA*     1.3    61.8    +      -       -      +
    101B  TRP*     3.3    41.5    -      -       +      -
    102B  THR*     3.7    11.7    +      -       -      +
    104B  GLU      5.1     3.1    -      -       -      +
    105B  PHE*     3.3    27.8    -      -       +      -
    106B  HIS      6.1     0.2    -      -       -      +
    109B  LEU*     4.5     6.5    -      -       +      -
    143B  ILE*     2.9    11.1    +      -       +      +
    144B  THR*     5.9     0.4    -      -       -      -
    145B  HIS*     3.6    25.8    -      -       +      +
    182B  VAL*     3.8     4.9    -      -       -      +
    185B  GLY      4.7     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  ALA      3.5     1.6    -      -       -      -
     82B  VAL*     1.3    81.9    -      -       -      +
     84B  LEU*     1.3    62.0    +      -       -      +
     99B  GLU*     4.9     0.7    -      -       +      -
    100B  VAL      3.2    13.7    -      -       -      +
    101B  TRP*     3.4    33.7    -      -       +      +
    142B  LEU*     3.2    11.6    -      -       -      +
    143B  ILE*     2.9    41.0    +      -       +      -
    182B  VAL*     3.8     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  ALA*     1.3    74.4    -      -       -      +
     85B  ARG*     1.3    66.5    +      -       -      +
     86B  ALA*     4.7     1.8    -      -       +      +
     98B  THR      3.9     0.5    -      -       -      +
     99B  GLU*     3.2     3.9    -      -       -      -
    100B  VAL*     2.9    44.2    +      -       +      +
    128B  ILE*     3.7    26.7    -      -       +      -
    140B  LEU*     4.5    12.3    -      -       +      -
    141B  ARG      3.3    23.1    -      -       -      +
    142B  LEU*     3.9     4.3    -      -       +      -
    166B  VAL*     5.4     0.4    -      -       +      -
    175B  LEU*     5.0     8.1    -      -       +      -
    178B  ALA*     3.6    30.1    -      -       +      -
    179B  LEU*     4.6    11.7    -      -       +      -
    182B  VAL*     3.9    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26700    G      3.3     8.3    -      -       -      +
   26710    U      2.8    33.7    +      -       -      -
   26720    C      3.6     9.3    +      -       -      -
   28190    C      2.9    19.1    +      -       -      -
     83B  ALA      4.0     1.6    -      -       -      -
     84B  LEU*     1.3    77.5    -      -       -      +
     86B  ALA*     1.3    67.5    +      -       -      +
     87B  TYR*     3.4    35.4    +      -       +      -
     96B  PRO*     4.0    18.7    -      -       +      +
     98B  THR      3.4     7.0    -      -       -      +
     99B  GLU*     2.6    42.5    +      -       +      -
    140B  LEU*     4.0     1.0    -      -       -      -
    141B  ARG      2.9    35.5    +      -       -      +
    142B  LEU*     4.9     0.2    -      -       -      +
    143B  ILE*     4.2    14.8    -      -       +      +
    163B  GLU*     2.7    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  LEU*     4.0     0.4    +      -       +      -
     85B  ARG*     1.3    74.7    -      -       -      +
     87B  TYR*     1.3    56.1    +      -       -      +
     96B  PRO*     3.6     3.5    -      -       -      +
     97B  LEU*     2.6    38.9    +      -       +      +
     98B  THR      2.9     9.3    +      -       -      +
    128B  ILE*     3.6    36.1    -      -       +      -
    137B  LEU*     3.9    18.4    -      -       +      -
    139B  ASP      4.5     0.2    -      -       -      -
    140B  LEU*     4.1     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26720    C      2.8    30.5    +      -       -      -
   26730    U      3.8    10.1    -      -       -      -
     85B  ARG*     3.4    26.0    +      -       +      -
     86B  ALA*     1.3    78.1    -      -       -      +
     88B  GLU*     1.3    56.2    +      -       -      +
     94B  GLN*     4.1    22.7    -      -       +      -
     95B  ARG      3.3    19.3    -      -       -      +
     96B  PRO*     3.6    11.4    -      -       +      -
     97B  LEU*     4.7     1.1    -      -       -      -
    137B  LEU*     3.4    10.4    -      -       -      +
    138B  GLY*     2.5    30.5    +      -       -      -
    139B  ASP*     3.5    33.7    +      -       -      +
    141B  ARG*     3.7    20.7    +      -       +      -
    163B  GLU*     2.4    39.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  TYR*     1.3    74.1    -      -       -      +
     89B  ASP*     1.3    66.5    +      -       -      +
     90B  THR*     3.4    22.9    +      -       +      +
     94B  GLN*     3.6     3.4    -      -       -      -
     95B  ARG*     2.9    37.4    +      -       +      +
     96B  PRO      5.3     1.2    -      -       -      +
     97B  LEU*     4.2    32.0    -      -       +      +
    131B  ALA*     5.8     0.2    -      -       +      -
    136B  ASP*     3.0    20.9    -      -       +      +
    137B  LEU*     4.5     0.2    -      -       -      +
    138B  GLY*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU*     1.3    74.8    -      -       -      +
     90B  THR*     1.3    61.5    +      -       -      +
     93B  GLY      4.3     2.7    -      -       -      -
     94B  GLN*     3.3    30.7    +      -       -      +
    135B  GLY      5.4     1.6    -      -       -      +
    136B  ASP*     2.7    30.8    +      -       -      +
    137B  LEU      3.7    15.4    -      -       -      +
    138B  GLY*     3.6     6.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU*     3.4    36.6    -      -       +      +
     89B  ASP*     1.3    80.3    -      -       -      +
     91B  PRO*     1.3    69.4    -      -       -      +
     92B  TYR*     2.9    25.2    +      -       -      +
     93B  GLY*     2.9    26.8    +      -       -      +
     95B  ARG*     4.3    19.4    +      -       +      -
    144J  THR*     2.8    16.3    +      -       -      -
----------------------------------------------------------
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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