Contacts of the strand formed by residues 80 - 94 (chain B) in PDB entry 1KY9


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 80 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  THR*     4.5     2.2    +      -       -      +
     37B  VAL*     3.1    38.4    +      -       +      +
     38B  ASN      3.8     1.6    -      -       -      +
     39B  THR*     3.7    14.7    -      -       -      +
     40B  PRO*     3.4    29.1    -      -       -      +
     79B  GLY*     1.3    77.0    -      -       -      +
     81B  GLN*     1.3    70.0    +      -       -      +
     82B  GLN*     3.2    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  SER*     3.4    26.6    +      -       -      +
     35B  THR*     3.0    17.5    -      -       -      +
     36B  THR*     2.4    29.4    +      -       -      +
     80B  GLN*     1.3    75.1    +      -       -      +
     82B  GLN*     1.3    76.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  SER*     3.0     6.0    -      -       -      -
     35B  THR*     2.7    41.2    +      -       +      +
     37B  VAL*     3.0    37.9    -      -       +      +
     80B  GLN*     3.2    27.7    +      -       -      +
     81B  GLN*     1.3    94.0    -      -       -      +
     83B  LYS*     1.3    68.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  GLU*     5.2    16.1    +      -       +      +
     33B  GLY      3.3    10.3    -      -       -      +
     34B  SER*     4.1     7.9    -      -       -      -
     82B  GLN*     1.3    82.8    +      -       -      +
     84B  PHE*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     31B  VAL*     4.5     7.0    -      -       +      -
     32B  GLU*     3.7     3.5    -      -       -      +
     33B  GLY*     2.8    62.0    +      -       -      -
     34B  SER*     3.3    22.0    -      -       -      -
     35B  THR*     4.0    16.2    -      -       +      -
     82B  GLN      4.8     0.4    -      -       -      +
     83B  LYS*     1.3    77.5    -      -       -      +
     85B  MSE      1.3    78.2    +      -       -      +
     86B  ALA*     4.2    19.3    -      -       +      -
    106B  VAL      5.1     0.2    -      -       -      -
    108B  ASP      3.9    15.7    -      -       -      -
    109B  ASN*     3.7    20.0    -      -       +      -
    110B  ALA      4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MSE 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  ASN*     6.0     5.4    -      -       -      +
     31B  VAL      3.4    10.3    -      -       -      +
     32B  GLU*     5.1     8.5    -      -       +      +
     84B  PHE*     1.3    86.5    -      -       -      +
     86B  ALA*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     30B  ASN*     3.6     3.8    +      -       -      +
     31B  VAL*     2.8    36.5    +      -       +      +
     84B  PHE*     4.2    12.5    -      -       +      -
     85B  MSE      1.3    76.6    -      -       -      +
     87B  LEU*     1.3    65.3    +      -       -      +
    105B  HIS      5.2     2.0    -      -       -      +
    106B  VAL*     3.6    30.5    -      -       +      +
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Residues in contact with LEU 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  ILE      3.1    11.9    -      -       -      +
     30B  ASN*     4.1    17.5    -      -       -      +
     86B  ALA*     1.3    80.7    -      -       -      +
     88B  GLY*     1.3    60.2    +      -       -      +
    106B  VAL*     3.8     9.3    -      -       -      +
    169B  ASN*     3.8    35.7    -      -       -      +
    172B  GLY*     3.8    26.7    -      -       -      +
    209B  ASN*     5.5    12.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  SER*     3.7     3.1    -      -       -      -
     29B  ILE*     2.9    33.2    +      -       -      +
     87B  LEU*     1.3    78.5    -      -       -      +
     89B  SER*     1.3    64.5    +      -       -      -
    103B  ASN*     6.0     0.2    -      -       -      -
    106B  VAL*     3.7    19.8    -      -       -      +
    169B  ASN*     4.8    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  VAL*     4.6     6.3    -      -       -      -
     27B  VAL      3.5     9.0    -      -       -      -
     29B  ILE*     4.0     4.5    -      -       -      -
     88B  GLY*     1.3    73.6    -      -       -      -
     90B  GLY*     1.3    55.3    +      -       -      +
    102B  THR*     2.6    28.8    +      -       -      -
    103B  ASN*     4.4     8.5    +      -       -      +
    167B  ILE      4.6     0.9    -      -       -      -
    168B  GLY*     3.5    12.8    -      -       -      -
    169B  ASN      3.4    21.1    +      -       -      +
    175B  GLU*     3.2    21.7    +      -       -      -
    211B  GLY*     4.9     4.0    +      -       -      -
    212B  GLY*     4.5    17.7    -      -       -      -
    213B  ALA      5.4     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  VAL*     3.6     5.2    -      -       -      +
     27B  VAL*     3.0    30.6    +      -       -      +
     29B  ILE*     4.0     4.3    -      -       -      +
     89B  SER*     1.3    77.7    -      -       -      +
     91B  VAL*     1.3    67.9    +      -       -      +
    100B  VAL*     3.7    13.7    -      -       -      -
    101B  VAL      3.0    13.7    -      -       -      -
    102B  THR*     3.9     2.9    -      -       -      -
    212B  GLY*     6.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  SER*     3.6     7.4    -      -       -      +
     26B  VAL*     4.5     9.2    -      -       +      -
     90B  GLY*     1.3    79.3    -      -       -      +
     92B  ILE*     1.3    66.1    +      -       -      +
     93B  ILE*     3.3     6.6    +      -       +      -
    100B  VAL*     3.2     5.5    -      -       -      +
    101B  VAL*     2.8    51.0    +      -       +      +
    150B  ILE*     3.3    41.1    -      -       +      -
    212B  GLY      5.4     0.2    -      -       -      -
    213B  ALA*     3.5    35.4    -      -       +      +
    221B  LEU*     4.5     7.2    -      -       +      -
    224B  ILE*     4.9     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PRO      3.9    11.0    -      -       -      +
     25B  SER*     2.9    15.1    +      -       -      +
     27B  VAL*     3.6    15.9    -      -       +      -
     90B  GLY      4.3     0.2    -      -       -      -
     91B  VAL*     1.3    70.0    -      -       -      +
     93B  ILE*     1.3    65.1    +      -       -      +
     94B  ASP      4.3     6.5    -      -       -      +
     95B  ALA*     4.3    11.2    -      -       -      -
     98B  GLY*     5.7     0.2    -      -       -      -
     99B  TYR      3.5     7.0    -      -       -      +
    100B  VAL*     3.9    10.8    -      -       +      -
    117B  LEU*     3.7    29.6    -      -       +      -
    141B  ILE*     4.6     2.5    -      -       +      -
    147B  LEU*     3.8    19.7    -      -       +      -
    148B  THR      3.0    35.0    -      -       -      +
    149B  ALA*     3.6    10.5    -      -       +      -
    150B  ILE      3.1    26.3    +      -       -      -
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Residues in contact with ILE 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  VAL*     3.6    16.8    -      -       +      +
     92B  ILE*     1.3    74.5    -      -       -      +
     94B  ASP*     1.3    57.4    +      -       +      +
     99B  TYR*     2.6    27.8    +      -       +      +
    101B  VAL*     4.3    13.2    -      -       +      +
    138B  LEU*     5.1     7.2    -      -       +      -
    149B  ALA*     4.0     9.0    -      -       -      +
    150B  ILE*     3.4    34.4    -      -       +      +
    152B  MSE      3.1    39.2    -      -       +      +
    221B  LEU*     3.9    12.1    -      -       +      -
    247B  VAL*     6.0     1.6    -      -       +      -
    251B  THR*     4.8    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  ILE*     3.7     3.5    -      -       -      +
     93B  ILE*     1.3    80.8    -      -       +      +
     95B  ALA*     1.3    58.1    +      -       -      +
     96B  ASP*     3.0    19.6    +      -       -      +
     97B  LYS*     3.0    32.6    +      -       -      +
     98B  GLY*     2.8    27.9    +      -       -      -
     99B  TYR*     3.1    34.9    +      -       +      +
    149B  ALA*     4.4     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