Contacts of the strand formed by residues 238 - 245 (chain B) in PDB entry 1KYO


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 238 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  PRO*     3.7    32.3    -      -       +      +
    139B  VAL*     4.4    10.1    -      -       +      -
    142B  ALA*     4.4     4.4    -      -       +      +
    237B  SER*     1.3    75.6    -      -       -      +
    239B  ALA*     1.3    66.3    +      -       -      +
    240B  ALA*     4.2     0.8    +      -       +      -
    288B  PHE*     4.5     9.6    -      -       +      -
    289B  VAL      3.2    27.1    -      -       -      +
    290B  ARG*     3.7    18.4    -      -       +      -
    297B  VAL*     4.2     1.1    -      -       -      -
    354B  VAL      4.0     1.0    -      -       -      +
    355B  ALA*     3.9     0.3    -      -       -      -
    356B  VAL*     2.6    58.6    +      -       +      +
    362B  LEU*     4.6     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  VAL*     1.3    73.5    -      -       -      +
    240B  ALA*     1.3    59.8    +      -       -      +
    289B  VAL*     2.7    40.6    +      -       +      +
    297B  VAL*     3.8    17.6    -      -       +      +
    301B  ILE*     3.6    27.3    -      -       +      +
    353B  TYR*     3.8    20.4    -      -       -      +
    354B  VAL      3.7     4.5    -      -       -      -
    355B  ALA*     4.6     0.9    -      -       -      +
    362B  LEU*     4.8     6.3    -      -       +      -
    363B  PRO*     5.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  ALA*     4.5     3.6    -      -       +      -
    146B  LEU*     4.5     1.1    -      -       +      -
    238B  VAL*     4.2     0.9    +      -       +      -
    239B  ALA*     1.3    75.3    -      -       -      +
    241B  ILE*     1.3    67.7    +      -       -      +
    287B  LEU      3.0    17.5    -      -       -      +
    288B  PHE*     3.2    33.2    -      -       +      -
    301B  ILE*     4.0     3.9    -      -       -      +
    353B  TYR*     3.5     2.1    -      -       -      -
    354B  VAL*     3.1    48.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  LEU*     4.0     5.4    -      -       -      -
    240B  ALA*     1.3    79.2    -      -       -      +
    242B  GLY*     1.3    58.8    -      -       -      +
    243B  ILE*     5.3     4.9    -      -       +      -
    285B  PHE*     3.5     8.3    -      -       +      +
    286B  THR*     3.5     1.2    -      -       -      -
    287B  LEU*     3.0    62.6    +      -       +      +
    301B  ILE*     4.8     4.5    -      -       +      -
    304B  ILE*     5.1     2.7    -      -       +      -
    305B  VAL*     4.1    23.6    -      -       +      -
    308B  LEU*     6.0     1.6    -      -       +      -
    348B  LEU*     5.5     8.5    -      -       +      -
    351B  PHE*     3.7    35.0    -      -       +      -
    352B  ASN      3.1    14.4    -      -       -      +
    353B  TYR*     3.8    17.3    -      -       +      -
    368B  LEU*     5.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 242 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  LEU*     3.8    19.7    -      -       -      +
    150B  THR*     4.9     0.9    -      -       -      -
    241B  ILE*     1.3    73.5    -      -       -      +
    243B  ILE*     1.3    63.5    +      -       -      +
    244B  PRO*     4.0     0.8    -      -       -      +
    284B  LEU*     4.3    10.3    -      -       -      -
    285B  PHE      3.0     8.7    -      -       -      -
    286B  THR*     4.6     0.2    -      -       -      -
    352B  ASN*     3.1    41.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 243 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225B  LEU*     5.1     1.1    -      -       +      -
    241B  ILE*     5.3     5.6    -      -       +      -
    242B  GLY*     1.3    73.7    -      -       -      +
    244B  PRO*     1.3    76.8    -      -       +      +
    245B  VAL*     3.7     3.8    +      -       -      +
    253B  TYR*     3.6    38.1    -      -       +      +
    284B  LEU*     3.8     3.1    -      -       -      +
    285B  PHE*     2.9    47.3    +      -       +      +
    346B  PHE*     5.2     1.6    -      -       +      -
    348B  LEU*     4.3    23.8    -      -       +      -
    349B  GLY      5.9     1.3    -      -       -      +
    350B  LYS      3.8    15.0    -      -       -      +
    351B  PHE*     3.4    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  THR*     4.8     1.3    -      -       +      -
    151B  PHE*     3.8    25.4    -      -       +      -
    223B  PHE*     3.9    32.2    -      -       +      +
    224B  PHE      4.6     2.7    -      -       -      +
    225B  LEU*     3.6    31.2    -      -       +      -
    242B  GLY      4.0     4.3    -      -       -      +
    243B  ILE*     1.3    95.5    -      -       +      +
    245B  VAL*     1.3    61.7    +      -       -      +
    253B  TYR*     5.2     1.2    -      -       -      -
    283B  GLY      3.3     7.9    -      -       -      +
    284B  LEU*     3.6     9.4    -      -       +      -
    352B  ASN*     4.4     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  GLU*     5.0     0.2    -      -       -      +
    223B  PHE*     3.6    20.6    -      -       -      -
    243B  ILE      3.7     9.6    -      -       -      +
    244B  PRO*     1.3    78.2    -      -       -      +
    246B  ASN*     1.3    71.4    +      -       -      +
    249B  SER*     4.6     1.6    -      -       -      -
    250B  LEU*     3.5    31.0    -      -       +      +
    253B  TYR*     3.5    42.8    -      -       +      -
    276B  LEU*     4.2     7.4    -      -       +      -
    282B  GLY*     4.2     3.3    -      -       -      -
    283B  GLY*     2.8    42.6    +      -       -      +
----------------------------------------------------------
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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