Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 3KYM


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 34 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     4.0    20.4    -      -       +      -
     22B  CYS*     4.4     5.6    -      -       -      -
     27B  PHE*     4.9     1.6    -      -       -      -
     29B  PHE*     4.0    20.6    -      -       +      -
     32B  TYR*     4.8     3.6    -      -       -      -
     33B  PRO*     1.3    78.8    -      -       -      +
     35B  PHE*     1.3    64.5    +      -       -      +
     50B  TRP*     3.3     7.3    -      -       -      -
     51B  ILE*     3.0    33.6    +      -       +      +
     70B  ILE*     4.3     1.1    -      -       -      +
     72B  ARG*     4.0    22.0    -      -       -      +
     79B  LEU*     3.5    38.1    -      -       +      -
     97B  ALA      3.9     7.2    -      -       -      +
     98B  ARG*     3.2    50.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  LEU*     4.1     4.3    -      -       +      -
     34B  MET*     1.3    77.6    -      -       -      +
     36B  TRP*     1.3    67.9    -      -       -      +
     47B  TRP*     3.8    19.1    -      +       -      -
     49B  SER      3.2     6.5    -      -       -      -
     50B  TRP*     3.5    21.5    -      +       +      -
     79B  LEU*     3.7     3.7    -      -       -      +
     96B  CYS*     3.1     9.7    -      -       -      +
     97B  ALA*     3.0    25.7    +      -       +      -
     98B  ARG      3.8     4.1    -      -       -      +
     99B  GLU*     3.2    37.5    -      -       +      -
    104B  TRP*     3.1    49.6    -      +       +      -
    105B  TYR      4.3     2.7    -      -       -      -
    106B  PHE*     3.3    45.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with TRP 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLU*     4.4     9.0    -      -       +      -
     20B  LEU*     3.9    29.4    -      -       +      -
     21B  SER      3.9     9.4    -      -       -      -
     22B  CYS*     3.8    20.9    -      -       +      -
     35B  PHE*     1.3    75.9    -      -       -      +
     37B  VAL*     1.3    65.9    +      -       -      +
     47B  TRP*     3.8     2.4    -      -       -      -
     48B  VAL*     3.1    31.1    +      -       +      -
     49B  SER*     2.9    23.9    +      -       -      +
     70B  ILE*     3.1    32.3    -      -       +      +
     79B  LEU*     3.6    25.0    -      -       +      +
     80B  TYR      3.5    16.4    +      -       -      -
     81B  LEU*     3.6    32.8    -      -       +      -
     94B  TYR*     4.3    17.0    -      -       +      -
     95B  TYR      3.3    22.0    -      -       -      -
     96B  CYS*     4.2    10.5    -      -       +      -
    113B  THR*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  PHE*     4.2    13.5    -      -       +      -
     35B  PHE*     4.3     2.9    -      -       +      -
     36B  TRP*     1.3    81.2    -      -       -      +
     38B  ARG*     1.3    69.8    +      -       -      +
     45B  LEU*     4.4    11.0    -      -       +      -
     46B  GLU      3.2    25.1    -      -       -      +
     47B  TRP*     4.0     5.2    -      -       +      +
     48B  VAL*     4.1     4.3    -      -       -      +
     94B  TYR*     3.6     3.7    -      -       -      +
     95B  TYR*     2.9    33.1    +      -       +      +
     97B  ALA*     4.8     3.1    -      -       +      -
    106B  PHE*     3.5    38.1    -      -       +      -
    109B  TRP*     4.3    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  VAL*     1.3    76.7    -      -       -      +
     39B  GLN*     1.3    59.3    +      -       -      +
     40B  ALA      5.4     0.4    -      -       -      +
     45B  LEU*     3.6     5.6    -      -       -      +
     46B  GLU*     2.7    85.9    +      -       -      +
     48B  VAL*     3.6    11.9    -      -       +      +
     63B  SER*     4.0    16.6    +      -       -      -
     64B  VAL*     4.2    11.4    -      -       -      +
     68B  PHE*     4.0     9.7    -      -       -      -
     89B  GLU*     4.3    12.7    +      -       -      +
     90B  ASP*     3.0    31.3    +      -       -      +
     91B  THR      5.3     0.7    -      -       -      -
     92B  ALA*     4.1    12.1    -      -       +      -
     93B  THR      3.5    11.4    -      -       -      +
     94B  TYR*     3.0    37.0    +      -       +      -
     95B  TYR*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLN*     3.0    32.0    +      -       -      +
     87A  TYR*     3.2    19.4    +      -       -      -
     38B  ARG*     1.3    72.1    -      -       -      +
     40B  ALA*     1.3    66.6    +      -       -      +
     42B  GLY      5.7     1.0    -      -       -      -
     43B  LYS      3.4    13.1    +      -       -      +
     44B  GLY      3.3    19.5    -      -       -      +
     45B  LEU*     3.4    18.3    -      -       +      +
     92B  ALA*     3.0    16.0    -      -       -      +
     93B  THR*     3.2    17.4    +      -       +      +
     95B  TYR*     2.7    37.2    +      -       +      +
----------------------------------------------------------
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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