Contacts of the strand formed by residues 537 - 544 (chain B) in PDB entry 1KT8


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 HIS 537 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513B  GLU      3.3    21.8    -      -       -      -
    514B  MET*     3.3    16.6    -      -       +      -
    515B  THR*     3.2    30.6    +      -       +      -
    535B  THR*     3.6    15.8    +      -       -      +
    536B  ASP*     1.3    95.9    -      -       +      +
    538B  MET*     1.3    63.9    +      -       -      +
    553B  ILE*     4.0    18.6    -      -       +      -
    554B  GLN      3.3    12.3    -      -       -      +
    555B  PRO      4.5     0.7    -      -       -      -
    556B  PHE*     3.9     8.4    -      -       -      +
    624B  LEU*     4.0    13.8    -      -       +      +
    627B  VAL*     3.9    19.5    -      -       +      +
    628B  ASP*     3.2    23.2    +      -       -      +
    665B  VAL      4.8     0.5    -      -       -      +
    667B  LEU*     4.8     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 538 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  PRO*     3.8    28.5    -      -       +      -
    537B  HIS*     1.3    76.3    -      -       -      +
    539B  LEU*     1.3    61.7    +      -       -      +
    540B  MET*     4.7     2.7    -      -       -      -
    553B  ILE*     3.2     4.5    -      -       -      -
    554B  GLN*     2.9    58.5    +      -       +      +
    555B  PRO      3.7     3.8    -      -       -      +
    556B  PHE*     3.9     4.3    -      -       +      -
    557B  GLN      3.5    35.0    -      -       -      +
    559B  LEU*     4.4    10.5    -      -       +      -
    624B  LEU*     3.5    10.2    -      -       -      +
    664B  PHE*     4.3    21.3    -      -       +      -
    665B  VAL      3.3    15.9    -      -       -      +
    666B  ILE*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 539 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    510B  LEU*     4.1     5.8    -      -       +      -
    538B  MET*     1.3    77.0    -      -       -      +
    540B  MET*     1.3    68.5    +      -       -      +
    541B  VAL*     4.4    11.4    -      -       +      -
    551B  PRO*     4.3     4.7    -      -       +      -
    552B  ARG      4.0    21.5    -      -       -      +
    553B  ILE*     4.1    12.3    -      -       +      +
    617B  LEU*     3.9    15.5    -      -       +      -
    620B  CYS*     3.8    38.1    -      -       +      +
    621B  ILE*     4.7     1.6    -      -       +      -
    624B  LEU*     3.9     9.6    -      -       +      +
    663B  LEU*     4.8     1.8    -      -       +      -
    664B  PHE*     3.0     9.6    -      -       -      +
    665B  VAL*     2.9    57.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 540 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538B  MET*     4.4     4.7    +      -       +      -
    539B  LEU*     1.3    78.8    -      -       -      +
    541B  VAL*     1.3    69.0    +      -       -      +
    542B  GLU*     4.8     6.5    -      -       +      +
    550B  GLN      4.0     2.6    -      -       -      +
    551B  PRO*     3.8    17.7    -      -       -      +
    552B  ARG*     3.8    30.0    +      -       -      +
    553B  ILE      4.9     0.2    -      -       -      +
    554B  GLN*     3.2    26.7    -      -       -      +
    557B  GLN*     5.1     4.5    -      -       +      +
    558B  ASN      5.4     2.5    -      -       -      +
    559B  LEU*     4.2    16.8    -      -       +      -
    662B  LEU*     3.3    33.9    -      -       +      -
    663B  LEU      3.3     5.2    -      -       -      -
    664B  PHE*     4.3     8.1    -      -       -      -
   1001B  ACY      3.5    29.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 541 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505B  PHE*     3.8    37.2    -      -       +      -
    539B  LEU*     4.4    12.1    -      -       +      -
    540B  MET*     1.3    80.1    -      -       -      +
    542B  GLU*     1.3    66.1    +      -       -      +
    548B  TRP*     3.5    28.3    -      -       +      -
    549B  GLY      3.7    21.1    -      -       -      +
    550B  GLN      4.6     2.5    -      -       -      -
    551B  PRO*     4.0    13.5    -      -       +      -
    662B  LEU*     3.4     3.9    -      -       -      +
    663B  LEU*     2.8    45.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 542 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540B  MET*     4.8     5.5    -      -       +      +
    541B  VAL*     1.3    78.2    -      -       -      +
    543B  TRP*     1.3    60.0    +      -       -      +
    544B  ASN*     5.9     3.4    -      -       -      +
    547B  GLY      3.7     0.6    -      -       -      +
    548B  TRP*     3.5     5.1    -      -       -      -
    549B  GLY*     2.7    37.7    +      -       -      +
    550B  GLN      5.2     1.0    +      -       -      -
    649B  ASN*     5.1     1.7    +      -       -      -
    660B  ARG*     3.3    31.0    +      -       -      +
    661B  ALA      3.8     6.4    -      -       -      +
    662B  LEU*     3.7    16.7    -      -       +      +
   1001B  ACY      2.8    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 543 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    503B  SER*     4.7     6.4    +      -       -      -
    542B  GLU*     1.3    77.0    -      -       -      +
    544B  ASN*     1.3    73.6    +      -       -      +
    547B  GLY*     3.3    33.0    -      -       -      -
    548B  TRP*     3.5    40.2    -      +       +      +
    610B  PRO*     3.5    36.7    -      -       +      +
    657B  GLN*     5.7     6.1    -      -       +      -
    658B  PRO*     3.5    17.5    -      -       +      -
    659B  ARG*     3.4    27.1    -      -       -      -
    660B  ARG*     3.2    11.3    -      -       -      +
    661B  ALA*     3.0    42.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 544 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542B  GLU*     5.9     3.4    -      -       -      +
    543B  TRP*     1.3    91.8    -      -       -      +
    545B  ASP*     1.3    62.2    +      -       +      +
    546B  LYS*     2.4    69.1    +      -       -      +
    547B  GLY*     2.8    24.6    +      -       -      +
    659B  ARG      3.3    19.7    -      -       -      +
    660B  ARG*     4.1    14.0    -      -       +      +
----------------------------------------------------------
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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