Contacts of the strand formed by residues 344 - 350 (chain A) in PDB entry 3KB5


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 GLU 344 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  PRO*     4.6    15.0    -      -       +      +
    343A  GLY*     1.3    81.9    -      -       -      -
    345A  HIS*     1.3    75.1    +      -       -      +
    416A  TYR*     3.3    33.4    -      -       +      +
    417A  LEU      3.2     4.7    -      -       -      +
    418A  SER*     3.7    14.0    +      -       -      +
    420A  GLY*     5.0     5.5    +      -       -      -
    421A  ASP*     5.2     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  PRO*     4.2     4.5    -      -       -      -
    287A  ALA      5.8     0.2    -      -       -      -
    289A  GLU*     2.8    31.5    +      -       -      +
    340A  LEU*     3.9    37.8    -      -       +      +
    341A  SER      5.1     0.2    +      -       -      -
    342A  GLU*     2.7    29.7    +      -       -      -
    343A  GLY*     3.8     6.7    -      -       -      -
    344A  GLU*     1.3    85.2    +      -       -      +
    346A  TYR*     1.3    62.3    +      -       -      +
    347A  TRP*     4.2    17.5    -      -       +      -
    415A  LEU      4.3     0.2    -      -       -      -
    416A  TYR*     3.3     6.1    -      -       -      -
    417A  LEU*     2.7    40.7    +      -       +      +
    419A  PHE*     4.5     5.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  ARG*     4.0     5.1    +      -       -      -
    285A  MET*     3.5    32.5    -      -       +      -
    286A  PRO*     3.7    36.5    -      -       +      +
    287A  ALA      4.6     2.2    +      -       -      +
    288A  LEU*     3.6    15.5    -      -       +      -
    289A  GLU*     2.7    34.7    +      -       -      +
    345A  HIS*     1.3    77.6    -      -       -      +
    347A  TRP*     1.3    56.7    +      -       -      +
    348A  GLU*     2.6    45.5    +      -       +      +
    414A  GLY*     3.5     8.1    -      -       -      -
    415A  LEU      3.2    34.8    -      -       -      -
    416A  TYR*     4.1     2.0    -      -       +      -
    427A  TYR*     4.7     3.8    -      +       -      -
    435A  LEU*     3.5    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  LEU*     4.1     6.7    -      -       +      -
    289A  GLU*     4.1    12.6    -      -       +      +
    291A  LEU*     3.6    30.7    -      -       +      +
    340A  LEU*     3.9    25.1    -      -       +      -
    345A  HIS*     4.2     6.5    -      -       +      -
    346A  TYR*     1.3    83.7    -      -       -      +
    348A  GLU*     1.3    66.9    +      -       -      +
    349A  VAL*     4.1    12.3    -      -       +      -
    360A  GLY      4.0     2.4    +      -       -      -
    361A  VAL*     3.8    25.4    -      -       +      -
    414A  GLY*     3.5     2.1    -      -       -      -
    415A  LEU*     2.8    83.4    +      -       +      +
    417A  LEU*     4.0    21.8    -      -       +      -
    424A  LEU*     4.7     1.8    -      -       +      -
    451A  PRO*     3.8    22.2    -      -       +      +
    453A  PHE*     4.2     7.9    -      +       -      -
    469A  LEU*     4.4     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  ARG*     2.8    24.6    +      -       -      -
    288A  LEU*     3.7    14.5    -      -       +      +
    346A  TYR*     2.6    39.2    +      -       +      +
    347A  TRP*     1.3    78.1    -      -       -      +
    349A  VAL*     1.3    68.0    +      -       -      +
    412A  ARG*     3.5    32.4    +      -       -      -
    413A  ILE      3.2     6.7    -      -       -      +
    414A  GLY*     4.2     2.7    -      -       -      -
    429A  ALA*     3.5     6.5    -      -       +      +
    469A  LEU*     3.8     7.1    -      -       -      +
    470A  VAL*     3.1    43.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  PHE*     5.8     0.2    -      -       +      -
    347A  TRP*     4.1    12.1    -      -       +      -
    348A  GLU*     1.3    80.9    -      -       -      +
    350A  ASP*     1.3    72.3    +      -       -      +
    351A  VAL*     3.5     7.0    +      -       +      +
    359A  LEU*     3.9    31.4    -      -       +      -
    412A  ARG*     3.3     4.6    -      -       -      -
    413A  ILE*     2.9    34.8    +      -       -      +
    415A  LEU*     4.2     9.6    -      -       +      -
    453A  PHE*     3.7    28.7    -      -       +      -
    467A  LEU*     4.3     7.9    -      -       +      -
    468A  LEU      3.3    16.8    -      -       -      +
    469A  LEU*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349A  VAL*     1.3    73.9    -      -       -      +
    351A  VAL*     1.3    59.7    +      -       -      +
    352A  GLY      4.8     1.8    -      -       -      +
    411A  THR*     3.6     7.0    +      -       -      +
    412A  ARG*     2.7    50.6    +      -       -      +
    466A  PRO      4.2     0.2    -      -       -      +
    467A  LEU*     3.9     4.3    -      -       -      -
    468A  LEU*     2.8    57.3    +      -       +      +
    470A  VAL*     3.8    10.0    -      -       -      +
----------------------------------------------------------
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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