Contacts of the strand formed by residues 423 - 429 (chain B) in PDB entry 3KCZ


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 ARG 423 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416B  PHE*     3.6    33.6    -      -       +      -
    417B  ARG      5.2     0.6    +      -       -      -
    418B  GLU*     3.0    43.8    +      -       -      +
    420B  LEU      4.6     9.7    +      -       -      +
    421B  HIS      3.3     1.4    -      -       -      -
    422B  ASN*     1.3    76.2    -      -       -      +
    424B  MET*     1.3    59.9    +      -       -      +
    489B  GLU*     4.4     8.6    +      -       -      -
    490B  VAL      3.3    15.0    -      -       -      +
    491B  ALA*     4.5     2.9    -      -       -      +
    532B  ASN      4.4     5.5    +      -       -      -
    533B  GLY*     4.1    28.6    +      -       -      +
    534B  SER*     3.1    24.0    -      -       -      +
    535B  THR*     2.9    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 424 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  ASN*     3.8    17.9    -      -       -      +
    423B  ARG*     1.3    78.6    -      -       -      +
    425B  LEU*     1.3    62.0    +      -       -      +
    426B  LEU*     3.6    17.7    +      -       +      -
    465B  ASP*     5.4     0.2    -      -       -      +
    488B  SER      3.4     1.7    -      -       -      +
    489B  GLU*     3.6     0.5    -      -       -      -
    490B  VAL*     2.8    33.9    +      -       -      +
    492B  LEU*     3.6    25.8    -      -       +      -
    528B  PHE*     4.5     8.3    -      -       +      -
    534B  SER*     4.1     4.9    -      -       -      -
    535B  THR*     3.4    25.6    -      -       +      +
    537B  PRO*     3.9    34.3    -      -       +      -
    559B  TYR*     4.2    22.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 425 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381B  VAL*     6.2     0.2    -      -       +      -
    382B  ILE*     5.1     1.3    -      -       +      -
    385B  TYR*     2.7    37.0    +      -       +      -
    424B  MET*     1.3    69.9    -      -       -      +
    426B  LEU*     1.3    56.6    +      -       -      +
    487B  LEU*     3.8    33.2    -      -       +      -
    488B  SER*     3.4    24.9    -      -       -      +
    489B  GLU*     3.9    18.4    -      -       +      +
    531B  LEU*     4.2    12.6    -      -       +      +
    534B  SER*     4.0     8.0    -      -       -      -
    535B  THR      2.9    14.6    +      -       -      +
    536B  VAL*     4.1    22.7    -      -       +      -
    537B  PRO*     3.7     3.5    -      -       -      +
    570B  ARG*     4.4     2.0    -      -       +      -
    571B  TYR*     4.1    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 426 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385B  TYR*     3.9     6.3    -      -       -      +
    424B  MET*     3.9    31.6    -      -       +      +
    425B  LEU*     1.3    85.0    -      -       -      +
    427B  TRP*     1.3    63.0    -      -       -      +
    463B  PHE*     3.7    32.9    -      -       +      -
    464B  ALA      3.6    13.5    -      -       -      +
    465B  ASP*     4.1    14.4    -      -       +      -
    486B  LEU      3.6     0.3    -      -       -      +
    487B  LEU*     3.4     8.6    -      -       -      -
    488B  SER*     2.9    30.4    +      -       -      +
    490B  VAL*     4.0    20.0    -      -       +      -
    492B  LEU*     4.6     1.8    -      -       +      -
    537B  PRO*     4.4     0.2    -      -       +      -
    559B  TYR*     3.8    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 427 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382B  ILE      4.4     1.8    -      -       -      -
    385B  TYR*     3.3    46.7    -      +       -      -
    386B  LEU*     3.6    31.6    -      -       +      -
    389B  THR*     3.5     0.6    +      -       -      -
    426B  LEU*     1.3    72.7    -      -       -      +
    428B  HIS*     1.3    60.2    -      -       -      +
    463B  PHE*     3.2    11.9    -      -       -      -
    464B  ALA*     2.9    45.6    +      -       +      +
    465B  ASP      3.9     1.8    -      -       -      -
    466B  MET      3.7     3.1    -      -       -      -
    467B  SER*     3.4    33.4    -      -       -      +
    470B  SER*     3.2    20.4    +      -       -      +
    485B  LEU*     3.8    22.2    -      -       +      -
    486B  LEU      3.4    11.0    -      -       -      -
    487B  LEU*     3.3    37.5    -      -       +      -
    573B  LEU*     3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 428 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  3AB      3.3    21.9    +      -       -      -
    427B  TRP*     1.3    75.7    -      -       -      +
    429B  GLY*     1.3    72.3    +      -       -      +
    430B  SER*     4.3    12.3    +      -       -      -
    435B  TRP*     4.0     5.0    -      +       -      -
    438B  ILE*     4.5     3.6    -      -       +      +
    443B  LEU*     3.7    37.5    -      -       +      +
    461B  ILE*     5.0     2.5    -      -       +      -
    462B  TYR*     2.9    30.1    +      -       +      -
    463B  PHE*     4.2    12.8    -      -       +      -
    470B  SER*     3.9     2.9    -      -       -      -
    485B  LEU*     3.9     1.8    -      -       -      -
    486B  LEU*     2.9    44.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 429 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  3AB      2.8    30.4    +      -       -      -
    428B  HIS*     1.3    79.4    +      -       -      +
    430B  SER*     1.3    64.3    +      -       -      -
    435B  TRP*     4.6     0.2    -      -       -      -
    470B  SER*     3.3    23.2    -      -       -      -
    473B  TYR*     3.8     5.3    -      -       -      +
    474B  CYS*     4.2     3.6    -      -       -      -
    484B  LEU      4.6     1.3    -      -       -      -
    485B  LEU*     3.9    11.4    -      -       -      -
----------------------------------------------------------
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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