Contacts of the strand formed by residues 482 - 491 (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 THR 482 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  LEU*     4.0    21.0    -      -       +      +
    402B  LEU*     4.7     9.4    -      -       +      +
    432B  MET*     3.8    17.3    -      -       -      +
    476B  ALA*     5.2     2.0    -      -       -      +
    480B  LYS*     3.5     7.2    -      -       -      +
    481B  ASN*     1.3    85.5    +      -       -      +
    483B  GLY*     1.3    61.4    +      -       -      +
    574B  LYS*     4.0    33.7    -      -       +      -
    575B  VAL      3.4    10.1    -      -       -      +
    576B  GLN*     5.3     1.2    -      -       -      +
    577B  PHE*     4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 483 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432B  MET*     4.0     9.6    -      -       -      -
    474B  CYS*     4.9     7.4    -      -       -      -
    476B  ALA*     5.2     2.0    -      -       -      -
    482B  THR*     1.3    75.3    -      -       -      +
    484B  LEU*     1.3    71.5    +      -       -      +
    574B  LYS*     3.7     0.2    -      -       -      -
    575B  VAL*     2.8    32.9    +      -       -      +
    577B  PHE*     3.8    21.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 484 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  LEU*     3.9    17.9    -      -       +      -
    244B  LEU*     4.9     5.8    -      -       +      -
    245B  ILE*     3.7    23.1    -      -       +      -
    405B  PHE*     6.2     0.2    -      -       +      -
    430B  SER      5.3     0.6    +      -       -      -
    432B  MET*     4.0    13.5    -      -       +      -
    435B  TRP*     3.2    50.2    -      -       +      +
    474B  CYS*     3.1    21.9    -      -       -      -
    483B  GLY*     1.3    85.7    -      -       -      +
    485B  LEU*     1.3    62.0    +      -       -      +
    572B  LEU*     4.0    19.5    -      -       +      -
    573B  LEU      3.1     6.5    -      -       -      +
    574B  LYS*     3.5    32.3    -      -       +      +
    575B  VAL*     5.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 485 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386B  LEU*     3.6    31.2    -      -       +      -
    399B  MET*     4.2    13.5    -      -       -      -
    427B  TRP*     3.8    22.0    -      -       +      -
    428B  HIS      3.9     5.4    -      -       -      +
    429B  GLY*     3.9    17.5    -      -       -      -
    435B  TRP*     4.6     0.7    -      -       -      -
    467B  SER      4.2     7.0    -      -       -      +
    470B  SER*     4.0     7.9    -      -       -      -
    471B  ALA*     3.7    32.3    -      -       +      +
    474B  CYS*     4.2     2.2    -      -       -      -
    484B  LEU*     1.3    76.0    -      -       -      +
    486B  LEU*     1.3    60.1    +      -       -      +
    572B  LEU*     3.5     5.6    -      -       -      -
    573B  LEU*     2.8    48.6    +      -       +      +
    575B  VAL*     4.4     8.5    -      -       +      +
    577B  PHE*     5.6     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 486 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407B  VAL*     4.5     5.8    -      -       +      -
    426B  LEU      3.6     0.9    -      -       -      +
    427B  TRP*     3.4     7.3    -      -       -      -
    428B  HIS*     2.9    42.9    +      -       +      +
    435B  TRP*     4.1    12.8    -      -       +      -
    438B  ILE*     4.2     9.9    -      -       +      -
    439B  LEU*     5.0     4.0    -      -       +      -
    443B  LEU*     3.9    22.7    -      -       +      -
    485B  LEU*     1.3    73.8    -      -       -      +
    487B  LEU*     1.3    65.5    +      -       -      +
    488B  SER*     3.8    17.2    +      -       -      +
    569B  MET*     3.8    37.2    -      -       +      -
    571B  TYR      3.4    16.6    -      -       -      +
    572B  LEU*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 487 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382B  ILE*     3.9    39.3    -      -       +      -
    385B  TYR*     3.6    21.3    -      -       +      -
    425B  LEU*     3.8    24.0    -      -       +      -
    426B  LEU*     3.4    15.3    -      -       -      +
    427B  TRP*     3.3    44.4    -      -       +      -
    485B  LEU      4.1     0.4    +      -       -      -
    486B  LEU*     1.3    75.3    -      -       -      +
    488B  SER*     1.3    61.2    +      -       -      +
    569B  MET*     4.0     0.7    -      -       -      -
    570B  ARG      2.9    21.3    +      -       -      -
    571B  TYR*     2.8    32.1    +      -       +      +
    573B  LEU*     4.2     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 488 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    424B  MET      3.4     0.7    -      -       -      +
    425B  LEU*     3.4     7.3    -      -       -      +
    426B  LEU      2.9    29.5    +      -       -      -
    443B  LEU*     4.4     0.2    -      -       -      +
    463B  PHE*     3.9    18.4    -      -       -      -
    486B  LEU*     3.8    15.8    -      -       -      +
    487B  LEU*     1.3    76.6    +      -       -      +
    489B  GLU*     1.3    65.1    +      -       -      +
    490B  VAL*     3.5     3.1    +      -       -      +
    567B  VAL*     3.9    20.4    -      -       -      +
    568B  ARG      3.3    12.1    -      -       -      -
    569B  MET*     3.6    14.4    -      -       -      +
    570B  ARG      4.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 489 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416B  PHE*     3.5    21.2    -      -       +      -
    423B  ARG*     4.4    10.8    +      -       -      -
    424B  MET      3.6     4.9    -      -       -      -
    425B  LEU*     3.9    11.1    -      -       +      +
    488B  SER*     1.3    72.5    -      -       -      +
    490B  VAL*     1.3    58.5    +      -       -      +
    491B  ALA      4.1     0.2    -      -       -      -
    531B  LEU      4.3     4.2    -      -       -      +
    532B  ASN*     4.1    17.3    -      -       -      +
    534B  SER*     3.5    28.0    +      -       -      +
    567B  VAL*     3.5     3.6    -      -       -      -
    568B  ARG*     2.8    59.2    +      -       +      +
    570B  ARG*     3.5    30.7    +      -       +      +
    571B  TYR*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 490 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  ASN      3.4     0.5    -      -       -      +
    423B  ARG*     3.3     3.5    -      -       -      -
    424B  MET      2.8    37.0    +      -       -      +
    426B  LEU*     4.0    14.4    -      -       +      -
    463B  PHE*     3.7    47.1    -      -       +      -
    488B  SER      3.6    13.2    -      -       -      +
    489B  GLU*     1.3    76.6    -      -       -      +
    491B  ALA*     1.3    62.2    +      -       -      +
    492B  LEU*     3.1    21.4    +      -       +      +
    561B  VAL*     3.6    29.4    -      -       +      -
    566B  GLN      3.4     6.1    -      -       -      +
    567B  VAL*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 491 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416B  PHE*     3.9    16.5    -      -       +      -
    417B  ARG*     3.5    29.8    -      -       +      +
    420B  LEU*     3.8    18.3    -      -       +      +
    421B  HIS      4.9     0.7    -      -       -      -
    422B  ASN      4.4     1.6    -      -       -      -
    423B  ARG*     4.5     5.8    -      -       +      +
    490B  VAL*     1.3    70.0    -      -       -      +
    492B  LEU*     1.3    62.2    +      -       -      +
    493B  GLY      3.4     2.8    +      -       -      +
    561B  VAL*     4.2     0.3    -      -       -      +
    566B  GLN*     2.9    41.2    +      -       +      +
----------------------------------------------------------
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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