Contacts of the strand formed by residues 120 - 128 (chain B) in PDB entry 4KZX


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 120 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110B  MET*     4.8    10.3    -      -       +      -
    114B  VAL*     3.3    27.1    -      -       +      -
    118B  GLN      3.7     3.1    +      -       -      +
    119B  THR*     1.3    77.9    -      -       -      +
    121B  ILE*     1.3    63.6    -      -       -      +
    122B  GLU*     4.1    24.4    +      -       -      +
    140B  VAL*     4.1    14.6    -      -       +      -
    142B  PHE*     3.0    44.6    -      -       +      -
    161B  VAL*     5.8     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  THR*     4.1     6.5    -      -       +      +
    120B  MET*     1.3    79.8    -      -       -      +
    122B  GLU*     1.3    65.9    +      -       -      +
    123B  ALA      4.4     0.2    +      -       -      -
    140B  VAL*     3.3     5.8    -      -       -      +
    141B  GLY*     2.8    45.5    +      -       -      +
    143B  THR*     4.6    12.8    -      -       +      -
    156B  ALA*     5.0     0.4    -      -       +      -
    161B  VAL*     3.8    46.0    -      -       +      +
    164B  ILE*     4.0    36.6    -      -       +      -
    165B  ARG*     4.4    12.3    -      -       +      -
    168B  MET*     4.9     8.2    -      -       +      +
    207B  LEU*     4.1    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110B  MET*     5.8     1.2    -      -       -      +
    120B  MET*     4.1    27.2    +      -       +      +
    121B  ILE*     1.3    79.0    -      -       -      +
    123B  ALA*     1.3    61.7    +      -       -      +
    124B  HIS*     5.4     3.5    +      -       -      +
    139B  CYS      3.6    12.3    -      -       -      +
    140B  VAL*     4.0    11.4    -      -       +      +
    165B  ARG*     3.3    24.5    +      -       -      +
    213B  ARG*     3.7    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  GLU*     1.3    75.3    -      -       -      +
    124B  HIS*     1.3    65.2    +      -       -      +
    138B  PHE*     3.8     0.3    -      -       -      +
    139B  CYS*     2.9    32.2    +      -       -      +
    165B  ARG*     3.4    33.2    -      -       +      +
    168B  MET*     3.5    27.1    -      -       +      -
    169B  MET*     4.7     7.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  GLU*     5.4     2.8    +      -       -      +
    123B  ALA*     1.3    76.9    -      -       -      +
    125B  VAL*     1.3    70.2    +      -       -      +
    126B  ASP*     4.5     3.8    -      -       -      -
    136B  HIS*     2.2    48.6    -      +       +      +
    137B  LEU      3.5     6.5    -      -       -      +
    138B  PHE*     3.3    29.7    -      +       +      -
    169B  MET*     5.3     1.9    -      -       -      +
    172B  MET*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  ALA      5.5     0.2    -      -       -      -
    124B  HIS*     1.3    83.6    -      -       -      +
    126B  ASP*     1.3    78.0    +      -       -      +
    127B  VAL*     4.3     3.7    +      -       +      +
    135B  LEU      4.0     0.5    -      -       -      +
    136B  HIS*     3.1     0.9    -      -       -      -
    137B  LEU*     2.7    36.7    +      -       -      +
    169B  MET*     3.2    49.8    -      -       +      +
    172B  MET*     4.4    14.0    -      -       +      +
    173B  THR*     2.9    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  HIS*     5.2     2.4    -      -       -      -
    125B  VAL*     1.3    81.1    -      -       -      +
    127B  VAL*     1.3    63.6    +      -       -      +
    135B  LEU      3.1     8.1    -      -       -      +
    136B  HIS*     2.2    53.8    +      -       +      -
    173B  THR*     5.2     0.3    -      -       -      +
    218B  LEU*     4.4    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  VAL*     4.7     3.6    -      -       +      +
    126B  ASP*     1.3    75.7    -      -       -      +
    128B  LYS*     1.3    72.9    +      -       -      +
    129B  THR*     3.9     0.5    +      -       -      +
    133B  TYR      3.8     0.9    -      -       -      +
    134B  LEU*     3.8     5.2    -      -       -      -
    135B  LEU*     2.7    39.0    +      -       +      +
    137B  LEU*     4.4     8.1    -      -       +      -
    172B  MET*     4.7     6.1    -      -       +      +
    173B  THR*     4.2    21.1    -      -       +      +
    176B  VAL*     3.2    34.3    -      -       +      -
    177B  GLN*     4.0    20.6    -      -       +      +
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Residues in contact with LYS 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  VAL*     1.3    85.3    -      -       -      +
    129B  THR*     1.3    69.2    +      -       -      +
    130B  THR      6.0     0.2    -      -       -      -
    132B  GLY*     2.6    40.6    -      -       -      +
    133B  TYR      3.4     2.9    -      -       -      -
    134B  LEU*     3.3    20.8    -      -       +      +
    177B  GLN*     3.9    12.8    -      -       -      +
----------------------------------------------------------
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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