Contacts of the strand formed by residues 180 - 184 (chain B) in PDB entry 1ZMC


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 LYS 180 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  PRO*     4.0     2.5    -      -       -      +
    179B  GLU*     1.3    83.6    -      -       +      +
    181B  MET*     1.3    65.8    +      -       -      +
    182B  VAL*     4.9     1.8    -      -       -      -
    203B  ASP*     3.3    27.6    -      -       +      +
    205B  THR*     4.9     6.3    -      -       -      -
    236B  LYS*     6.2     0.2    -      -       -      +
    269B  ILE*     3.7    27.8    -      -       -      +
    270B  THR*     2.9    29.0    +      -       -      +
    271B  CYS*     3.8     7.9    -      -       +      -
    272B  ASP*     2.9    35.0    +      -       -      +
    273B  VAL      3.5     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ALA*     6.0     1.3    -      -       -      -
    174B  LEU*     4.7     2.5    -      -       -      -
    178B  PRO*     4.3    18.2    -      -       +      -
    179B  GLU      4.3     0.2    -      -       -      -
    180B  LYS*     1.3    76.5    -      -       -      +
    182B  VAL*     1.3    70.1    +      -       -      +
    183B  VAL*     3.3    29.4    -      -       +      -
    193B  LEU      4.4     0.2    -      -       -      +
    194B  GLY*     4.1    17.0    -      -       -      -
    197B  TRP*     4.1    31.4    -      -       +      -
    202B  ALA*     4.6     2.2    -      -       +      -
    203B  ASP      2.7    14.7    +      -       -      +
    204B  VAL*     3.4    13.7    -      -       +      +
    205B  THR*     3.1    24.8    +      -       -      +
    271B  CYS*     4.1     0.4    -      -       -      -
    273B  VAL*     3.5    25.8    -      -       +      +
    275B  LEU*     3.8    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  LYS*     4.9     3.6    -      -       -      -
    181B  MET*     1.3    75.3    -      -       -      +
    183B  VAL*     1.3    68.7    +      -       -      +
    184B  ILE*     4.9     1.8    -      -       +      +
    205B  THR*     3.3    13.9    -      -       +      +
    207B  VAL*     4.3    16.8    -      -       +      -
    256B  VAL*     4.2    14.4    -      -       +      -
    269B  ILE*     3.5    32.3    -      -       +      -
    271B  CYS*     3.6    27.6    -      -       +      +
    273B  VAL      3.2     7.3    +      -       -      +
    274B  LEU*     3.3    19.7    -      -       +      +
    275B  LEU*     3.0    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181B  MET*     3.3    31.6    -      -       +      -
    182B  VAL*     1.3    73.8    -      -       -      +
    184B  ILE*     1.3    63.8    +      -       -      +
    185B  GLY      3.5    21.0    +      -       -      +
    190B  GLY*     4.0    22.0    -      -       -      +
    194B  GLY*     4.4     0.9    -      -       -      -
    204B  VAL*     4.3    16.4    -      -       +      -
    205B  THR      3.0     5.8    +      -       -      +
    206B  ALA*     3.3    12.1    -      -       +      -
    207B  VAL*     2.7    33.1    +      -       -      +
    275B  LEU*     3.5    24.5    -      -       +      +
    277B  CYS*     4.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  PHE*     4.0    11.2    -      -       +      -
    158B  ILE*     4.0    27.6    -      -       +      -
    182B  VAL*     5.1     2.2    -      -       +      -
    183B  VAL*     1.3    71.5    -      -       -      +
    185B  GLY*     1.3    59.7    +      -       -      +
    207B  VAL*     3.8     4.3    -      -       -      -
    243B  VAL*     4.0    24.7    -      -       +      -
    256B  VAL*     5.3     0.2    -      -       +      -
    274B  LEU*     3.9    22.4    -      -       +      -
    275B  LEU      2.9    12.2    +      -       -      +
    276B  VAL*     4.0    20.2    -      -       +      -
    277B  CYS*     3.0    30.1    +      -       -      +
    278B  ILE*     3.6    22.2    -      -       +      -
    481B  NAD      4.0    20.0    -      -       +      -
----------------------------------------------------------
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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