Contacts of the strand formed by residues 381 - 387 (chain A) 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 TYR 381 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371A  GLU*     2.5    40.0    +      -       +      +
    374A  LEU*     3.5    41.1    -      -       +      -
    375A  LYS*     2.9    34.9    +      -       +      +
    379A  ILE      3.4    16.8    -      -       -      -
    380A  GLU*     1.3    75.8    -      -       -      +
    382A  LYS*     1.3    71.7    +      -       -      +
    383A  VAL*     3.7    16.3    -      -       +      +
    407A  LEU*     4.2     6.3    -      -       +      -
    408A  GLY      3.1    17.3    -      -       -      +
    410A  LYS*     3.7    15.8    +      -       -      +
    416A  LEU*     4.3     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  TYR*     1.3    75.3    -      -       -      +
    383A  VAL*     1.3    69.4    +      -       -      +
    407A  LEU*     3.5     4.2    -      -       -      -
    408A  GLY*     2.8    39.2    +      -       -      +
    409A  GLN      4.0    14.8    -      -       -      +
    410A  LYS*     4.3    22.3    +      -       +      +
    413A  ASP*     2.9    38.7    +      -       -      +
    442A  CYS*     4.7     4.0    -      -       -      -
    466A  ALA*     3.1    32.9    +      -       +      +
    467A  SER      4.0     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371A  GLU*     4.4     7.2    -      -       -      +
    381A  TYR*     3.7    25.1    -      -       +      +
    382A  LYS*     1.3    83.6    -      -       -      +
    384A  GLY*     1.3    69.8    +      -       -      +
    385A  LYS*     4.2    25.4    +      -       +      -
    405A  LYS*     4.2    13.2    -      -       +      -
    406A  ILE      3.3     8.1    -      -       -      +
    407A  LEU*     3.8     8.3    -      -       +      -
    465A  ALA      4.8     1.7    -      -       -      +
    466A  ALA*     4.2     8.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383A  VAL*     1.3    75.8    -      -       -      +
    385A  LYS*     1.3    62.6    +      -       -      +
    404A  VAL      3.7     0.2    -      -       -      +
    405A  LYS*     3.3     4.2    -      -       -      -
    406A  ILE*     2.8    34.9    +      -       -      +
    462A  ALA*     3.4    24.9    -      -       -      +
    465A  ALA*     4.0     3.6    -      -       -      -
    466A  ALA*     3.6    14.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 385 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  GLU*     3.1    39.6    +      -       -      +
    371A  GLU*     5.3     1.6    +      -       -      -
    383A  VAL*     4.2    20.8    +      -       +      -
    384A  GLY*     1.3    77.9    -      -       -      +
    386A  PHE*     1.3    66.1    +      -       -      +
    387A  PRO*     4.5     2.9    -      -       +      +
    403A  MET*     4.3    21.1    -      -       -      -
    404A  VAL      3.3     5.2    -      -       -      +
    405A  LYS*     4.3     9.2    -      -       +      +
    462A  ALA*     4.4     2.7    -      -       -      -
    465A  ALA*     4.1    13.4    -      -       -      +
    471A  SER*     4.9     1.7    +      -       -      -
    474A  PHE*     4.6     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 386 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  LYS*     1.3    75.3    -      -       -      +
    387A  PRO*     1.3    88.4    -      -       -      +
    390A  ALA*     3.5    34.5    -      -       +      -
    391A  ASN*     3.8    10.5    -      -       +      -
    403A  MET*     3.2     4.1    -      -       -      +
    404A  VAL*     2.7    38.1    +      -       -      +
    457A  GLU      5.5     0.2    -      -       -      -
    458A  ALA*     3.7    37.8    -      -       +      +
    461A  GLU*     3.3    38.1    -      -       +      -
    462A  ALA*     3.9     7.9    -      -       +      +
    471A  SER*     3.3    23.8    -      -       -      -
    473A  ASN*     3.9     6.1    -      -       +      -
    474A  PHE*     3.6    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 387 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  LYS*     4.6     0.7    -      -       +      -
    386A  PHE*     1.3   101.1    -      -       +      +
    388A  PHE*     1.3    64.4    +      -       -      +
    389A  ALA*     3.0    13.7    -      -       +      +
    390A  ALA*     3.0    20.3    +      -       +      +
    402A  GLY      3.4     9.9    -      -       -      +
    403A  MET*     3.7     6.1    -      -       +      -
    474A  PHE*     3.6    50.9    -      -       +      -
----------------------------------------------------------
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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