Contacts of the strand formed by residues 387 - 393 (chain A) in PDB entry 4ZZ7


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 VAL 387 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  ALA*     4.5     6.0    +      -       -      +
    273A  PHE*     4.0     3.2    -      -       -      -
    283A  LEU      4.9     0.7    -      -       -      +
    284A  SER*     4.0    19.6    -      -       -      +
    332A  VAL*     4.3     4.5    -      -       +      -
    336A  ILE*     4.0    22.2    -      -       +      -
    367A  THR*     3.4    22.9    -      -       +      +
    369A  ILE*     3.8    26.2    -      -       +      -
    383A  ILE*     4.0    34.2    -      -       +      +
    385A  GLY      2.7    19.7    +      -       -      +
    386A  PRO*     1.3    80.6    -      -       +      +
    388A  LEU*     1.3    63.9    +      -       -      +
    389A  GLN*     4.6     2.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 388 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  LEU*     4.7    13.0    -      -       +      -
    272A  ALA*     3.7    21.5    -      -       +      -
    273A  PHE*     3.6    17.9    -      -       +      -
    283A  LEU*     4.2     5.4    -      -       +      +
    284A  SER      3.7    11.4    -      -       -      +
    285A  VAL      4.2     0.9    -      -       -      +
    286A  ALA*     3.9    21.5    -      -       +      +
    297A  LEU*     6.0     2.7    -      -       +      -
    301A  MET*     4.2    32.5    -      -       +      -
    367A  THR      3.0     9.0    +      -       -      +
    368A  LEU*     3.5    14.7    -      -       +      +
    369A  ILE      2.9    25.1    +      -       -      -
    387A  VAL*     1.3    74.1    -      -       -      +
    389A  GLN*     1.3    76.8    +      -       -      +
    390A  VAL*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 389 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  LYS*     3.5    30.0    +      -       -      -
    284A  SER*     2.9    16.0    +      -       -      +
    285A  VAL*     3.3     9.6    -      -       +      +
    286A  ALA      2.8    25.1    +      -       -      -
    339A  ALA*     5.0     0.6    -      -       -      +
    369A  ILE*     3.6    22.8    -      -       +      +
    372A  VAL*     3.9    27.2    -      -       +      +
    376A  MET*     6.0     0.4    -      -       -      -
    378A  SER*     3.2    40.0    +      -       -      +
    379A  TYR*     3.6    10.4    -      -       -      +
    383A  ILE*     3.9    10.2    -      -       -      +
    387A  VAL*     4.1     3.5    -      -       +      +
    388A  LEU*     1.3    77.1    -      -       -      +
    390A  VAL*     1.3    60.3    +      -       -      +
    391A  VAL      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  ALA*     3.2    17.7    -      -       +      +
    288A  ALA*     4.4     7.9    -      -       +      -
    294A  GLY      5.1     1.6    -      -       -      +
    297A  LEU*     4.2    17.9    -      -       +      -
    298A  VAL*     4.0    13.9    -      -       +      -
    368A  LEU*     3.6    18.8    -      -       +      -
    369A  ILE      3.1    20.0    +      -       -      +
    370A  ASP*     3.6    19.2    -      -       -      +
    371A  HIS*     3.4    21.0    +      -       -      -
    372A  VAL*     3.6     6.9    +      -       -      +
    388A  LEU*     5.5     1.8    -      -       +      -
    389A  GLN*     1.3    73.6    -      -       -      +
    391A  VAL*     1.3    70.9    +      -       -      +
    392A  ARG*     4.7     4.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  VAL*     4.0    17.7    -      -       +      -
    286A  ALA      2.9     7.5    +      -       -      +
    287A  VAL*     3.5     5.9    -      -       +      -
    288A  ALA*     2.7    34.1    +      -       -      +
    372A  VAL*     3.2    40.8    -      -       +      +
    373A  THR*     5.3     1.8    -      -       -      -
    374A  PRO*     5.5     7.9    -      -       +      -
    379A  TYR*     4.3    11.7    -      -       +      -
    390A  VAL*     1.3    73.7    -      -       -      +
    392A  ARG*     1.3    73.0    +      -       -      +
    393A  VAL*     4.1     5.6    -      -       +      -
    402A  LEU*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ALA*     3.4     7.6    -      -       +      +
    290A  GLY      5.1     1.1    -      -       -      +
    291A  ASP*     3.0    43.1    +      -       +      +
    294A  GLY*     3.4    30.0    +      -       -      -
    295A  ASP*     2.9    30.0    +      -       -      +
    298A  VAL*     3.7     5.8    -      -       -      +
    370A  ASP*     3.0    37.7    +      -       -      +
    371A  HIS*     3.6    33.7    +      -       -      +
    372A  VAL      4.9     1.4    +      -       -      -
    390A  VAL*     4.7     2.0    -      -       +      +
    391A  VAL*     1.3    83.4    -      -       -      +
    393A  VAL*     1.3    67.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 393 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  VAL*     3.8    21.3    -      -       +      -
    288A  ALA      3.0    11.2    +      -       -      +
    289A  VAL*     3.4     7.4    -      -       -      -
    290A  GLY*     2.7    33.1    +      -       -      -
    391A  VAL*     4.1    14.6    -      -       +      -
    392A  ARG*     1.3    80.0    -      -       -      +
    394A  ALA*     1.3    57.4    +      -       -      +
    395A  THR      3.6    19.7    -      -       -      +
    398A  ASP*     4.0    17.3    -      -       +      +
    399A  ALA*     3.8    14.1    -      -       +      +
    402A  LEU*     4.6     7.0    -      -       +      -
----------------------------------------------------------
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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