Contacts of the strand formed by residues 472 - 480 (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 THR 472 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  LEU*     4.0    10.5    -      -       +      -
    136A  PHE*     3.4    39.2    -      -       +      +
    137A  GLN      3.2    11.9    -      -       -      +
    139A  MET*     3.7     7.0    -      -       -      -
    165A  CYS*     4.0    21.1    -      -       +      +
    242A  ARG*     2.8    25.3    +      -       -      -
    468A  VAL      2.9    23.7    +      -       -      +
    469A  ARG*     3.0    15.6    +      -       -      +
    470A  PHE      3.2     0.4    -      -       -      -
    471A  TYR*     1.3    85.6    -      -       -      +
    473A  LYS*     1.3    59.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  ARG*     6.1     0.4    -      -       -      +
    135A  GLU      3.4     0.9    -      -       -      +
    136A  PHE*     4.3     3.4    -      -       -      -
    137A  GLN      2.8    40.9    +      -       -      +
    138A  PRO      3.2    19.5    -      -       -      +
    139A  MET*     3.7    36.1    +      -       +      +
    218A  LYS*     5.9     3.4    -      -       -      +
    242A  ARG*     3.9    11.0    -      -       -      +
    469A  ARG*     5.3     0.2    -      -       -      +
    472A  THR*     1.3    74.7    -      -       -      +
    474A  ARG*     1.3    63.9    +      -       -      +
    475A  LYS      3.5     0.3    +      -       -      -
    430B  GLN*     3.5    15.4    +      -       -      +
    452B  TRP*     3.3    62.2    -      -       +      +
    453B  LYS*     5.8     4.6    -      -       -      +
    461B  HIS*     5.5     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  GLU*     4.4     9.3    +      -       -      -
    134A  SER*     3.5    24.9    +      -       -      -
    135A  GLU      3.4     5.2    -      -       -      +
    136A  PHE*     3.8    29.2    -      -       +      -
    469A  ARG*     3.7    12.3    -      -       -      +
    473A  LYS*     1.3    72.9    -      -       -      +
    475A  LYS*     1.3    64.1    +      -       -      +
    476A  THR*     4.2    15.8    +      -       -      +
    432B  GLY*     4.3     2.9    -      -       -      +
    447B  HIS*     4.5     5.1    +      -       -      -
    448B  SER*     4.0    27.4    -      -       -      +
    450B  GLY      4.7     0.5    -      -       -      +
    452B  TRP*     2.9    19.0    +      -       -      -
    461B  HIS*     3.5    32.8    +      -       +      +
    465B  PRO*     4.1    18.2    -      -       -      +
    466B  ASP*     2.8    40.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  TRP      3.8     0.5    -      -       -      +
    134A  SER*     3.2     4.9    -      -       -      -
    135A  GLU*     2.7    49.3    +      -       +      +
    137A  GLN*     3.2    32.6    +      -       -      +
    473A  LYS      3.5     0.2    +      -       -      -
    474A  ARG*     1.3    75.1    -      -       -      +
    476A  THR*     1.3    67.5    +      -       -      +
    477A  VAL*     4.1     8.5    +      -       +      -
    426B  SER      2.7    29.3    +      -       -      +
    427B  ASP      3.2     8.7    +      -       -      -
    428B  ASN      4.3     0.2    -      -       -      -
    429B  ILE*     2.7    24.3    +      -       -      +
    431B  VAL      3.4    18.4    -      -       -      -
    432B  GLY      3.3    13.0    -      -       -      +
    434B  VAL*     3.8    14.1    -      -       +      -
    452B  TRP*     3.6    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  SER*     3.5    21.1    -      -       -      +
    133A  TRP      3.6     9.6    -      -       -      +
    134A  SER*     4.7     3.5    -      -       -      -
    474A  ARG*     4.2    12.6    +      -       -      +
    475A  LYS*     1.3    77.7    +      -       -      +
    477A  VAL*     1.3    58.5    -      -       -      +
    478A  THR*     4.7     2.4    +      -       -      +
    432B  GLY      2.9     8.8    +      -       -      +
    433B  MET*     3.3     7.8    -      -       -      +
    434B  VAL*     2.8    32.4    +      -       -      +
    441B  PRO      5.3     1.5    -      -       -      +
    443B  PRO*     3.9    30.1    -      -       +      -
    447B  HIS*     4.5    11.4    -      -       +      +
    448B  SER      3.6    15.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  SER*     2.6    24.5    +      -       -      -
    133A  TRP*     2.9    70.7    +      -       +      +
    135A  GLU*     5.1     6.5    -      -       +      -
    475A  LYS*     4.3    17.9    -      -       +      -
    476A  THR*     1.3    77.9    -      -       -      +
    478A  THR*     1.3    59.5    +      -       -      +
    426B  SER*     4.1    27.8    -      -       -      +
    434B  VAL*     3.2    11.9    -      -       +      +
    436B  ILE*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  VAL*     4.7     4.7    -      -       +      -
    130A  ILE*     3.5    25.4    -      -       +      -
    131A  ASP      3.5     6.5    -      -       -      +
    132A  SER*     3.2    17.5    +      -       -      -
    476A  THR*     4.7     4.2    +      -       -      +
    477A  VAL*     1.3    71.1    -      -       -      +
    479A  GLN*     1.3    56.2    +      -       -      +
    434B  VAL      2.9     7.3    +      -       -      +
    435B  GLY*     3.2     3.3    -      -       -      -
    436B  ILE*     2.7    32.2    +      -       -      +
    438B  ILE*     4.2    17.0    -      -       +      +
    441B  PRO*     4.2    28.6    +      -       +      +
    442B  VAL      4.6     6.4    +      -       -      +
    443B  PRO*     5.1     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  GLY      4.4     0.2    -      -       -      +
    130A  ILE*     3.5     9.4    -      -       -      +
    131A  ASP*     2.8    36.1    +      -       +      +
    133A  TRP*     3.5    38.4    -      -       +      -
    478A  THR*     1.3    76.4    -      -       -      +
    480A  ARG*     1.3    64.2    +      -       -      +
    481A  TRP*     3.2    41.2    +      -       +      +
    422B  ALA*     5.2     3.2    -      -       -      +
    436B  ILE*     3.7    24.6    -      -       +      +
    438B  ILE*     4.5     0.4    -      -       -      -
    423C  ARG*     5.0     9.4    -      -       -      +
    479D  GLN*     5.3     9.6    +      -       -      +
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Residues in contact with ARG 480 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PRO      5.4     2.0    +      -       -      -
    129A  GLY      4.2    12.1    +      -       -      +
    130A  ILE*     3.9    20.1    -      -       +      +
    479A  GLN*     1.3    77.4    -      -       -      +
    481A  TRP*     1.3    73.3    +      -       -      +
    482A  PRO*     3.7    19.0    -      -       +      +
    263B  ASN*     3.6    30.9    +      -       -      +
    267B  GLN*     3.4    24.0    +      -       -      +
    436B  ILE*     2.9    10.8    +      -       -      +
    437B  ASN*     2.9    28.3    +      -       -      +
    438B  ILE*     3.4    31.2    -      -       +      -
    423C  ARG*     6.3     0.7    -      -       -      +
----------------------------------------------------------
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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