Contacts of the strand formed by residues 472 - 480 (chain J) 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 J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118J  LEU*     4.0     7.9    -      -       +      -
    136J  PHE*     3.6    35.1    -      -       +      +
    137J  GLN      3.2    13.2    -      -       -      +
    139J  MET*     3.6     5.6    -      -       -      -
    165J  CYS*     3.9    22.9    -      -       +      +
    242J  ARG*     2.7    27.0    +      -       -      -
    468J  VAL      2.5    26.0    +      -       -      +
    469J  ARG*     3.0    16.2    +      -       -      +
    470J  PHE      3.2     0.2    -      -       -      -
    471J  TYR*     1.3    84.2    -      -       -      +
    473J  LYS*     1.3    57.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 473 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57J  ARG*     6.2     0.2    -      -       -      +
    135J  GLU      3.3     1.0    -      -       -      +
    136J  PHE*     3.3     4.6    -      -       -      -
    137J  GLN*     2.8    44.8    +      -       -      +
    138J  PRO      3.3    21.1    +      -       -      -
    139J  MET*     3.7    33.8    +      -       +      +
    218J  LYS*     5.9     1.6    -      -       -      +
    242J  ARG*     3.9    11.4    -      -       -      +
    469J  ARG*     5.3     1.3    -      -       -      +
    472J  THR*     1.3    74.3    -      -       -      +
    474J  ARG*     1.3    64.5    +      -       -      +
    475J  LYS      3.5     0.2    +      -       -      -
    430K  GLN*     3.4    23.0    +      -       -      -
    452K  TRP*     3.4    53.7    -      -       +      +
    453K  LYS*     6.1     2.4    -      -       -      +
    461K  HIS*     5.4     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 474 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121J  GLU*     4.7     7.9    +      -       -      -
    134J  SER*     3.6    25.0    +      -       -      -
    135J  GLU      3.6     4.0    -      -       -      -
    136J  PHE*     3.8    28.8    -      -       +      -
    469J  ARG*     3.8    13.5    -      -       -      +
    473J  LYS*     1.3    72.1    -      -       -      +
    475J  LYS*     1.3    68.7    +      -       -      +
    476J  THR*     4.1     6.9    +      -       -      +
    432K  GLY*     4.1     3.1    -      -       -      +
    447K  HIS*     4.8     5.1    +      -       -      -
    448K  SER*     3.7    37.3    -      -       -      +
    450K  GLY      4.8     0.3    -      -       -      +
    452K  TRP*     2.8    21.0    +      -       -      -
    461K  HIS*     3.6    33.2    +      -       +      +
    465K  PRO*     3.9    18.3    -      -       -      +
    466K  ASP*     2.6    41.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 475 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134J  SER*     3.3     7.1    -      -       -      -
    135J  GLU*     2.7    42.1    +      -       +      +
    137J  GLN*     3.0    28.3    +      -       -      +
    473J  LYS      3.5     0.2    +      -       -      -
    474J  ARG*     1.3    75.1    -      -       -      +
    476J  THR*     1.3    67.9    +      -       -      +
    477J  VAL*     4.2    10.1    -      -       +      -
    426K  SER      2.6    29.5    +      -       -      +
    427K  ASP      2.9    19.2    +      -       -      -
    429K  ILE*     2.8    28.1    +      -       -      +
    431K  VAL      3.5    11.2    -      -       -      -
    432K  GLY      3.1    13.2    -      -       -      +
    434K  VAL*     4.0    13.7    -      -       +      -
    452K  TRP*     3.6    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 476 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132J  SER*     3.8    19.1    -      -       -      +
    133J  TRP      3.7     7.6    -      -       -      +
    134J  SER*     5.0     2.1    -      -       -      -
    474J  ARG*     4.1    10.9    +      -       -      +
    475J  LYS*     1.3    76.9    +      -       -      +
    477J  VAL*     1.3    64.1    +      -       -      +
    478J  THR*     4.8     3.0    +      -       -      +
    432K  GLY      2.9    11.1    +      -       -      -
    433K  MET*     3.5     6.2    -      -       -      +
    434K  VAL      3.0    24.1    +      -       -      +
    441K  PRO      5.0     1.6    -      -       -      +
    443K  PRO*     4.0    31.2    -      -       +      -
    447K  HIS*     4.3    15.7    -      -       +      +
    448K  SER      3.4    18.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 477 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132J  SER*     2.8    24.7    +      -       -      -
    133J  TRP*     3.0    68.8    +      -       +      +
    135J  GLU*     4.9     5.4    -      -       +      +
    475J  LYS*     4.4    15.0    -      -       +      -
    476J  THR*     1.3    75.3    -      -       -      +
    478J  THR*     1.3    60.7    +      -       -      +
    426K  SER*     4.0    22.9    -      -       -      +
    434K  VAL*     3.4    16.2    -      -       +      +
    436K  ILE*     4.2    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 478 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126J  VAL*     4.8     4.7    -      -       +      -
    130J  ILE*     3.7    24.9    -      -       +      -
    131J  ASP      3.7     5.6    -      -       -      +
    132J  SER*     3.5    11.4    +      -       -      -
    476J  THR*     4.8     4.3    +      -       -      +
    477J  VAL*     1.3    77.9    +      -       -      +
    479J  GLN*     1.3    60.5    +      -       -      +
    434K  VAL      2.9    11.9    +      -       -      -
    435K  GLY*     3.4     2.8    -      -       -      -
    436K  ILE      2.9    27.2    +      -       -      +
    438K  ILE*     3.8    18.7    -      -       +      +
    441K  PRO*     4.3    22.9    +      -       +      +
    442K  VAL      4.9     6.5    +      -       -      +
    443K  PRO*     5.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 479 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133I  TRP*     6.0     3.0    -      -       -      -
    479I  GLN*     4.9    15.7    +      -       -      +
    130J  ILE*     3.4     8.5    -      -       -      +
    131J  ASP*     3.1    35.8    +      -       +      +
    133J  TRP*     3.6    38.5    -      -       +      -
    478J  THR*     1.3    73.4    -      -       -      +
    480J  ARG*     1.3    65.4    +      -       -      +
    481J  TRP*     3.4    39.2    +      -       +      +
    422K  ALA*     5.3     3.6    -      -       -      +
    436K  ILE*     3.9    22.0    -      -       +      +
    438K  ILE*     4.6     0.2    -      -       -      -
    423L  ARG*     4.9    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 480 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128J  PRO      5.6     1.0    +      -       -      -
    129J  GLY      4.3     8.3    -      -       -      +
    130J  ILE*     4.0    21.7    -      -       +      +
    479J  GLN*     1.3    77.7    -      -       -      +
    481J  TRP*     1.3    72.6    +      -       -      +
    482J  PRO*     3.5    36.0    -      -       +      +
    263K  ASN*     3.7     8.1    -      -       -      +
    267K  GLN*     3.3    34.5    +      -       -      +
    436K  ILE*     3.1     9.4    +      -       -      +
    437K  ASN*     3.0    27.2    +      -       -      +
    438K  ILE*     3.5    33.2    -      -       +      -
    423L  ARG*     6.4     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