Contacts of the strand formed by residues 65 - 76 (chain R) in PDB entry 4PJO


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 MET 65 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3Q  LEU*     4.3     3.1    -      -       -      -
     32R  LEU*     4.5    21.5    -      -       +      -
     42R  VAL*     4.3     2.9    -      -       +      -
     44R  ILE*     3.6    26.0    -      -       +      -
     56R  VAL*     3.6    24.7    -      -       +      -
     58R  ALA      3.3     5.8    -      -       -      +
     59R  PHE*     3.9    15.5    -      -       +      -
     63R  CYS*     3.2    13.2    +      -       -      +
     64R  ASN*     1.3    78.7    -      -       -      +
     66R  VAL*     1.3    61.9    +      -       -      +
     67R  LEU*     3.5    33.6    +      -       +      -
    100R  PHE*     3.4     5.6    -      -       -      -
    101R  LEU*     2.8    38.9    +      -       +      +
    106R  VAL*     4.8     6.5    -      -       -      -
    109R  VAL*     4.7     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 66 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3Q  LEU*     4.2     8.9    -      -       +      +
      6Q  PHE*     4.2    20.0    -      -       +      -
     70Q  LEU*     5.3     1.3    -      -       +      -
     76Q  LEU*     4.2    26.7    -      -       +      -
     80Q  LEU*     4.6    12.1    -      -       +      -
     56R  VAL*     3.7     0.7    -      -       -      -
     57R  LYS*     2.9    41.9    +      -       +      -
     58R  ALA*     3.0    17.8    +      -       +      +
     65R  MET*     1.3    73.4    -      -       -      +
     67R  LEU*     1.3    69.0    +      -       -      +
     99R  MET      3.3    11.0    -      -       -      +
    100R  PHE*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 67 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42R  VAL*     4.9     2.7    -      -       +      -
     44R  ILE*     4.0    20.9    -      -       +      -
     52R  LEU*     4.2    17.3    -      -       +      -
     54R  GLY*     5.1     2.5    -      -       -      +
     55R  ARG      3.2    17.3    -      -       -      +
     56R  VAL*     3.9     5.6    -      -       +      -
     57R  LYS*     5.1     0.7    -      -       -      -
     65R  MET*     3.5    33.4    -      -       +      +
     66R  VAL*     1.3    83.2    -      -       -      +
     68R  GLU*     1.3    64.9    +      -       -      +
     70R  VAL*     3.4    22.4    -      -       +      -
     98R  LYS*     3.4     5.2    -      -       -      +
     99R  MET*     2.9    49.3    +      -       +      +
    101R  LEU*     4.5     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 68 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76Q  LEU*     3.8    20.3    -      -       +      +
     54R  GLY*     3.8     0.7    -      -       -      -
     55R  ARG*     2.9    36.5    +      -       +      +
     57R  LYS*     3.3    44.6    +      -       +      +
     67R  LEU*     1.3    73.7    -      -       -      +
     69R  ASN*     1.3    89.8    +      -       -      +
     70R  VAL*     3.2     4.3    +      -       -      -
     97R  SER      3.2     9.6    -      -       -      +
     98R  LYS*     4.1    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 69 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41R  GLN*     5.6     2.9    +      -       -      -
     53R  LEU      3.6     8.0    -      -       -      +
     54R  GLY*     3.7     4.3    -      -       -      -
     55R  ARG*     4.3    22.4    -      -       +      +
     68R  GLU*     1.3    95.1    +      -       -      +
     70R  VAL*     1.3    63.1    +      -       -      +
     71R  LYS*     5.2     0.7    -      -       -      +
     95R  TYR*     3.0    36.0    +      -       +      -
     96R  ILE      3.8     1.1    -      -       -      -
     97R  SER*     2.9    13.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52R  LEU*     3.8    28.5    -      -       +      -
     53R  LEU      3.3     9.6    -      -       -      +
     54R  GLY*     4.1     4.0    -      -       -      +
     67R  LEU*     3.4    36.1    -      -       +      +
     68R  GLU      3.8     9.4    -      -       -      +
     69R  ASN*     1.3    75.7    -      -       -      +
     71R  LYS*     1.3    67.8    +      -       -      +
     72R  GLU*     4.0     2.2    -      -       -      +
     95R  TYR*     3.3    10.4    -      -       -      -
     96R  ILE*     2.8    37.2    +      -       +      +
     99R  MET*     3.5    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47N  GLU*     3.4    28.5    +      -       +      +
     51R  LYS      3.4     2.8    -      -       -      +
     53R  LEU*     2.9    37.9    +      -       +      +
     69R  ASN      5.2     1.1    -      -       -      +
     70R  VAL*     1.3    75.6    -      -       -      +
     72R  GLU*     1.3    64.2    +      -       -      +
     73R  MET*     3.8    30.7    -      -       +      +
     93R  ASP*     4.0    26.2    +      -       +      +
     94R  ARG      3.4     9.6    -      -       -      +
     95R  TYR*     4.5     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 72 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67Q  TYR*     2.4    33.0    +      -       -      -
     48R  ASN*     4.1     1.4    +      -       -      -
     50R  LYS*     3.2    27.9    +      -       +      +
     51R  LYS      3.3     4.7    -      -       -      -
     52R  LEU*     4.0    18.9    -      -       +      +
     70R  VAL*     4.0     3.1    -      -       +      +
     71R  LYS*     1.3    74.2    -      -       -      +
     73R  MET*     1.3    61.7    +      -       -      +
     74R  TRP*     3.5    13.7    -      -       +      -
     93R  ASP*     3.1     5.7    -      -       -      +
     94R  ARG*     2.5    73.8    +      -       +      +
     96R  ILE*     4.6    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 73 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44N  TYR*     3.8    33.4    -      -       +      -
     47N  GLU*     3.5    33.7    -      -       +      -
     43R  LEU*     4.1    12.8    -      -       +      -
     50R  LYS*     3.6     0.7    -      -       -      -
     51R  LYS*     2.7    42.3    +      -       +      +
     53R  LEU*     3.8    29.8    -      -       +      -
     71R  LYS*     3.8    31.9    -      -       +      +
     72R  GLU*     1.3    81.2    -      -       -      +
     74R  TRP*     1.3    65.3    +      -       -      +
     92R  LYS      3.3     7.6    -      -       -      +
     93R  ASP*     4.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 74 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44N  TYR*     4.1    11.5    +      -       -      -
     49R  ASN      4.4     5.4    -      -       -      +
     50R  LYS*     3.6    44.2    -      -       +      +
     51R  LYS*     5.5     1.1    -      -       -      +
     72R  GLU*     3.5    40.2    -      -       +      -
     73R  MET*     1.3    83.4    -      -       -      +
     75R  THR*     1.3    77.2    +      -       -      +
     76R  GLU*     3.2    34.6    +      -       +      +
     91R  ASN*     3.8     4.2    -      -       -      +
     92R  LYS*     2.9    47.8    +      -       +      +
     93R  ASP*     3.8    13.7    -      -       -      -
     94R  ARG*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 75 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36N  GLN*     2.9    26.1    +      -       +      +
     39N  CYS*     5.4    11.9    -      -       -      -
     44N  TYR*     4.6     8.8    +      -       -      +
     49R  ASN*     5.6     5.3    +      -       -      +
     74R  TRP*     1.3    86.2    +      -       -      +
     76R  GLU*     1.3    63.1    +      -       -      +
     89R  PRO*     4.7    13.4    -      -       +      +
     90R  VAL      3.3    13.7    +      -       -      -
     91R  ASN*     3.8    11.8    +      -       -      -
     92R  LYS      4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36N  GLN*     4.4     6.5    -      -       -      +
     74R  TRP*     3.2    31.5    +      -       +      +
     75R  THR*     1.3    78.0    -      -       -      +
     77R  VAL*     1.3    61.8    +      -       -      +
     89R  PRO*     3.4     7.3    -      -       -      +
     90R  VAL*     2.8    38.7    +      -       +      +
     92R  LYS*     3.6    37.1    +      -       +      +
----------------------------------------------------------
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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