Contacts of the strand formed by residues 65 - 72 (chain p) 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 ARG 65 (chain p).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19n  ILE*     4.1    15.8    -      -       +      +
     20n  PRO*     2.8    47.6    +      -       +      -
     21n  TYR*     3.4     2.4    -      -       -      +
     22n  LEU*     2.9    47.5    +      -       +      +
     21o  GLU*     5.0     3.6    +      -       -      -
     27o  VAL*     6.0     4.2    -      -       -      +
     70o  PHE*     6.0     1.0    -      -       -      -
     25p  ARG*     4.1     6.5    -      -       -      +
     46p  ASP*     3.9     0.2    -      -       -      -
     47p  GLU*     2.9    54.4    +      -       +      +
     49p  ARG*     3.0    29.5    -      -       -      +
     63p  GLU      4.9     0.2    -      -       -      +
     64p  LYS*     1.3    81.3    -      -       -      +
     66p  VAL*     1.3    65.8    +      -       -      +
     67p  LEU*     3.4    15.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16n  ARG*     3.4    33.6    -      -       -      +
     19n  ILE*     3.6    16.5    -      -       -      +
     20n  PRO*     5.4     3.5    -      -       -      +
     44p  ASP*     5.7     1.3    -      -       -      -
     45p  CYS      4.2     2.0    -      -       -      -
     46p  ASP*     4.0    28.3    -      -       -      +
     64p  LYS*     4.5    13.7    -      -       -      -
     65p  ARG*     1.3    74.2    -      -       -      +
     67p  LEU*     1.3    67.8    +      -       -      +
     68p  GLY*     3.8     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 67 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16n  ARG*     4.3    10.2    +      -       -      -
     19n  ILE*     4.5    11.0    -      -       +      +
     70o  PHE*     4.5     6.3    -      -       +      -
     72o  ILE*     3.1    44.8    -      -       +      +
     27p  PHE*     3.7    25.1    -      -       +      -
     45p  CYS*     3.0    11.4    +      -       -      +
     47p  GLU*     3.5    41.5    -      -       +      +
     65p  ARG*     3.4    22.9    -      -       +      +
     66p  VAL*     1.3    83.6    -      -       -      +
     68p  GLY*     1.3    59.3    +      -       -      +
     69p  LEU      3.7     0.2    +      -       -      -
     70p  VAL*     3.5    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 68 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16n  ARG*     3.7    30.1    -      -       -      -
     75o  ASP*     4.0     0.4    -      -       -      -
     42p  LEU      3.5     0.3    -      -       -      +
     44p  ASP*     3.2     9.1    +      -       -      -
     45p  CYS*     2.7    43.7    +      -       -      +
     66p  VAL*     3.8     4.2    -      -       -      +
     67p  LEU*     1.3    76.8    -      -       -      +
     69p  LEU*     1.3    59.7    +      -       -      -
     70p  VAL      3.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9o  VAL*     4.6    10.1    -      -       +      -
     72o  ILE*     3.6     3.3    -      -       -      +
     73o  LEU*     2.8    55.2    +      -       +      +
     74o  PRO      3.8     7.0    -      -       -      +
     75o  ASP*     3.4    20.2    +      -       -      +
     77o  LEU*     3.8    29.4    -      -       +      -
     78o  LYS*     4.1    12.8    -      -       +      +
     83o  LEU*     5.7     1.6    -      -       +      -
     41p  ILE*     3.8    20.9    -      -       +      -
     42p  LEU      3.5    15.0    -      -       -      +
     43p  CYS*     3.5    26.7    -      -       -      +
     67p  LEU      3.7     2.4    +      -       -      -
     68p  GLY*     1.3    68.9    -      -       -      -
     70p  VAL*     1.3    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70o  PHE*     4.1     8.3    -      -       +      -
     71o  LEU      3.4    12.3    -      -       -      +
     72o  ILE*     4.8     2.5    -      -       +      -
     73o  LEU*     5.7     0.7    -      -       -      -
     27p  PHE*     3.8    27.4    -      -       +      -
     40p  LEU      3.7     0.5    -      -       -      +
     41p  ILE*     3.4     8.3    -      -       -      +
     42p  LEU*     2.9    38.0    +      -       +      +
     45p  CYS*     3.5    30.1    -      -       +      -
     67p  LEU*     3.5    27.6    -      -       +      +
     68p  GLY      3.6     0.9    -      -       -      +
     69p  LEU*     1.3    79.4    -      -       -      +
     71p  LEU*     1.3    71.0    +      -       -      +
     72p  LEU*     4.1     3.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 71 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6o  PRO*     3.8    20.4    -      -       +      +
      7o  ILE*     5.3     2.0    -      -       +      -
     10o  LEU*     3.8    31.9    -      -       +      -
     39o  MET*     4.4    20.0    -      -       +      -
     70o  PHE*     3.3     4.0    -      -       -      -
     71o  LEU*     3.0    37.8    +      -       +      +
     73o  LEU*     4.2    17.2    -      -       +      +
     39p  ASN*     4.3    14.1    -      -       +      +
     40p  LEU      3.3     6.5    -      -       -      +
     41p  ILE*     3.8    19.1    -      -       +      -
     69p  LEU      4.4     0.4    +      -       -      -
     70p  VAL*     1.3    75.9    -      -       -      +
     72p  LEU*     1.3    74.9    +      -       -      +
     73p  ARG      3.9     1.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 72 (chain p). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69o  ARG      3.7    11.9    -      -       -      +
     70o  PHE*     4.1     4.7    -      -       +      -
     19p  CYS*     4.8     2.0    -      -       +      -
     21p  LEU*     4.0    34.8    -      -       +      -
     27p  PHE*     4.0    30.5    -      -       +      -
     38p  MET      4.4     0.4    -      -       -      +
     39p  ASN*     3.1     6.6    -      -       -      +
     40p  LEU*     3.0    60.0    +      -       +      -
     42p  LEU*     5.2     3.1    -      -       +      -
     70p  VAL*     4.0     3.2    -      -       +      -
     71p  LEU*     1.3    73.9    -      -       -      +
     73p  ARG*     1.3    77.1    +      -       -      +
     74p  GLY*     5.6     0.2    -      -       -      -
     76p  ASN*     4.5     5.6    -      -       +      -
     77p  LEU*     4.1    16.4    -      -       +      -
----------------------------------------------------------
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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