Contacts of the strand formed by residues 41 - 49 (chain O) 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 CYS 41 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10O  LEU*     4.5     7.4    -      -       -      -
     20O  CYS*     6.0     0.4    -      -       -      -
     32O  LEU*     3.9    23.8    -      -       +      -
     34O  GLU      3.6     2.9    -      -       -      -
     35O  ALA*     4.1    10.3    -      -       -      -
     39O  MET      3.3    17.5    +      -       -      -
     40O  ASN*     1.3    77.0    -      -       -      +
     42O  GLN*     1.3    59.5    +      -       -      +
     43O  MET*     4.5    11.0    -      -       +      -
     62O  TYR*     3.2     5.7    -      -       -      -
     63O  ILE*     2.7    47.9    +      -       +      +
     68O  ILE*     4.3    10.8    -      -       +      -
     71O  LEU*     4.4    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 42 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32O  LEU*     3.5     5.7    -      -       -      +
     33O  ILE*     3.0    51.7    +      -       -      +
     34O  GLU*     2.9    24.0    +      -       +      +
     40O  ASN      4.3     0.2    -      -       -      -
     41O  CYS*     1.3    74.4    -      -       -      +
     43O  MET*     1.3    63.4    +      -       -      +
     60O  GLN*     3.3    30.5    +      -       -      +
     61O  VAL      3.3    14.6    -      -       -      +
     62O  TYR*     3.8    15.7    -      -       +      -
      8U  GLU      5.6     1.9    -      -       -      +
     11U  LYS*     4.3    20.9    -      -       -      +
     12U  PHE*     4.0    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 43 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18O  VAL*     3.4    42.4    -      -       +      +
     20O  CYS*     4.5     9.2    -      -       +      -
     28O  TYR*     3.7    13.7    -      -       -      +
     30O  GLY      3.6    18.8    -      -       -      +
     31O  LYS      3.2     9.0    -      -       -      +
     32O  LEU*     4.2    11.9    -      -       +      -
     33O  ILE*     4.3     2.2    -      -       -      +
     41O  CYS*     4.1    10.7    +      -       +      +
     42O  GLN*     1.3    80.3    -      -       -      +
     44O  SER*     1.3    62.5    +      -       -      +
     46O  ILE*     3.3    22.7    -      -       +      -
     60O  GLN*     3.3     7.6    -      -       -      +
     61O  VAL*     2.8    37.1    +      -       +      +
     63O  ILE*     4.1    23.6    -      -       -      -
     71O  LEU*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 44 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31O  LYS*     2.9    32.0    +      -       -      +
     33O  ILE*     3.5    26.1    -      -       -      +
     43O  MET*     1.3    71.1    -      -       -      +
     45O  ASN*     1.3    84.3    +      -       -      +
     46O  ILE*     3.5     4.4    -      -       -      +
     59O  GLU      3.2     6.7    -      -       -      -
     60O  GLN*     2.7    27.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 45 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29O  ARG      3.6     1.2    -      -       -      +
     30O  GLY*     3.6    11.1    -      -       -      -
     31O  LYS*     4.2    21.1    -      -       +      +
     44O  SER*     1.3    84.7    +      -       -      +
     46O  ILE*     1.3    61.7    +      -       -      +
     47O  THR*     4.0     1.7    +      -       -      -
     57O  GLN*     4.9     6.5    +      -       -      +
     58O  LEU      3.5     5.2    -      -       -      -
     59O  GLU*     3.0    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 46 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28O  TYR*     3.9    27.6    -      -       +      -
     29O  ARG      3.1     4.7    -      -       -      +
     30O  GLY*     3.8     3.8    -      -       -      -
     43O  MET*     3.3    47.8    -      -       +      -
     44O  SER*     3.7    15.0    -      -       -      +
     45O  ASN*     1.3    75.1    -      -       -      +
     47O  THR*     1.3    65.3    +      -       -      +
     48O  VAL*     3.5    15.5    -      -       +      +
     56O  ALA      3.7     0.2    -      -       -      +
     57O  GLN*     3.2    12.2    +      -       -      -
     58O  LEU*     2.8    44.1    +      -       +      +
     59O  GLU      4.9     0.4    -      -       -      +
     61O  VAL*     3.6    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 47 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27O  VAL      3.4     3.8    -      -       -      +
     29O  ARG*     2.8    40.4    +      -       -      +
     45O  ASN      4.8     1.7    +      -       -      -
     46O  ILE*     1.3    73.9    -      -       -      +
     48O  VAL*     1.3    70.6    +      -       -      +
     49O  THR*     3.7     6.8    +      -       -      +
     55O  VAL*     4.2    18.4    -      -       +      -
     56O  ALA      3.4     8.3    -      -       -      +
     57O  GLN*     3.5    22.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26O  GLU*     4.3     2.2    -      -       +      -
     27O  VAL      3.3     6.1    -      -       -      +
     28O  TYR*     3.6    38.6    -      -       +      +
     46O  ILE*     3.5     8.5    +      -       -      +
     47O  THR*     1.3    76.4    -      -       -      +
     49O  THR*     1.3    66.3    +      -       -      +
     50O  TYR*     3.6    37.9    -      -       +      +
     55O  VAL*     3.3     5.9    -      -       -      +
     56O  ALA*     3.2    48.7    +      -       +      +
     58O  LEU*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 49 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21N  TYR*     4.0    22.9    -      -       +      -
     25O  GLY      4.3     0.9    -      -       -      +
     26O  GLU*     3.5     2.6    -      -       -      -
     27O  VAL*     2.8    49.3    +      -       +      +
     47O  THR*     3.8     9.2    +      -       -      +
     48O  VAL*     1.3    78.8    +      -       -      +
     50O  TYR*     1.3    73.7    +      -       -      +
     53O  GLY      3.9    20.6    -      -       -      +
     54O  ARG      3.5     3.1    -      -       -      +
     55O  VAL*     4.0    12.3    -      -       +      +
----------------------------------------------------------
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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