Contacts of the strand formed by residues 41 - 49 (chain a) 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 a).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10a  LEU*     4.5     7.6    -      -       -      -
     20a  CYS*     6.0     0.2    -      -       -      -
     32a  LEU*     3.9    23.6    -      -       +      -
     34a  GLU      3.6     3.1    -      -       -      -
     35a  ALA*     4.1    10.1    -      -       -      -
     39a  MET      3.3    17.3    -      -       -      -
     40a  ASN*     1.3    77.7    -      -       -      +
     42a  GLN*     1.3    60.6    +      -       -      +
     43a  MET*     4.5    12.3    -      -       +      -
     62a  TYR*     3.2     6.6    -      -       -      -
     63a  ILE*     2.7    47.5    +      -       +      +
     68a  ILE*     4.3    10.3    -      -       +      -
     71a  LEU*     4.4    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 42 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32a  LEU*     3.5     5.0    -      -       -      +
     33a  ILE*     3.0    55.6    +      -       +      +
     34a  GLU*     2.9    14.7    +      -       -      +
     41a  CYS*     1.3    74.7    -      -       -      +
     43a  MET*     1.3    62.7    +      -       -      +
     60a  GLN*     3.4    24.5    +      -       -      +
     61a  VAL      3.3    14.4    -      -       -      +
     62a  TYR*     3.8    12.0    -      -       +      -
      8g  GLU*     3.2    29.3    +      -       -      +
     11g  LYS*     4.1    15.9    -      -       -      +
     12g  PHE*     4.0    22.2    -      -       +      -
     76g  VAL*     5.7     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 43 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18a  VAL*     3.4    41.5    -      -       +      +
     20a  CYS*     4.5     7.0    -      -       +      -
     28a  TYR*     3.7    13.7    -      -       -      +
     30a  GLY      3.6    19.5    -      -       -      +
     31a  LYS      3.2    10.1    -      -       -      +
     32a  LEU*     4.2    11.4    -      -       +      -
     33a  ILE*     4.3     2.5    -      -       -      +
     41a  CYS*     4.5     9.4    -      -       +      -
     42a  GLN*     1.3    80.3    -      -       -      +
     44a  SER*     1.3    61.3    +      -       -      +
     46a  ILE*     3.3    24.2    -      -       +      -
     60a  GLN*     3.3     7.4    -      -       -      +
     61a  VAL*     2.8    38.2    +      -       +      +
     63a  ILE*     4.0    24.7    -      -       -      -
     71a  LEU*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 44 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31a  LYS*     2.9    32.5    +      -       -      -
     33a  ILE*     3.5    26.6    -      -       -      +
     43a  MET*     1.3    70.1    -      -       -      +
     45a  ASN*     1.3    84.8    +      -       -      +
     46a  ILE*     3.5     4.1    -      -       -      +
     59a  GLU      3.2     7.4    -      -       -      -
     60a  GLN*     2.7    27.3    +      -       -      -
     75g  ARG*     5.3     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 45 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29a  ARG      3.6     6.6    -      -       -      +
     30a  GLY*     3.6     5.7    -      -       -      -
     31a  LYS*     5.1    13.8    -      -       +      +
     44a  SER*     1.3    87.0    +      -       -      +
     46a  ILE*     1.3    62.1    -      -       -      +
     47a  THR*     4.0     1.7    +      -       -      -
     57a  GLN*     4.9     5.6    +      -       -      +
     58a  LEU      3.5     5.4    -      -       -      -
     59a  GLU*     3.0    16.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 46 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28a  TYR*     3.9    28.5    -      -       +      -
     29a  ARG      3.1     4.7    -      -       -      +
     30a  GLY*     3.8     4.0    -      -       -      -
     43a  MET*     3.3    47.6    -      -       +      +
     44a  SER      3.7    13.9    -      -       -      +
     45a  ASN*     1.3    73.6    -      -       -      +
     47a  THR*     1.3    64.2    +      -       -      +
     48a  VAL*     3.5    15.5    -      -       +      +
     56a  ALA      3.7     0.2    -      -       -      +
     57a  GLN*     3.2    11.9    +      -       -      -
     58a  LEU*     2.9    42.5    +      -       +      +
     59a  GLU      5.0     0.2    -      -       -      +
     61a  VAL*     3.7    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 47 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27a  VAL      3.4     3.6    -      -       -      +
     29a  ARG*     2.8    40.5    +      -       -      +
     45a  ASN      4.8     1.9    +      -       -      -
     46a  ILE*     1.3    73.5    -      -       -      +
     48a  VAL*     1.3    71.2    +      -       -      +
     49a  THR*     3.8     6.1    +      -       -      +
     55a  VAL*     4.2    17.7    -      -       +      -
     56a  ALA      3.4     8.5    -      -       -      +
     57a  GLN*     3.5    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26a  GLU*     4.3     3.4    -      -       +      -
     27a  VAL      3.3     6.5    -      -       -      +
     28a  TYR*     3.6    37.9    -      -       +      +
     46a  ILE*     3.5     7.4    +      -       -      +
     47a  THR*     1.3    76.8    -      -       -      +
     49a  THR*     1.3    64.9    +      -       -      +
     50a  TYR*     3.6    35.9    -      -       +      +
     55a  VAL*     3.2     6.9    -      -       -      +
     56a  ALA*     3.2    49.8    +      -       +      +
     58a  LEU*     4.1    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 49 (chain a). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25a  GLY      4.3     1.6    -      -       -      +
     26a  GLU*     3.5     2.8    -      -       -      -
     27a  VAL*     2.9    43.8    +      -       +      +
     47a  THR*     3.8     9.0    +      -       -      +
     48a  VAL*     1.3    77.0    +      -       -      +
     50a  TYR*     1.3    74.3    +      -       -      +
     53a  GLY      3.9    19.5    -      -       -      +
     54a  ARG      3.5     3.4    -      -       -      +
     55a  VAL*     4.0    12.0    -      -       +      +
     21k  TYR*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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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