Contacts of the strand formed by residues 41 - 46 (chain d) 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 GLN 41 (chain d).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40d  THR*     1.3    85.1    +      -       -      +
     42d  VAL*     1.3    63.7    +      -       -      +
     53d  LEU*     3.6    26.1    +      -       +      +
     54d  GLY*     3.3    12.9    -      -       -      +
     55d  ARG*     3.5    18.1    -      -       +      +
     69d  ASN      5.6     2.0    +      -       -      -
    112d  ASN*     3.4    20.6    +      -       +      +
     47k  GLU      4.9     1.6    +      -       -      -
     48k  PHE*     3.3    22.9    -      -       +      -
     49k  GLU*     2.7    58.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32d  LEU*     5.4     1.3    -      -       +      -
     35d  SER*     3.9    19.1    -      -       -      +
     40d  THR      4.3     1.1    -      -       -      +
     41d  GLN*     1.3    80.5    -      -       -      +
     43d  LEU*     1.3    58.9    +      -       -      +
     44d  ILE*     4.1    23.3    -      -       +      -
     52d  LEU      3.5     0.9    -      -       -      +
     53d  LEU*     3.1     6.2    -      -       -      +
     54d  GLY      2.9    36.5    +      -       -      +
     56d  VAL*     3.6    28.3    -      -       +      -
     65d  MET*     4.3     2.2    -      -       +      -
     67d  LEU*     5.0     1.6    -      -       +      -
    109d  VAL*     3.5    23.1    -      -       +      -
    110d  LEU      3.4    14.8    -      -       -      +
    111d  ARG*     4.1     3.1    -      -       +      +
     48k  PHE*     3.8     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42d  VAL*     1.3    73.5    -      -       -      +
     44d  ILE*     1.3    60.7    +      -       -      +
     45d  ASN      4.2     0.2    +      -       -      -
     51d  LYS*     4.3     9.6    -      -       +      -
     52d  LEU      3.4     6.5    -      -       -      +
     53d  LEU*     3.9    25.4    -      -       +      -
     73d  MET*     4.1    15.0    -      -       +      -
    108d  VAL      3.8     0.9    -      -       -      +
    109d  VAL*     3.6     1.0    -      -       -      -
    110d  LEU*     2.8    42.1    +      -       +      +
     41k  ILE*     3.7    46.8    -      -       +      +
     44k  TYR*     4.1    14.8    -      -       +      +
     45k  ILE      4.8     0.4    -      -       -      +
     48k  PHE*     3.3    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 44 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42d  VAL*     4.1    14.1    -      -       +      -
     43d  LEU*     1.3    77.4    -      -       -      +
     45d  ASN*     1.3    70.9    +      -       -      +
     46d  CYS*     3.7     4.5    +      -       +      +
     50d  LYS      3.9     0.2    -      -       -      +
     51d  LYS*     3.2     5.6    -      -       -      -
     52d  LEU*     2.7    43.9    +      -       +      +
     65d  MET*     3.6    36.1    -      -       +      -
     67d  LEU*     4.0    20.6    -      -       +      -
    101d  LEU*     4.3    11.7    -      -       +      -
    106d  VAL*     4.1    24.5    -      -       +      -
    108d  VAL      3.3     9.9    -      -       -      +
    109d  VAL*     4.2     9.0    -      -       +      -
     41k  ILE*     4.7     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 45 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43d  LEU      4.2     0.4    +      -       -      -
     44d  ILE*     1.3    74.7    -      -       -      +
     46d  CYS*     1.3    65.4    +      -       -      +
     49d  ASN*     4.2     1.2    -      -       -      +
     50d  LYS      3.8     1.5    -      -       -      +
     51d  LYS*     3.1    27.8    +      -       -      +
    107d  ILE*     3.0    51.3    +      -       +      +
    108d  VAL*     3.0    18.9    +      -       +      +
     27f  MET*     4.3    10.7    -      -       -      -
     29f  TYR*     4.5     3.2    +      -       -      -
     38k  TYR*     5.9     0.2    -      -       -      +
     39k  CYS      3.1    20.6    +      -       -      +
     40k  GLY*     4.0     8.9    -      -       -      -
     41k  ILE*     3.5    22.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 46 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66c  ARG*     4.1    14.6    -      -       -      -
     67c  TYR*     5.2     0.7    -      -       -      -
     44d  ILE*     4.3     7.2    -      -       +      +
     45d  ASN*     1.3    76.9    +      -       -      +
     47d  ARG*     1.3    62.7    +      -       -      +
     48d  ASN*     3.3    22.4    -      -       -      +
     49d  ASN*     2.8    23.4    +      -       -      -
     50d  LYS      3.1    19.4    +      -       -      +
     52d  LEU*     4.3    24.0    -      -       +      -
    101d  LEU*     4.3    13.9    -      -       -      -
    105d  SER      3.4    12.6    -      -       -      -
    106d  VAL*     5.5     0.2    -      -       -      -
    107d  ILE*     3.7     9.6    -      -       -      +
----------------------------------------------------------
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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