Contacts of the strand formed by residues 41 - 45 (chain D) in PDB entry 1JIQ


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 SER 41 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  PHE*     2.7    37.8    +      -       -      -
     38D  ASN*     3.8    13.7    +      -       -      +
     39D  HIS      3.6     1.8    -      -       -      +
     40D  PHE*     1.3    78.4    -      -       -      +
     42D  LEU*     1.3    65.9    +      -       -      +
     43D  THR*     5.3     3.0    -      -       -      +
     52D  LEU*     4.0    12.5    -      -       -      +
     53D  VAL      3.2    11.7    -      -       -      -
     54D  ASP*     4.0    11.0    -      -       -      -
     55D  TYR*     3.6     8.2    +      -       -      -
    314D  LYS*     5.6     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  SER*     1.3    79.4    -      -       -      +
     43D  THR*     1.3    63.6    +      -       -      +
     44D  LEU*     4.1    13.7    -      -       +      -
     51D  ILE      3.5     0.9    -      -       -      +
     52D  LEU*     3.4     4.3    -      -       -      +
     53D  VAL*     2.8    48.3    +      -       +      +
     55D  TYR*     4.6     3.6    -      -       +      +
    313D  GLU      5.0     0.2    -      -       -      +
    314D  LYS*     3.1    61.2    -      -       +      +
    315D  ASN      4.0     0.7    -      -       -      -
    316D  ALA*     3.6    33.4    -      -       +      +
    319D  LEU*     4.3    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 43 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    548C  PHE*     5.1    13.2    -      -       +      -
     37D  PHE*     6.1     1.3    -      -       +      -
     41D  SER*     5.3     3.1    -      -       -      +
     42D  LEU*     1.3    79.0    -      -       -      +
     44D  LEU*     1.3    66.3    +      -       -      +
     45D  ASN      4.1     0.9    +      -       -      -
     50D  HIS*     5.4     8.1    -      -       -      -
     51D  ILE      3.4     5.2    -      -       -      +
     52D  LEU*     3.9    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  LEU*     4.2    21.3    -      -       +      +
     43D  THR*     1.3    81.9    -      -       -      +
     45D  ASN*     1.3    59.8    +      -       -      +
     46D  THR*     3.7     1.3    +      -       +      -
     49D  GLY      4.0     0.2    -      -       -      +
     50D  HIS*     3.1    10.1    -      -       -      +
     51D  ILE*     2.7    59.3    +      -       +      +
     53D  VAL*     5.1     1.8    -      -       +      -
    302D  TRP*     3.9    24.7    -      -       +      -
    303D  MET*     4.1    12.6    -      -       +      -
    306D  HIS*     3.5    41.5    -      -       +      +
    314D  LYS      4.9     0.9    -      -       -      +
    316D  ALA*     4.0    15.3    -      -       +      -
    493D  MET*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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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  THR      4.1     2.0    +      -       -      -
     44D  LEU*     1.3    73.4    -      -       -      +
     46D  THR*     1.3    60.1    +      -       -      +
     47D  ASN*     2.9    34.0    +      -       -      +
     49D  GLY      3.9     2.7    +      -       -      +
     50D  HIS*     3.4    40.8    +      -       +      +
    302D  TRP*     3.6    13.8    +      -       -      -
----------------------------------------------------------
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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