Contacts of the strand formed by residues 40 - 44 (chain D) in PDB entry 1JLH


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 40 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  PHE*     2.7    44.2    +      -       -      -
     37D  ASN*     3.8    13.0    +      -       -      +
     38D  HIS      3.7     1.3    -      -       -      +
     39D  PHE*     1.3    75.8    -      -       -      +
     41D  LEU*     1.3    73.0    +      -       -      +
     42D  THR*     5.5     2.3    -      -       -      +
     51D  LEU*     4.1     7.3    -      -       -      +
     52D  VAL      3.3    12.3    -      -       -      -
     53D  ASP*     4.0    10.5    -      -       -      -
     54D  TYR*     3.5     3.9    +      -       -      -
    313D  LYS*     4.9     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 41 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  SER*     1.3    82.4    -      -       -      +
     42D  THR*     1.3    62.3    +      -       -      +
     43D  LEU*     4.0    12.6    -      -       +      -
     50D  ILE      3.6     0.9    -      -       -      +
     51D  LEU*     3.3     6.8    -      -       -      +
     52D  VAL*     2.8    45.7    +      -       +      +
     54D  TYR*     4.0    13.0    -      -       +      +
    305D  HIS*     5.4     0.7    -      -       +      -
    313D  LYS*     3.6    53.8    -      -       +      +
    315D  ALA*     3.7    31.2    -      -       +      +
    318D  LEU*     3.9    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547C  PHE*     5.1    12.8    -      -       +      -
     36D  PHE*     6.1     1.1    -      -       +      -
     40D  SER*     5.5     2.5    -      -       -      +
     41D  LEU*     1.3    76.5    -      -       -      +
     43D  LEU*     1.3    65.4    -      -       -      +
     44D  ASN      4.1     1.2    +      -       -      -
     49D  HIS*     5.5     7.6    -      -       -      -
     50D  ILE      3.6     3.4    -      -       -      -
     51D  LEU*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     41D  LEU*     4.7    13.9    -      -       +      -
     42D  THR*     1.3    81.7    -      -       -      +
     44D  ASN*     1.3    58.9    +      -       -      +
     45D  THR*     3.8     1.5    +      -       -      -
     48D  GLY      4.0     0.2    -      -       -      +
     49D  HIS*     3.1     8.6    +      -       -      +
     50D  ILE*     2.8    59.7    +      -       +      +
     52D  VAL*     5.0     3.1    -      -       +      -
    301D  TRP*     3.9    23.6    -      -       +      -
    302D  MET*     4.4     9.6    -      -       +      -
    305D  HIS*     3.3    47.1    -      -       +      +
    313D  LYS      5.3     1.8    -      -       -      +
    315D  ALA*     4.3    13.0    -      -       +      -
    492D  MET*     5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  THR      4.1     1.8    +      -       -      -
     43D  LEU*     1.3    71.7    -      -       -      +
     45D  THR*     1.3    61.1    +      -       -      +
     46D  ASN*     2.9    36.1    +      -       -      +
     48D  GLY      4.0     1.6    +      -       -      +
     49D  HIS*     3.3    42.9    +      -       +      -
    301D  TRP*     3.5    14.3    +      -       -      -
----------------------------------------------------------
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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