Contacts of the strand formed by residues 46 - 51 (chain D) in PDB entry 5JMO


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 GLU 46 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  VAL*     3.3     4.3    -      -       -      -
     38D  ARG*     2.8    87.6    +      -       +      +
     43D  LYS*     6.0     2.3    -      -       -      +
     44D  GLY      4.2     5.4    -      -       -      +
     45D  LEU*     1.3    76.4    -      -       -      +
     47D  TRP*     1.3    75.6    +      -       -      +
     48D  VAL*     3.5     1.4    +      -       -      +
     61D  ALA*     5.0     2.0    -      -       +      +
     63D  SER*     3.5    13.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496B  ASN*     6.4     0.7    -      -       -      -
    525B  ALA*     3.7    33.7    -      -       +      -
    526B  ASP*     5.4     7.0    -      -       -      +
     35D  TYR*     3.9    16.6    -      +       -      -
     36D  TRP      4.0     4.9    -      -       -      -
     37D  VAL*     4.3     6.1    -      -       +      -
     46D  GLU*     1.3    80.7    -      -       -      +
     48D  VAL*     1.3    64.4    +      -       -      +
     49D  SER      3.3    25.7    +      -       -      -
     50D  SER*     3.6    24.0    -      -       -      -
     59D  ASP*     3.8    24.0    -      -       +      -
     60D  TYR*     3.3    23.8    -      -       -      -
     61D  ALA*     3.3    40.5    -      -       +      +
    100D  MET*     3.7    36.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  TRP*     2.8    23.2    +      -       +      +
     37D  VAL      3.9     1.8    -      -       -      -
     38D  ARG*     3.7    44.6    -      -       +      +
     46D  GLU      3.7     6.3    -      -       -      +
     47D  TRP*     1.3    75.7    -      -       -      +
     49D  SER*     1.3    63.2    +      -       -      +
     60D  TYR*     3.5     2.3    -      -       -      -
     61D  ALA*     3.0    27.4    +      -       -      -
     64D  VAL*     3.6    11.6    -      -       +      +
     68D  PHE*     3.6    37.2    -      -       +      -
     81D  LEU*     4.3    11.0    -      -       +      -
     94D  TYR*     4.2     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 49 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  TYR*     3.4     2.3    -      -       -      -
     36D  TRP*     2.8    29.6    +      -       -      +
     47D  TRP*     3.3    12.1    +      -       -      +
     48D  VAL*     1.3    88.9    -      -       -      +
     50D  SER*     1.3    63.5    +      -       -      +
     59D  ASP      2.9    15.4    +      -       -      -
     60D  TYR*     3.2    15.6    -      -       -      -
     68D  PHE*     5.7     0.2    -      -       -      -
     70D  ILE*     3.2    32.9    -      -       -      +
     81D  LEU*     4.5     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496B  ASN*     5.0     3.5    -      -       -      +
    560B  TYR*     2.6    29.3    +      -       -      -
     34D  MET      3.3     6.7    -      -       -      -
     35D  TYR*     3.6    23.3    -      -       -      -
     47D  TRP*     3.6    14.6    -      -       -      -
     49D  SER*     1.3    77.6    +      -       -      +
     51D  ILE*     1.3    62.5    +      -       -      +
     58D  THR*     3.3     3.6    -      -       -      -
     59D  ASP*     3.0    37.8    +      -       -      +
     70D  ILE*     3.6     8.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    560B  TYR*     3.5     5.3    -      -       -      -
     33D  SER*     3.2     5.5    -      -       -      -
     34D  MET*     2.9    54.1    +      -       +      +
     50D  SER*     1.3    77.6    -      -       -      +
     52D  ASN*     1.3    74.4    +      -       -      +
     55D  GLY*     3.6    26.0    -      -       -      +
     57D  ASN      3.5     9.9    -      -       -      +
     58D  THR*     3.8    13.0    -      -       +      -
     70D  ILE*     3.8    16.2    -      -       +      +
     71D  SER*     3.8    29.2    -      -       -      +
     72D  ARG*     3.9    15.3    -      -       +      +
     79D  LEU*     3.9     7.2    -      -       +      -
----------------------------------------------------------
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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