Contacts of the strand formed by residues 49 - 58 (chain D) in PDB entry 4JDA


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 THR 49 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  ARG*     5.1     0.2    -      -       -      -
     46D  SER*     2.8    53.7    +      -       -      +
     47D  PRO      3.4     9.2    -      -       -      +
     48D  ASN*     1.3    80.4    -      -       -      +
     50D  CYS*     1.3    63.1    +      -       -      +
    173D  ILE*     4.1    15.6    -      -       +      +
    174D  VAL      3.4     9.4    -      -       -      +
    175D  ASP*     4.1    18.4    -      -       -      +
    176D  ILE*     3.0    15.7    -      -       -      +
    182D  GLU*     4.7     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  THR*     1.3    78.3    -      -       -      +
     51D  THR*     1.3    62.6    +      -       -      +
    172D  TYR*     4.2     8.8    -      -       -      -
    173D  ILE*     3.3     4.7    -      -       -      +
    174D  VAL*     2.9    43.4    +      -       +      +
    176D  ILE*     3.7    18.8    -      -       +      -
    182D  GLU*     4.0    12.6    -      -       +      +
    185D  THR*     4.1     5.2    -      -       -      -
    186D  ARG*     3.7    47.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  PHE*     3.6    30.1    +      -       +      +
     50D  CYS*     1.3    77.7    -      -       -      +
     52D  SER*     1.3    67.1    +      -       -      +
    172D  TYR*     2.5    25.0    +      -       -      -
    173D  ILE*     3.9    10.0    -      -       -      +
    182D  GLU*     5.7     0.2    +      -       -      -
    186D  ARG*     3.9    15.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 52 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51D  THR*     1.3    81.3    +      -       -      +
     53D  LEU*     1.3    63.2    +      -       -      +
     54D  ILE*     4.2     2.0    -      -       -      +
    171D  SER*     3.4     3.6    -      -       -      -
    172D  TYR*     2.8    47.1    +      -       -      +
    186D  ARG*     3.7    17.0    -      -       -      +
    190D  ASP*     2.8    30.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 53 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  TYR      4.6    22.8    +      -       -      +
     37D  ILE*     3.7    39.0    -      -       +      -
     41D  HIS*     4.8     4.9    -      -       +      -
     52D  SER*     1.3    76.3    -      -       -      +
     54D  ILE*     1.3   103.0    +      -       -      +
     55D  ALA*     4.2     4.8    +      -       +      +
    169D  LEU*     3.9    22.4    -      -       +      -
    170D  GLU      3.4    10.8    -      -       -      +
    171D  SER*     4.1    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  SER*     4.2     5.6    -      -       -      +
     53D  LEU*     1.3    87.3    -      -       -      +
     55D  ALA*     1.3    66.6    +      -       -      +
     56D  HIS*     4.9     2.5    -      -       +      -
    168D  VAL      3.8     0.5    -      -       -      +
    169D  LEU*     3.4     0.7    -      -       -      -
    170D  GLU      2.8    35.8    +      -       -      +
    172D  TYR*     4.9     4.0    -      -       +      -
    190D  ASP*     3.4    40.2    -      -       +      +
    193D  VAL*     3.8    20.9    -      -       +      -
    194D  LYS*     4.1    29.4    -      -       +      -
    197D  LEU*     3.4    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  TYR      5.6     2.4    -      -       -      +
     24D  GLY*     4.7    25.6    -      -       -      +
     25D  LEU*     5.2     8.1    -      -       +      +
     53D  LEU*     4.6     4.0    -      -       +      -
     54D  ILE*     1.3    77.4    -      -       -      +
     56D  HIS*     1.3    62.5    +      -       -      +
     57D  ARG      4.3     0.6    +      -       -      -
    167D  VAL*     4.3    13.2    -      -       +      -
    168D  VAL      3.3     8.5    -      -       -      +
    169D  LEU*     4.5     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 56 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191C  THR*     5.8     0.7    -      -       +      -
     54D  ILE*     4.9     2.0    -      -       +      -
     55D  ALA*     1.3    75.6    -      -       -      +
     57D  ARG*     1.3    77.5    +      -       -      +
     58D  VAL*     3.5     9.7    -      -       -      +
    167D  VAL*     4.4     2.8    -      -       -      +
    168D  VAL*     3.1    29.3    +      -       +      +
    194D  LYS*     5.4     5.8    -      -       +      -
    197D  LEU*     3.7    39.0    +      -       +      +
    198D  GLN*     3.3    44.4    +      -       +      -
    201D  ALA*     3.9    22.1    -      -       +      +
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Residues in contact with ARG 57 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  GLY      3.8     8.9    +      -       -      -
     25D  LEU*     3.8    19.2    -      -       -      +
     26D  THR*     4.0    13.7    +      -       -      +
     29D  GLU*     3.0    36.9    +      -       -      -
     55D  ALA      4.3     0.4    -      -       -      -
     56D  HIS*     1.3    90.3    +      -       -      +
     58D  VAL*     1.3    58.8    +      -       -      +
     59D  ASP*     4.3     6.4    +      -       -      +
    165D  TYR*     3.9    25.8    -      -       +      -
    166D  SER      3.7     3.6    -      -       -      -
    167D  VAL*     4.1    11.1    -      -       +      +
    201D  ALA*     5.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56D  HIS*     3.5    20.6    -      -       -      +
     57D  ARG*     1.3    77.4    -      -       -      +
     59D  ASP*     1.3    63.3    +      -       -      +
     60D  ALA*     2.8    17.5    +      -       +      +
     65D  ILE*     3.7    25.1    -      -       +      -
    165D  TYR*     3.3     2.6    -      -       -      +
    166D  SER      2.9    33.7    +      -       -      +
    168D  VAL*     3.7    22.2    -      -       +      -
    197D  LEU*     5.3     1.3    -      -       +      +
    200D  LEU*     5.7     1.3    -      -       +      -
    201D  ALA*     3.9    35.0    -      -       +      +
    204D  SER*     4.0     8.5    -      -       -      +
    205D  THR*     4.6     0.2    -      -       -      +
----------------------------------------------------------
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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