Contacts of the strand formed by residues 47 - 53 (chain C) in PDB entry 5J1T


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 47 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  TYR*     5.7     0.4    -      -       -      -
     38C  TYR*     3.2     7.7    -      -       -      -
     39C  ARG*     2.9    77.1    +      -       +      +
     44C  LYS*     5.3     8.3    -      -       -      +
     45C  GLN      4.2     7.4    -      -       -      +
     46C  ARG*     1.4    75.0    -      -       -      +
     48C  LEU*     1.3    71.9    +      -       -      +
     49C  VAL*     4.0     0.2    -      -       -      +
     63C  SER*     4.8     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346B  LEU*     4.1    25.6    -      -       +      -
    349B  LEU*     4.2    28.0    -      -       +      -
    350B  GLU*     4.2    23.1    +      -       -      +
    353B  TYR*     6.1     0.2    -      -       -      -
     37C  TRP      3.7     4.7    -      -       -      +
     38C  TYR*     3.5    37.2    -      -       +      +
     47C  GLU*     1.3    79.4    -      -       -      +
     49C  VAL*     1.3    66.9    +      -       -      +
     50C  ALA*     3.6    27.4    -      -       -      +
     51C  ALA*     4.3     7.6    -      -       +      -
     59C  THR*     4.8     6.5    -      -       +      -
     61C  ALA*     3.3    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 49 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  TRP*     2.8    19.6    +      -       +      +
     38C  TYR      4.0     1.8    -      -       -      -
     39C  ARG*     3.5    53.6    -      -       +      +
     47C  GLU      4.9     0.2    -      -       -      -
     48C  LEU*     1.3    78.6    -      -       -      +
     50C  ALA*     1.3    61.5    +      -       +      +
     60C  TYR*     3.5     2.4    -      -       -      -
     61C  ALA*     3.0    26.7    +      -       -      -
     64C  VAL*     3.6    12.0    -      -       +      +
     68C  PHE*     3.5    37.0    -      -       +      -
     81C  LEU*     4.3    11.2    -      -       +      -
     94C  TYR*     4.2     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 50 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  GLY*     3.2     2.3    -      -       -      -
     37C  TRP*     2.8    29.1    +      -       +      +
     48C  LEU*     3.6     7.2    -      -       -      +
     49C  VAL*     1.3    84.3    -      -       +      +
     51C  ALA*     1.3    63.8    +      -       -      +
     59C  THR      3.3     6.7    -      -       -      -
     60C  TYR*     3.6    27.8    -      -       +      +
     70C  ILE*     3.8    17.5    -      -       +      -
     81C  LEU*     4.0    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345B  LEU*     4.5     2.9    -      -       +      -
    349B  LEU*     3.4    33.7    -      -       +      -
     34C  VAL*     3.8     7.0    -      -       +      -
     35C  MET      3.3    11.7    -      -       -      +
     36C  GLY*     4.3     1.6    -      -       -      -
     48C  LEU*     4.3     6.7    -      -       +      -
     50C  ALA*     1.3    77.1    -      -       -      +
     52C  ILE*     1.3    63.4    +      -       -      +
     58C  THR*     3.3     4.0    -      -       -      -
     59C  THR*     3.0    36.4    +      -       +      +
     70C  ILE*     3.7     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345B  LEU*     4.7     0.4    -      -       -      -
     34C  VAL*     3.5     4.2    -      -       -      -
     35C  MET*     2.9    43.1    +      -       +      +
     51C  ALA*     1.3    76.7    -      -       -      +
     53C  THR*     1.3    75.1    +      -       -      +
     56C  ASP*     3.7    27.1    -      -       +      +
     57C  THR      3.3    12.3    -      -       -      +
     58C  THR*     3.7    18.6    -      -       +      -
     70C  ILE*     3.7    20.4    -      -       +      +
     71C  SER*     4.0    17.7    -      -       -      -
     72C  ARG*     3.3    32.2    +      -       +      -
     79C  VAL*     4.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 53 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  HIS*     4.6     7.6    -      -       +      -
    142A  SER*     2.7    28.4    +      -       -      +
    143A  ASN*     3.5    18.8    -      -       -      +
    345B  LEU*     3.9    29.2    -      -       +      -
     33C  ASN      3.4     8.5    -      -       -      +
     34C  VAL*     4.7     1.3    -      -       +      -
     52C  ILE*     1.3    83.7    -      -       -      +
     54C  SER*     1.3    65.1    +      -       -      +
     55C  GLY      3.3     5.5    +      -       -      -
     56C  ASP*     3.1     9.5    +      -       -      -
     57C  THR*     2.9    32.8    +      -       +      +
     72C  ARG*     3.4     8.7    +      -       -      -
----------------------------------------------------------
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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