Contacts of the strand formed by residues 39 - 52 (chain B) in PDB entry 5JTP


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 39 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TRP*     5.4     1.6    -      -       -      +
     37B  GLN      3.6     2.2    +      -       -      -
     38B  PRO*     1.4    68.9    -      -       -      +
     40B  VAL*     1.3    83.1    +      -       -      +
     41B  LYS*     3.8     2.4    +      -       +      +
     65B  THR      3.3     2.4    -      -       -      +
     66B  ALA*     3.2    20.3    -      -       -      -
     67B  SER*     3.1    23.9    +      -       -      +
     69B  GLY      6.0     0.9    -      -       -      +
    467F  ALA*     5.1    10.4    -      -       -      +
    470F  LEU*     3.8    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  PRO      3.6    13.0    -      -       -      +
     39B  GLU*     1.3    89.5    +      -       -      +
     41B  LYS*     1.3    67.0    +      -       -      +
     42B  LEU*     4.8     5.6    -      -       +      +
     64B  VAL*     4.0    21.8    -      -       +      -
     65B  THR      3.6     4.0    -      -       -      -
     66B  ALA*     4.9     1.3    -      -       +      +
    126B  LEU*     3.8    20.9    -      -       +      -
    128B  LEU*     5.6     7.2    -      -       +      -
    467F  ALA*     6.1     1.2    -      -       -      +
    468F  LEU*     3.8    23.3    -      -       +      +
    470F  LEU*     3.8    25.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  GLU*     4.8     2.5    -      -       +      +
     40B  VAL*     1.3    77.7    -      -       -      +
     42B  LEU*     1.3    67.3    +      -       -      +
     43B  ASP*     2.8    37.7    +      -       -      +
     63B  THR      3.7     0.5    -      -       -      +
     64B  VAL*     3.6     3.5    -      -       -      -
     65B  THR*     2.8    54.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  VAL*     4.3     6.4    -      -       +      +
     41B  LYS*     1.3    85.0    +      -       -      +
     43B  ASP*     1.3    77.7    +      -       -      +
     44B  LEU*     5.3     5.2    -      -       +      -
     62B  VAL*     3.6    30.1    -      -       +      -
     63B  THR      3.7     4.3    -      -       -      +
     64B  VAL*     4.3     8.1    -      -       +      +
    128B  LEU*     3.6    36.3    -      -       +      -
    131B  VAL*     4.9    11.4    -      -       +      -
    462F  TYR*     3.3    37.0    +      -       +      -
    464F  MET*     6.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  LYS*     2.8    38.1    +      -       -      +
     42B  LEU*     1.3    80.8    -      -       -      +
     44B  LEU*     1.3    62.2    +      -       -      +
     45B  ASP*     5.1     6.5    -      -       -      +
     62B  VAL*     3.5     5.0    -      -       -      +
     63B  THR*     2.8    53.4    +      -       -      +
     65B  THR*     4.1     9.5    +      -       -      -
    462F  TYR*     3.1     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  LEU*     5.3     6.3    -      -       +      -
     43B  ASP*     1.3    76.7    -      -       -      +
     45B  ASP*     1.3    79.7    +      -       -      +
     46B  THR*     3.8    15.3    -      -       +      -
     60B  LEU*     3.7    16.8    -      -       +      -
     61B  ARG      3.3    11.0    -      -       -      +
     62B  VAL*     3.8    17.5    -      -       +      -
    107B  PHE*     5.2     5.2    -      -       +      -
    128B  LEU*     5.7     0.2    -      -       +      -
    131B  VAL*     6.2     2.0    -      -       +      -
    133B  PHE*     3.7    35.2    -      -       +      -
    458F  THR      4.0     1.7    -      -       -      +
    460F  LEU*     3.5    21.0    +      -       +      +
    462F  TYR*     3.3    37.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  ASP*     5.1     4.2    -      -       -      +
     44B  LEU*     1.3    80.1    +      -       -      +
     46B  THR*     1.3    68.7    +      -       -      +
     47B  ALA      4.4     0.2    -      -       -      -
     61B  ARG*     2.9    71.6    +      -       +      +
     63B  THR*     5.0     3.3    +      -       -      -
    458F  THR*     3.1    35.0    -      -       +      +
    460F  LEU*     3.6     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  LEU*     3.8    17.9    -      -       +      -
     45B  ASP*     1.3    80.5    -      -       -      +
     47B  ALA*     1.3    60.1    +      -       -      +
     59B  VAL      3.5     7.2    -      -       -      +
     60B  LEU*     4.7     2.9    -      -       -      -
     98B  LEU      5.2     0.7    -      -       -      -
     99B  GLY      5.1     1.1    -      -       -      +
    103B  PRO*     3.6    34.3    -      -       +      -
    133B  PHE*     5.3     1.1    -      -       +      -
    456F  ASP*     4.0     5.0    -      -       -      +
    457F  GLN*     2.8    67.2    +      -       -      +
    458F  THR*     4.1     2.0    +      -       -      +
    460F  LEU*     3.3    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  THR*     1.3    73.6    -      -       -      +
     48B  SER*     1.3    62.1    +      -       -      +
     58B  VAL*     3.3    11.8    -      -       -      +
     59B  VAL*     2.8    46.4    +      -       +      +
     98B  LEU      5.0     1.5    -      -       -      +
    456F  ASP*     3.5    17.3    -      -       -      +
    457F  GLN*     5.7     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ALA*     1.3    77.4    -      -       -      +
     49B  SER*     1.3    65.9    +      -       -      +
     56B  TYR*     5.5     1.1    -      -       -      -
     57B  GLU      3.2    11.0    -      -       -      -
     58B  VAL*     3.9    19.3    -      -       -      +
     59B  VAL*     5.4     0.9    -      -       -      -
     98B  LEU*     4.5    22.4    -      -       -      +
    454F  LEU*     5.0     9.5    +      -       -      +
    456F  ASP*     2.9    23.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PRO*     5.4     0.2    -      -       -      +
     48B  SER*     1.3    75.8    -      -       -      +
     50B  GLN*     1.3    60.1    +      -       -      +
     51B  LEU*     3.7    10.6    -      -       -      +
     56B  TYR*     3.2    14.3    -      -       -      +
     57B  GLU*     2.9    55.8    +      -       -      +
     59B  VAL*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  SER*     1.3    74.1    -      -       -      +
     51B  LEU*     1.3    66.1    +      -       -      +
     52B  ALA      2.7    28.4    +      -       -      +
     54B  ASP      4.0     2.8    -      -       -      +
     55B  VAL      2.9    20.2    +      -       -      +
     56B  TYR*     3.1    25.3    -      -       +      -
    450F  ASN*     2.7    51.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PRO*     3.6    39.5    -      -       +      +
     30A  HIS*     5.3     5.6    -      -       +      -
     32A  PHE*     5.8     0.4    -      -       +      -
     33A  GLN*     3.7    31.9    +      -       +      +
     49B  SER*     3.7    20.6    -      -       -      +
     50B  GLN*     1.3    78.1    -      -       -      +
     52B  ALA*     1.3    62.6    +      -       -      +
     55B  VAL*     3.2    28.0    +      -       +      +
     57B  GLU*     3.7    19.7    -      -       +      -
     83B  ILE*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLN*     4.3    11.2    -      -       -      +
     50B  GLN*     2.7    30.5    +      -       -      -
     51B  LEU*     1.3    78.0    -      -       +      +
     53B  ASP*     1.3    57.5    +      -       -      +
     55B  VAL*     2.9    25.9    +      -       +      +
    450F  ASN*     4.5     2.5    -      -       -      -
----------------------------------------------------------
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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