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


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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  GLN      3.8     2.2    +      -       -      -
     38D  PRO*     1.3    70.3    -      -       -      +
     40D  VAL*     1.3    64.6    +      -       -      +
     65D  THR      4.1     0.5    -      -       -      +
     66D  ALA*     3.8     0.2    -      -       -      -
     67D  SER*     3.0    52.5    +      -       -      +
     68D  LEU*     4.4     1.5    -      -       -      +
    293G  PRO*     3.4    22.3    -      -       +      +
    294G  LYS*     3.5    33.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  PRO*     4.5     7.2    -      -       +      +
     39D  GLU*     1.3    79.3    -      -       -      +
     41D  LYS*     1.3    60.6    +      -       -      +
     64D  VAL*     5.0     2.5    -      -       +      -
     65D  THR      3.7     3.4    -      -       -      +
     66D  ALA*     4.3    19.5    -      -       +      -
     74D  PHE*     5.2     2.0    -      -       +      -
    126D  LEU*     3.8    23.1    -      -       +      -
    307E  THR*     6.0     0.7    -      -       +      -
    290G  TRP*     3.2    49.1    -      -       +      +
    292G  GLY      4.2     4.5    -      -       -      +
    293G  PRO*     3.0    22.9    +      -       -      +
    294G  LYS*     5.2     0.4    -      -       -      -
    295G  ALA      5.4     1.6    -      -       -      +
    296G  THR*     4.3    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 41 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  VAL*     1.3    73.2    -      -       -      +
     42D  LEU*     1.3    80.1    +      -       -      +
     43D  ASP*     2.9    35.6    +      -       -      +
     63D  THR      3.8     0.3    -      -       -      +
     64D  VAL*     3.6     5.5    -      -       -      +
     65D  THR*     2.9    48.3    +      -       +      +
    285G  ASN*     4.7     3.8    -      -       -      +
    288G  VAL      5.2     5.2    -      -       -      +
    290G  TRP*     3.3    11.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 42 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  LYS*     1.3    88.5    -      -       -      +
     43D  ASP*     1.3    75.5    +      -       -      +
     44D  LEU*     3.8    23.6    -      -       +      +
     62D  VAL*     3.8    18.8    -      -       +      -
     63D  THR      3.4     8.1    -      -       -      +
     64D  VAL*     5.1     2.0    -      -       +      -
    107D  PHE*     5.3     8.5    -      -       +      -
    128D  LEU*     3.6    27.4    -      -       +      -
    286G  MET      5.4     1.7    -      -       -      +
    288G  VAL*     3.8    37.1    +      -       +      +
    290G  TRP*     3.3    30.5    -      -       +      +
    291G  LEU*     6.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 43 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  LYS*     2.9    40.4    +      -       -      +
     42D  LEU*     1.3    76.5    -      -       -      +
     44D  LEU*     1.3    62.9    +      -       -      +
     62D  VAL      3.9     0.2    -      -       -      -
     63D  THR*     2.9    49.8    +      -       +      +
     65D  THR*     4.4    10.2    +      -       -      -
    285G  ASN*     2.9    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 44 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  LEU*     3.8    25.8    -      -       +      +
     43D  ASP*     1.3    80.5    -      -       -      +
     45D  ASP*     1.3    63.3    +      -       -      +
     60D  LEU*     5.0    12.6    -      -       +      -
     61D  ARG      3.6     7.6    -      -       -      +
     62D  VAL*     5.5     2.0    -      -       +      -
     63D  THR*     5.8     0.4    -      -       -      -
    107D  PHE*     5.3     7.4    -      -       +      -
    133D  PHE*     4.2    14.8    -      -       +      -
    284G  GLY*     3.7     1.2    -      -       -      -
    285G  ASN*     2.9    32.2    +      -       -      +
    286G  MET*     3.5    54.1    -      -       +      +
    288G  VAL*     3.8    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 45 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  LEU*     1.3    77.1    -      -       -      +
     46D  THR*     1.3    82.7    +      -       -      +
     60D  LEU*     3.8     7.9    -      -       -      +
     61D  ARG*     2.8    77.9    +      -       -      +
    281G  PHE*     5.7     1.1    -      -       -      -
    282G  ALA      4.1    11.4    -      -       -      +
    283G  ASP      4.2     8.8    -      -       -      +
    284G  GLY*     4.5     6.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 46 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  ASP*     1.3    92.7    +      -       -      +
     47D  ALA*     1.3    74.0    +      -       -      +
     48D  SER*     5.6     0.5    -      -       -      -
     58D  VAL*     4.5     5.7    -      -       -      +
     59D  VAL*     2.9    17.2    +      -       -      -
     60D  LEU*     4.3     2.5    -      -       -      +
     61D  ARG*     4.6     1.3    -      -       -      +
    281G  PHE*     3.3    60.9    +      -       +      +
    282G  ALA*     3.7    19.8    +      -       -      +
    284G  GLY      5.5     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 47 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  ASP*     5.5     0.2    -      -       -      +
     46D  THR*     1.3    83.0    +      -       -      +
     48D  SER*     1.3    63.4    +      -       -      +
     58D  VAL*     3.9     2.9    -      -       -      +
     59D  VAL*     2.9    52.1    +      -       +      +
     61D  ARG*     5.8     4.3    -      -       -      +
     79D  GLN*     5.5     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 48 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  THR*     5.6     0.9    -      -       -      -
     47D  ALA*     1.3    77.9    -      -       -      +
     49D  SER*     1.3    66.7    +      -       -      +
     57D  GLU*     3.6     7.0    -      -       -      -
     58D  VAL*     6.4     0.2    -      -       -      -
     59D  VAL*     5.0     1.3    -      -       -      +
    278G  LEU*     3.6    35.9    +      -       -      -
    279G  GLY*     5.1     4.7    -      -       -      -
    281G  PHE      5.6     2.6    +      -       -      -
    282G  ALA*     5.9     2.9    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     29C  PRO*     5.7     0.2    -      -       -      +
     19D  LYS*     5.3     0.5    +      -       -      -
     48D  SER*     1.3    77.3    -      -       -      +
     50D  GLN*     1.3    66.4    +      -       -      +
     51D  LEU*     3.5     9.4    +      -       -      +
     57D  GLU*     3.2    44.5    +      -       -      +
    278G  LEU*     3.4     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 50 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  SER*     1.3    73.0    -      -       -      +
     51D  LEU*     1.3    60.6    -      -       -      +
     52D  ALA*     3.0    32.3    +      -       -      +
     53D  ASP*     4.5     2.2    -      -       -      +
     54D  ASP      4.3     3.8    -      -       -      +
     55D  VAL      3.5     7.9    -      -       -      +
     56D  TYR*     3.5    30.1    +      -       +      -
    274G  GLN*     2.9    41.6    +      -       -      -
    278G  LEU*     3.7     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  PRO*     3.8    32.8    -      -       +      -
     49D  SER*     3.7    23.3    -      -       -      +
     50D  GLN*     1.3    75.8    -      -       -      +
     52D  ALA*     1.3    64.1    +      -       +      +
     55D  VAL*     3.0    16.2    +      -       +      -
     57D  GLU*     3.7    24.5    -      -       +      +
     83D  ILE*     3.6    46.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 52 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  GLN*     3.0    25.4    +      -       -      +
     51D  LEU*     1.3    79.2    -      -       +      +
     53D  ASP*     1.3    67.9    +      -       +      +
     55D  VAL*     3.0    31.2    +      -       +      +
----------------------------------------------------------
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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