Contacts of the strand formed by residues 39 - 52 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  GLN      4.1     0.2    +      -       -      -
     38A  PRO*     1.3    70.4    -      -       -      +
     40A  VAL*     1.3    59.2    +      -       -      +
     41A  LYS*     3.2    13.0    +      -       +      +
     65A  THR      3.1    11.7    -      -       -      +
     66A  ALA*     4.4     0.9    -      -       -      -
     67A  SER*     3.0    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  PRO*     3.7    10.8    +      -       +      +
     39A  GLU*     1.3    69.2    -      -       -      +
     41A  LYS*     1.3    60.7    +      -       -      +
     42A  LEU*     3.7     3.9    +      -       +      +
     64A  VAL*     3.8    29.2    -      -       +      -
     65A  THR      3.1     6.1    -      -       -      +
     66A  ALA*     4.3    13.7    -      -       +      -
     74A  PHE*     5.5     0.9    -      -       +      -
    126A  LEU*     4.7     4.0    -      -       +      -
    290E  TRP*     3.2    56.8    +      -       +      +
    292E  GLY      5.4     1.6    -      -       -      +
    295E  ALA*     5.2     1.3    -      -       -      -
    296E  THR*     3.7    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  GLU*     3.2    11.7    +      -       +      +
     40A  VAL*     1.3    72.0    -      -       -      +
     42A  LEU*     1.3    65.8    +      -       +      +
     43A  ASP*     2.8    36.2    +      -       -      +
     63A  THR      3.7     1.7    -      -       -      +
     65A  THR*     2.8    46.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     3.7     3.7    +      -       +      +
     41A  LYS*     1.3    79.8    +      -       -      +
     43A  ASP*     1.3    68.7    +      -       -      +
     62A  VAL*     6.1     3.4    -      -       +      -
     63A  THR      3.4     5.8    -      -       -      +
     64A  VAL*     4.8     7.2    -      -       +      +
    128A  LEU*     5.7     5.4    -      -       +      -
    131A  VAL*     5.7     1.1    -      -       +      -
    288E  VAL*     3.8    43.3    -      -       +      +
    289E  ARG      3.9     4.9    -      -       -      +
    290E  TRP*     3.7    53.6    -      -       +      -
    291E  LEU*     5.4     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LYS*     2.8    43.1    +      -       -      +
     42A  LEU*     1.3    77.8    -      -       -      +
     44A  LEU*     1.3    62.2    +      -       -      +
     45A  ASP*     4.7     7.0    -      -       -      +
     61A  ARG*     4.0     1.8    -      -       -      +
     62A  VAL*     3.5     9.0    -      -       -      +
     63A  THR*     2.8    49.5    +      -       -      +
     65A  THR*     4.3     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ASP*     1.3    76.1    -      -       -      +
     45A  ASP*     1.3    77.4    +      -       -      +
     46A  THR*     3.9    16.2    +      -       +      +
     60A  LEU*     3.9    28.3    -      -       +      -
     61A  ARG      3.3     5.6    -      -       -      +
     62A  VAL*     5.1     9.2    -      -       +      -
    103A  PRO*     6.2     0.4    -      -       +      -
    107A  PHE*     5.1    10.1    -      -       +      -
    133A  PHE*     3.6    35.4    -      -       +      -
    284E  GLY*     5.4     7.1    -      -       -      -
    288E  VAL*     4.5    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ASP*     4.7     4.9    -      -       -      +
     44A  LEU*     1.3    83.1    +      -       -      +
     46A  THR*     1.3    63.2    +      -       -      +
     47A  ALA*     5.3     2.0    -      -       +      +
     59A  VAL      3.7     1.7    -      -       -      +
     60A  LEU*     3.4    10.2    -      -       -      -
     61A  ARG*     3.0    80.5    +      -       +      +
     63A  THR*     4.7     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     3.9    19.1    -      -       +      +
     45A  ASP*     1.3    75.6    -      -       -      +
     47A  ALA*     1.3    63.0    +      -       -      +
     59A  VAL      4.2     0.9    -      -       -      -
     60A  LEU*     4.3     1.1    -      -       +      -
    281E  PHE*     3.2    42.0    +      -       +      +
    282E  ALA*     3.5    13.2    -      -       -      +
    283E  ASP*     2.8    39.7    +      -       -      +
    284E  GLY*     4.8     5.8    -      -       -      -
    285E  ASN*     4.0     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASP*     5.3     2.2    -      -       +      +
     46A  THR*     1.3    74.6    -      -       -      +
     48A  SER*     1.3    62.5    +      -       -      +
     59A  VAL*     2.9    47.8    +      -       +      +
    281E  PHE*     3.5    11.2    +      -       -      -
    282E  ALA*     5.0     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  ALA*     1.3    76.2    -      -       -      +
     49A  SER*     1.3    63.8    +      -       -      +
     56A  TYR*     5.8     1.1    -      -       -      -
     57A  GLU      3.3    11.7    -      -       -      -
     58A  VAL*     4.7     1.6    -      -       -      -
     59A  VAL*     6.4     0.2    -      -       -      -
     98A  LEU*     4.2     5.2    -      -       -      -
    278E  LEU*     3.3    44.3    -      -       -      +
    280E  LEU      4.0     3.8    +      -       -      -
    281E  PHE*     3.5    28.1    +      -       -      -
    282E  ALA*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LYS*     5.5     0.6    +      -       -      -
     48A  SER*     1.3    76.6    -      -       -      +
     50A  GLN*     1.3    67.7    +      -       -      +
     51A  LEU*     3.9     9.9    -      -       -      +
     56A  TYR*     3.2    13.9    -      -       -      +
     57A  GLU*     2.9    53.1    +      -       -      +
     59A  VAL*     5.9     1.8    -      -       -      -
    275E  LYS*     5.4     2.2    -      -       -      +
    278E  LEU*     5.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  SER*     1.3    78.5    +      -       -      +
     51A  LEU*     1.3    61.7    +      -       -      +
     52A  ALA*     3.4    30.1    +      -       -      +
     53A  ASP*     4.6     9.5    +      -       -      +
     55A  VAL      3.9     3.4    -      -       -      +
     56A  TYR*     4.7     7.9    -      -       +      +
     30B  HIS*     5.4     2.8    -      -       -      -
    273E  GLN*     4.8    10.1    -      -       -      +
    275E  LYS*     2.9    50.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LYS*     5.3     0.4    -      -       -      +
     49A  SER*     3.9    17.7    -      -       -      +
     50A  GLN*     1.3    76.0    -      -       -      +
     52A  ALA*     1.3    63.4    +      -       +      +
     55A  VAL*     3.1    16.0    +      -       +      +
     57A  GLU*     3.7    27.6    -      -       +      +
     83A  ILE*     3.6    40.6    -      -       +      -
     29B  PRO*     3.7    37.2    -      -       +      -
     30B  HIS*     4.3    23.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLN*     3.4    20.2    -      -       -      +
     51A  LEU*     1.3    79.8    -      -       +      +
     53A  ASP*     1.3    67.1    +      -       -      +
     54A  ASP      3.4     1.2    +      -       -      -
     55A  VAL*     3.0    39.1    +      -       +      +
     56A  TYR*     4.9     1.0    -      -       -      -
----------------------------------------------------------
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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