Contacts of the strand formed by residues 115 - 124 (chain A) 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 115 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  GLU*     3.2    30.5    +      -       -      +
    105A  VAL      3.1     9.4    +      -       -      +
    106A  SER*     4.5     4.7    -      -       -      -
    107A  VAL*     3.6     6.6    -      -       -      +
    114A  SER*     1.3    91.8    +      -       -      +
    116A  SER*     1.3    60.3    +      -       -      +
    117A  VAL*     4.8     1.8    -      -       +      +
    137A  GLY*     3.8    16.8    -      -       -      -
    138A  GLU*     3.1    22.0    +      -       +      +
    139A  HIS*     2.6    29.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ARG      3.8     0.7    -      -       -      +
    104A  GLU*     3.3     1.1    -      -       -      -
    105A  VAL*     2.5    56.6    +      -       -      +
    107A  VAL*     5.6     0.4    -      -       -      -
    115A  THR*     1.3    80.0    -      -       -      +
    117A  VAL*     1.3    64.0    +      -       -      +
    118A  GLU*     4.1     3.4    +      -       -      +
    134A  VAL*     3.6    16.8    -      -       -      +
    136A  GLY      3.6     6.7    +      -       -      -
    139A  HIS*     3.3    20.0    -      -       -      -
    301A  A9S      3.7    18.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  ARG*     6.0     1.6    -      -       +      -
    102A  ILE*     3.7    23.8    -      -       +      -
    103A  ARG      3.3     6.5    -      -       -      +
    104A  GLU*     4.6    13.0    -      -       +      +
    115A  THR*     5.2     3.8    -      -       +      -
    116A  SER*     1.3    73.9    -      -       -      +
    118A  GLU*     1.3    56.1    +      -       -      +
    134A  VAL*     3.6     2.8    -      -       -      -
    135A  LEU*     2.7    45.9    +      -       +      -
    136A  GLY*     3.0    33.9    +      -       -      +
    137A  GLY*     3.7     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     3.9     3.7    -      -       +      -
    101A  THR      3.8     0.5    -      -       -      +
    102A  ILE*     3.3     7.2    -      -       -      +
    103A  ARG*     2.9    52.6    +      -       +      +
    105A  VAL*     6.4     0.9    -      -       +      -
    116A  SER*     4.1     4.9    -      -       -      +
    117A  VAL*     1.3    74.9    -      -       -      +
    119A  ILE*     1.3    59.9    +      -       -      +
    132A  PHE*     3.6    32.3    -      -       +      -
    133A  ARG      3.2     5.6    -      -       -      +
    134A  VAL*     4.6     4.0    -      -       +      -
    135A  LEU*     4.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     4.3     0.2    -      -       -      -
    100A  GLY*     3.4    38.4    -      -       -      +
    101A  THR      3.4     3.1    -      -       -      +
    102A  ILE*     3.6    16.8    -      -       +      -
    118A  GLU*     1.3    72.6    -      -       -      +
    120A  LEU*     1.3    65.0    +      -       -      +
    121A  GLU*     3.5    20.6    +      -       +      +
    132A  PHE*     3.2     5.3    -      -       -      -
    133A  ARG*     2.7    43.6    +      -       +      +
    135A  LEU*     3.5    35.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     3.6    32.4    -      -       +      -
     97A  ILE*     3.5    31.6    -      -       +      -
     98A  LYS      3.8    17.7    -      -       -      +
     99A  VAL*     3.6     6.4    -      -       -      +
    100A  GLY*     2.7    31.5    +      -       -      -
    101A  THR*     3.0    13.2    +      -       -      +
    119A  ILE*     1.3    70.9    -      -       -      +
    121A  GLU*     1.3    59.0    +      -       -      +
    122A  VAL      3.1    31.4    -      -       -      +
    123A  LEU*     4.2    12.8    -      -       +      -
    130A  LEU*     4.2    15.3    -      -       +      -
    131A  SER      3.4     9.6    -      -       -      +
    132A  PHE*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  VAL*     3.7    19.2    -      -       -      +
    119A  ILE*     3.5    20.0    +      -       +      +
    120A  LEU*     1.3    77.9    -      -       -      +
    122A  VAL*     1.3    71.5    +      -       +      +
    131A  SER*     2.9    19.6    +      -       -      +
    132A  PHE      4.9     0.2    -      -       -      -
    133A  ARG*     3.0    57.1    +      -       +      +
    145A  ARG*     4.6     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  HIS*     6.1     2.2    -      -       +      +
     99A  VAL*     4.2     2.2    -      -       -      -
    120A  LEU*     3.1    16.3    -      -       -      +
    121A  GLU*     1.3    87.7    -      -       +      +
    123A  LEU*     1.3    61.9    +      -       -      +
    124A  ASP*     4.4     9.4    -      -       +      +
    129A  ILE*     3.7    28.9    -      -       +      +
    130A  LEU*     3.5     3.8    -      -       -      -
    131A  SER*     3.1    35.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  TRP*     3.9    26.2    -      -       +      -
     70A  ARG*     4.3    17.0    -      -       +      +
     97A  ILE*     4.3    33.7    -      -       +      +
     98A  LYS*     5.0     4.5    -      -       -      -
     99A  VAL*     3.8    19.6    -      -       +      +
    120A  LEU*     4.2     9.4    -      -       +      -
    122A  VAL*     1.3    74.5    -      -       -      +
    124A  ASP*     1.3    59.0    +      -       -      +
    125A  GLU*     3.6    27.2    +      -       +      +
    129A  ILE      3.7     1.6    -      -       -      -
    130A  LEU*     4.4    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  HIS*     5.7     1.2    -      -       -      -
     66A  TRP*     4.2     2.5    -      -       -      -
    122A  VAL*     4.6     7.4    -      -       +      -
    123A  LEU*     1.3    73.6    -      -       -      +
    125A  GLU*     1.3    51.5    +      -       -      +
    126A  GLU*     3.1    10.6    +      -       -      +
    127A  LYS*     2.5    54.5    +      -       +      +
    128A  ARG*     2.6    37.1    +      -       -      -
    129A  ILE*     3.2    26.2    +      -       +      +
----------------------------------------------------------
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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