Contacts of the strand formed by residues 116 - 123 (chain E) in PDB entry 3J7Y


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 LYS 116 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3150A    U      3.3    24.8    +      -       -      -
   3151A    A      4.5    12.6    -      -       +      -
   3165A    C      5.4     3.6    +      -       -      -
    108E  PRO*     3.7    17.6    -      -       +      +
    109E  LEU      3.7     4.3    -      -       -      -
    110E  TRP*     3.3    20.6    -      -       +      +
    115E  GLN*     1.3    72.4    +      -       -      +
    117E  HIS*     1.3    70.8    +      -       -      +
    118E  VAL*     3.6    18.9    -      -       +      +
     95L  ARG*     4.8     9.4    -      -       +      -
    165Q  GLU*     3.2    33.9    -      -       -      +
    168Q  ASN*     4.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 117 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3165A    C      5.5    11.0    +      -       -      -
    108E  PRO*     4.6     1.1    -      -       -      -
    109E  LEU*     2.8    39.1    +      -       +      +
    111E  THR*     3.5    30.9    +      -       +      +
    115E  GLN*     3.8    27.1    +      -       -      +
    116E  LYS*     1.3    79.5    +      -       -      +
    118E  VAL*     1.3    66.2    +      -       -      +
    119E  VAL*     3.3     5.2    -      -       -      +
    274E  TRP*     3.6    34.4    +      +       +      +
    286E  ASN*     5.3     8.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 118 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3150A    U      3.5    41.3    -      -       +      +
   3164A    C      3.8    21.9    +      -       -      +
   3165A    C      5.8     4.4    -      -       -      +
    106E  MET*     3.5    38.1    -      -       +      -
    107E  MET      3.7     6.1    -      -       -      +
    108E  PRO*     4.3     1.3    -      -       +      -
    116E  LYS*     3.6    17.1    +      -       +      +
    117E  HIS*     1.3    72.1    -      -       -      +
    119E  VAL*     1.3    63.4    +      -       -      +
    286E  ASN*     3.6     5.5    -      -       -      +
    287E  GLY*     2.8    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  MET*     3.2     5.5    -      -       -      +
    107E  MET*     2.8    37.8    +      -       +      +
    109E  LEU*     3.4    23.6    -      -       +      -
    117E  HIS      3.3    17.7    -      -       -      +
    118E  VAL*     1.3    76.0    -      -       -      +
    120E  THR*     1.3    60.6    +      -       -      +
    121E  LEU*     4.0     4.6    -      -       +      +
    274E  TRP*     3.6    18.2    -      -       +      -
    284E  TYR*     3.4    27.8    -      -       +      +
    285E  VAL      3.1    36.6    -      -       -      +
    286E  ASN      4.2     0.2    -      -       -      +
    287E  GLY      4.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 120 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  LYS*     4.1    11.2    -      -       -      +
    105E  GLY      3.4     8.6    +      -       -      -
    106E  MET*     3.6    18.2    -      -       -      +
    119E  VAL*     1.3    74.5    -      -       -      +
    121E  LEU*     1.3    63.6    +      -       -      +
    122E  LEU*     3.8    20.4    +      -       -      +
    285E  VAL*     2.8    34.6    +      -       -      +
    286E  ASN      5.0     0.2    -      -       -      -
    287E  GLY      3.0    29.2    -      -       -      +
    288E  SER*     3.7     7.9    -      -       -      -
    289E  VAL*     3.8    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 121 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  LYS*     3.7     2.6    -      -       -      -
    104E  LEU*     2.8    41.1    +      -       +      +
    105E  GLY      2.8    18.3    +      -       -      +
    107E  MET*     3.5    32.1    -      -       +      -
    119E  VAL*     4.0     5.6    -      -       +      +
    120E  THR*     1.3    75.9    +      -       -      +
    122E  LEU*     1.3    58.7    +      -       -      +
    123E  GLN      4.0     0.7    -      -       -      -
    282E  ILE*     3.8    13.9    -      -       +      -
    283E  ILE      3.5     4.3    -      -       -      -
    284E  TYR*     3.2    38.1    -      -       +      -
     91Q  LYS*     3.7    26.7    -      -       +      -
     94Q  ILE*     4.3    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 122 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101E  ALA*     3.8    11.4    -      -       +      -
    102E  LEU      3.3     2.0    -      -       -      -
    103E  LYS*     3.7    26.2    -      -       +      +
    120E  THR*     3.8    15.3    -      -       -      +
    121E  LEU*     1.3    71.9    -      -       -      +
    123E  GLN*     1.3    62.0    +      -       -      +
    124E  VAL*     3.6     2.1    +      -       -      +
    206E  VAL*     4.1    14.1    -      -       +      -
    281E  ASN      3.7     0.2    -      -       -      +
    282E  ILE*     3.5     2.0    -      -       -      -
    283E  ILE*     2.8    47.3    +      -       +      +
    285E  VAL*     3.6    28.0    -      -       +      -
    289E  VAL*     4.3     8.3    -      -       +      -
    297E  VAL*     3.7    17.9    -      -       +      -
    299E  VAL*     3.7    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 123 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101E  ALA*     3.7     1.3    -      -       -      -
    102E  LEU*     2.8    39.3    +      -       +      +
    104E  LEU*     3.9    21.9    -      -       +      +
    121E  LEU      4.0     1.6    +      -       -      -
    122E  LEU*     1.3    70.5    -      -       -      +
    124E  VAL*     1.3    60.0    +      -       -      +
    125E  GLN*     2.7    47.6    +      -       +      +
    280E  HIS      4.0    12.3    +      -       -      +
    281E  ASN*     3.6     3.6    -      -       +      -
    282E  ILE*     3.5    19.0    -      -       +      +
     88Q  ASP*     5.3     1.4    -      -       -      +
     90Q  LEU*     3.2    45.7    -      -       -      +
----------------------------------------------------------
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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