Contacts of the strand formed by residues 109 - 114 (chain E) in PDB entry 6GJH


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 LEU 109 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101E  VAL*     3.8    38.4    -      -       +      -
    104E  PHE*     3.8    23.8    -      -       +      +
    105E  ALA      3.5    17.7    -      -       -      +
    106E  PRO*     3.4    14.8    +      -       +      +
    107E  ASP      3.6     1.4    -      -       -      -
    108E  GLU*     1.3    79.5    -      -       -      +
    110E  THR*     1.3    68.9    +      -       -      +
    111E  VAL*     5.5     1.6    -      -       +      -
    120E  ILE*     4.9     6.1    -      -       +      -
    121E  THR      3.3     3.4    -      -       -      +
    122E  GLY*     4.0    16.4    -      -       -      -
    138E  PHE*     4.4     4.9    -      -       +      -
    157E  LEU*     4.2    20.2    -      -       +      -
    163E  LEU*     4.9    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 110 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  ILE      5.7     4.5    -      -       -      +
    107E  ASP      6.1     0.9    -      -       -      +
    108E  GLU      5.3     1.8    -      -       -      -
    109E  LEU*     1.3    81.6    -      -       -      +
    111E  VAL*     1.3    65.9    +      -       -      +
    112E  LYS*     4.2    19.6    -      -       -      +
    119E  GLU      3.6     0.5    -      -       -      +
    120E  ILE*     3.4     7.1    -      -       -      +
    121E  THR*     3.0    49.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109E  LEU*     5.5     2.5    -      -       +      -
    110E  THR*     1.3    78.7    -      -       -      +
    112E  LYS*     1.3    66.8    +      -       -      +
    113E  THR*     5.7     0.4    -      -       -      +
    118E  VAL*     4.0    23.8    -      -       +      -
    119E  GLU      3.6     3.1    -      -       -      +
    120E  ILE*     4.3    13.0    -      -       +      -
    153E  VAL*     4.6     9.2    -      -       +      -
    154E  SER*     5.8     0.7    -      -       -      -
    155E  SER*     3.6    27.1    -      -       -      +
    163E  LEU*     4.3    13.2    -      -       +      -
    165E  VAL*     4.3    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 112 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110E  THR*     4.3    18.6    -      -       -      +
    111E  VAL*     1.3    84.1    -      -       -      +
    113E  THR*     1.3    63.1    +      -       -      +
    114E  LYS*     3.8    29.6    -      -       +      +
    117E  VAL      3.7     0.3    -      -       -      +
    118E  VAL*     3.4     4.3    -      -       -      +
    119E  GLU*     2.7    55.3    +      -       +      +
    121E  THR*     5.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 113 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111E  VAL*     5.7     0.3    -      -       -      +
    112E  LYS*     1.3    77.3    +      -       -      +
    114E  LYS*     1.3    71.5    +      -       -      +
    115E  ASP      4.4     0.4    -      -       -      +
    116E  GLY      4.5     4.0    -      -       -      +
    117E  VAL      3.2    18.4    -      -       -      +
    118E  VAL*     4.3     5.4    -      -       -      +
    144E  LEU*     4.1    14.6    -      -       +      -
    150E  PRO*     3.6    41.9    +      -       +      -
    153E  VAL*     4.0    15.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 114 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112E  LYS*     3.8    34.8    -      -       +      +
    113E  THR*     1.3    81.6    -      -       -      +
    115E  ASP*     1.3    76.4    +      -       +      +
    116E  GLY      3.2     1.3    -      -       -      -
    117E  VAL*     2.8    31.1    +      -       +      +
    119E  GLU*     4.0    25.4    +      -       +      +
----------------------------------------------------------
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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