Contacts of the strand formed by residues 110 - 117 (chain G) in PDB entry 6S1M


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 110 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143E  GLU*     3.8    27.0    -      -       +      +
    146E  ARG*     4.3    20.8    -      -       -      +
    147E  ILE*     4.2    16.0    -      -       -      +
    150E  ASP*     4.4     5.4    +      -       -      -
    180E  ILE*     3.7    30.7    -      -       +      -
    181E  LYS      3.3     4.9    -      -       -      -
    182E  LEU*     3.7    14.1    -      -       +      -
     81G  CYS      6.2     0.2    -      -       -      -
     86G  ASP*     6.1     0.7    -      -       -      -
    105G  ALA*     3.3    36.7    +      -       +      +
    108G  GLN*     3.3     3.8    -      -       -      +
    109G  GLU*     1.3    88.5    +      -       -      +
    111G  VAL*     1.3    71.2    +      -       -      +
    112G  SER*     3.9    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 111 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179E  ASN      3.8     0.9    -      -       -      +
    180E  ILE*     3.4     2.7    -      -       -      -
    181E  LYS*     2.9    41.6    +      -       +      +
    102G  VAL*     3.7    28.0    -      -       +      -
    103G  PHE      3.4     6.1    -      -       -      +
    104G  GLU*     4.3     3.6    -      -       +      -
    108G  GLN*     3.2    39.5    -      -       +      +
    109G  GLU      5.6     0.2    -      -       -      -
    110G  LYS*     1.3    74.9    -      -       -      +
    112G  SER*     1.3    67.9    +      -       -      +
    113G  ASP*     5.4     3.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 112 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150E  ASP*     5.5     0.5    +      -       -      -
    179E  ASN      3.5     4.3    -      -       -      -
    180E  ILE*     3.8    21.2    -      -       -      +
     81G  CYS      4.6     5.2    +      -       -      -
    102G  VAL*     3.2     7.3    -      -       -      +
    103G  PHE*     2.7    51.1    +      -       -      +
    110G  LYS*     3.9    12.6    -      -       -      -
    111G  VAL*     1.3    75.9    -      -       -      +
    113G  ASP*     1.3    59.7    +      -       -      +
    114G  TYR*     3.4    25.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 113 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178E  GLY*     3.0     3.5    -      -       -      -
    179E  ASN*     2.8    58.3    +      -       -      +
    181E  LYS*     6.5     0.2    -      -       -      -
     91G  ARG*     4.3     5.0    +      -       -      -
    100G  ALA*     4.6     0.3    -      -       -      +
    101G  LEU      3.5     1.9    -      -       -      +
    102G  VAL*     3.2    27.5    -      -       +      +
    111G  VAL*     5.4     3.4    -      -       +      +
    112G  SER*     1.3    75.6    -      -       -      +
    114G  TYR*     1.3    61.9    +      -       -      +
    115G  GLU*     2.9    31.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 114 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150E  ASP*     3.6    15.0    -      -       -      +
    151E  LEU*     4.5     5.0    -      -       +      +
    154E  ILE*     3.6    38.6    -      -       +      -
    177E  ASN      3.7     2.7    -      -       -      +
    178E  GLY*     3.8    16.4    -      -       -      -
    179E  ASN      5.0     0.7    -      -       -      -
    180E  ILE*     4.1    16.1    -      -       +      +
     78G  ILE*     3.8    27.4    -      -       +      -
     81G  CYS*     3.4    24.9    +      -       +      +
     99G  LEU      3.8     0.7    -      -       -      +
    100G  ALA*     3.2     2.6    -      -       -      -
    101G  LEU*     2.5    48.8    +      -       +      +
    103G  PHE*     3.7    27.1    -      +       -      -
    112G  SER*     3.4    24.6    -      -       -      -
    113G  ASP*     1.3    78.5    -      -       -      +
    115G  GLU*     1.3    63.1    -      -       -      +
    116G  MET      3.9     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 115 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175E  LEU      4.2     0.5    -      -       -      +
    176E  GLY*     3.5     4.5    -      -       -      -
    177E  ASN*     2.8    52.0    +      -       -      +
    178E  GLY*     5.6     0.4    -      -       -      -
    179E  ASN*     6.0     1.1    -      -       -      +
     78G  ILE*     5.1     1.0    -      -       -      +
     91G  ARG*     5.2     1.4    +      -       -      -
     98G  THR*     4.1    14.8    +      -       -      +
     99G  LEU      3.4     4.5    -      -       -      -
    100G  ALA*     3.6    20.3    -      -       -      +
    113G  ASP*     2.9    38.1    -      -       -      +
    114G  TYR*     1.3    71.4    -      -       -      +
    116G  MET*     1.3    61.4    +      -       -      +
    117G  LYS*     3.9     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 116 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175E  LEU      4.3     6.1    -      -       -      +
     70G  VAL*     3.6    29.8    -      -       +      -
     71G  ASN*     4.8     0.9    -      -       +      +
     74G  SER*     4.3     8.7    -      -       -      -
     75G  MET*     3.6    42.2    -      -       +      -
     78G  ILE*     3.4    26.0    -      -       +      -
     98G  THR*     3.4     3.9    -      -       -      -
     99G  LEU*     2.7    70.3    +      -       +      +
    101G  LEU*     4.3     8.5    -      -       +      -
    114G  TYR      3.9     1.0    -      -       -      -
    115G  GLU*     1.3    73.0    -      -       -      +
    117G  LYS*     1.3    71.8    +      -       -      +
    118G  LEU*     3.4     5.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 117 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173E  GLY      3.8     8.8    +      -       -      -
    174E  GLU*     3.5    27.3    +      -       -      +
    175E  LEU*     4.5     2.7    +      -       -      +
    176E  GLY*     3.9    23.9    -      -       -      +
    177E  ASN*     6.3     0.2    -      -       -      +
     70G  VAL*     5.9     0.2    -      -       -      -
     71G  ASN*     5.6     4.9    +      -       -      +
     97G  ASP      4.2     4.5    -      -       -      +
     98G  THR*     4.6     3.8    -      -       -      +
    115G  GLU      3.9     0.8    +      -       -      +
    116G  MET*     1.3    82.3    -      -       -      +
    118G  LEU*     1.3    68.4    +      -       -      +
    119G  MET*     4.9     8.4    -      -       +      +
----------------------------------------------------------
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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