Contacts of the strand formed by residues 103 - 109 (chain G) in PDB entry 6AHU


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 SER 103 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82F  GLU*     3.7    14.7    +      -       -      +
     85F  LYS*     5.6     3.4    -      -       -      +
    101G  ASN      4.2     0.4    +      -       -      -
    102G  THR*     1.3    75.9    -      -       -      +
    104G  THR*     1.3    77.0    +      -       -      +
    105G  VAL*     4.2     1.5    -      -       -      +
    128G  SER*     4.0     5.5    -      -       -      -
    129G  ALA*     3.5    28.4    +      -       -      +
    131G  HIS*     4.6    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 104 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A    C      4.2     7.0    -      -       -      +
     82F  GLU*     2.4    36.2    +      -       -      +
     85F  LYS*     4.1     6.7    +      -       -      +
     86F  ARG*     5.4     6.0    -      -       -      -
    103G  SER*     1.3    82.6    +      -       -      +
    105G  VAL*     1.3    65.7    +      -       -      +
    106G  GLU*     4.0    16.7    +      -       -      +
    126G  ASN*     3.9    31.2    -      -       +      +
    127G  ASN      3.9     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A    A      3.4    34.1    -      -       -      +
     21G  THR*     3.9    14.4    -      -       +      -
     22G  LEU      3.9     8.3    -      -       -      +
     74G  LEU*     4.0    10.1    -      -       +      -
    103G  SER*     5.4     1.8    -      -       -      +
    104G  THR*     1.3    77.0    -      -       -      +
    106G  GLU*     1.3    74.5    +      -       -      +
    107G  LEU*     4.5     0.4    -      -       +      +
    126G  ASN*     3.4     2.3    -      -       -      -
    127G  ASN*     2.9    39.9    +      -       +      +
    129G  ALA*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 106 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    498B  GLU*     4.7     6.1    -      -       -      +
    533B  ASN*     5.9     1.3    -      -       -      +
    537B  ARG*     3.0    37.2    +      -       -      +
    540B  LEU*     5.8     6.1    -      -       +      -
     21G  THR*     4.1    11.3    -      -       -      -
     22G  LEU*     4.6     2.8    +      -       +      +
    104G  THR*     4.0    18.6    +      -       +      +
    105G  VAL*     1.3    87.9    -      -       -      +
    107G  LEU*     1.3    58.4    +      -       -      +
    108G  VAL*     4.3     6.1    -      -       +      -
    124G  ILE*     3.5    28.0    -      -       +      +
    125G  ARG      3.8     6.9    -      -       -      +
    126G  ASN*     4.5     6.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 107 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A    C      3.3    27.8    -      -       +      +
    498B  GLU*     4.7     1.3    -      -       -      -
     18G  VAL*     4.6     4.9    -      -       +      -
     20G  TYR      4.9     0.9    -      -       -      +
     21G  THR*     3.8    21.8    -      -       +      -
    105G  VAL      4.5     2.2    -      -       -      +
    106G  GLU*     1.3    77.4    +      -       -      +
    108G  VAL*     1.3    64.3    +      -       -      +
    109G  ASP*     3.3    38.7    +      -       -      +
    124G  ILE*     4.1     1.3    -      -       -      +
    125G  ARG*     2.8    64.3    +      -       -      +
    126G  ASN*     4.7     0.2    -      -       -      -
    127G  ASN*     4.3    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 108 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    498B  GLU*     3.3    28.5    +      -       +      +
    500B  PRO*     6.5     0.7    -      -       +      -
    537B  ARG*     6.4     0.7    -      -       +      -
    540B  LEU*     3.5    37.9    -      -       +      +
    541B  LEU*     3.8    29.4    -      -       +      -
     18G  VAL*     5.0     0.7    -      -       -      +
     19G  GLU*     4.1    25.8    +      -       +      +
     20G  TYR      4.6     5.3    +      -       -      +
    106G  GLU*     5.5     3.4    -      -       +      -
    107G  LEU*     1.3    75.8    -      -       -      +
    109G  ASP*     1.3    74.2    +      -       -      +
    110G  GLU*     4.2     1.5    +      -       +      -
    122G  THR*     4.8     7.0    -      -       +      -
    123G  ARG      4.0     4.3    -      -       -      +
    124G  ILE*     5.1     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 109 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A    A      5.0     5.9    +      -       -      -
     16G  ASP*     4.7    10.3    -      -       -      +
     17G  PRO      4.8     1.6    -      -       -      +
     18G  VAL*     3.4    32.7    -      -       -      +
    107G  LEU*     3.3    30.9    +      -       -      +
    108G  VAL*     1.3    74.8    -      -       -      +
    110G  GLU*     1.3    59.5    +      -       -      +
    111G  LEU*     5.9     3.1    -      -       +      -
    121G  LEU      4.2     0.5    -      -       -      +
    122G  THR*     3.4     9.5    -      -       -      -
    123G  ARG*     3.2    44.7    +      -       +      +
    125G  ARG*     3.6    20.2    +      -       +      +
----------------------------------------------------------
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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