Contacts of the strand formed by residues 43 - 48 (chain G) in PDB entry 6A5T


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 GLY 43 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38G  CYS*     5.4     1.1    -      -       -      -
     39G  THR*     2.7    45.7    +      -       -      -
     42G  PHE*     1.3    77.6    -      -       -      +
     44G  TYR*     1.3    68.9    +      -       -      -
     45G  ILE      3.8     0.2    +      -       -      -
     79G  TRP      3.4     9.6    -      -       -      -
     80G  LYS*     3.3    21.9    -      -       -      +
     81G  PRO*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 44 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101D  VAL*     4.9    20.9    -      -       +      -
     36G  GLY      4.4     5.4    -      -       -      -
     37G  THR      3.3    16.4    -      -       -      +
     38G  CYS*     3.6    32.6    -      -       +      -
     43G  GLY*     1.3    74.9    -      -       -      -
     45G  ILE*     1.3    61.1    +      -       -      +
     46G  VAL*     3.0    16.9    +      -       +      +
     78G  VAL*     3.2    22.3    -      -       -      -
     79G  TRP*     2.8    51.8    +      +       +      +
     81G  PRO*     5.1     3.8    -      -       +      -
    105G  PRO*     4.4    14.3    -      -       +      +
    106G  LEU*     4.3    23.0    +      -       +      +
    156G  GLU*     5.0    11.7    -      -       +      +
    157G  ILE*     5.6     3.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 45 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  SER*     6.0     2.5    -      -       -      +
      7G  LEU*     4.2    15.3    -      -       +      -
     34G  VAL*     3.2    42.8    -      -       +      +
     35G  GLU*     4.1     4.0    -      -       +      -
     36G  GLY*     2.6    35.7    +      -       -      -
     37G  THR*     3.2    18.7    +      -       -      +
     39G  THR*     4.5    20.2    -      -       +      +
     42G  PHE*     5.2     3.8    -      -       +      -
     43G  GLY      3.8     1.0    +      -       -      -
     44G  TYR*     1.3    68.9    -      -       -      +
     46G  VAL*     1.3    58.2    +      -       -      +
     47G  THR      4.9     1.3    -      -       -      +
     74G  TYR*     3.8    18.6    -      -       -      +
     76G  ALA*     4.6    17.0    -      -       +      -
     77G  VAL      4.0     3.1    -      -       -      -
     78G  VAL*     4.4     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 46 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  ILE*     4.6    18.2    -      -       +      -
     93D  THR*     4.8     1.9    -      -       -      +
    101D  VAL*     5.5     8.7    -      -       +      +
    102D  VAL*     4.8     9.8    -      -       +      +
    105D  THR*     5.0    13.7    -      -       +      +
      2G  PHE*     4.5     7.4    -      -       +      -
     35G  GLU*     3.8     6.6    -      -       -      +
     36G  GLY*     3.8    10.4    +      -       -      -
     44G  TYR*     3.3     9.6    -      -       +      +
     45G  ILE*     1.3    75.0    -      -       -      +
     47G  THR*     1.3    80.7    +      -       +      +
     77G  VAL*     2.7    20.0    +      -       +      +
     78G  VAL      3.7     2.2    -      -       -      -
     79G  TRP*     3.3    41.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 47 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  ILE*     4.1    22.2    -      -       +      +
     63D  ALA*     5.7     1.6    -      -       -      +
     64D  LEU*     4.4    12.1    -      -       +      -
     67D  ARG*     4.3     3.1    -      -       -      -
     93D  THR*     3.6    27.8    -      -       +      -
    102D  VAL*     4.8     4.3    -      -       +      -
     35G  GLU*     3.9    10.1    -      -       -      -
     45G  ILE*     5.4     0.4    -      -       -      -
     46G  VAL*     1.3    97.2    -      -       +      +
     48G  VAL*     1.3    70.6    +      -       -      +
     49G  LEU*     6.1     0.2    -      -       -      +
     76G  ALA*     3.2     7.9    -      -       -      +
     77G  VAL*     2.9    38.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63D  ALA*     4.0    10.2    -      -       -      +
     67D  ARG*     2.3    34.7    +      -       -      +
     30G  LEU*     5.7     4.3    -      -       +      -
     31G  LEU*     4.0    11.0    -      -       +      -
     34G  VAL*     5.1    10.8    -      -       +      -
     35G  GLU*     3.1    22.4    +      -       +      +
     45G  ILE*     5.8     0.2    -      -       +      -
     47G  THR*     1.3    83.4    +      -       -      +
     49G  LEU*     1.3    77.4    +      -       -      +
     50G  ASP      4.0     0.2    +      -       -      -
     51G  GLY*     3.9    15.3    -      -       -      -
     54G  ILE*     4.1    15.0    -      -       +      -
     74G  TYR*     5.3    11.9    -      -       +      -
     75G  ARG      5.0     4.0    -      -       -      +
     76G  ALA*     4.4     9.4    -      -       +      -
     77G  VAL*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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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