Contacts of the strand formed by residues 93 - 101 (chain D) in PDB entry 3B94


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 93 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92D  ASN*     1.3    78.8    -      -       -      +
     94D  LEU*     1.3    61.3    +      -       -      -
     95D  TYR*     3.4    12.8    -      -       -      -
    141D  GLU*     3.4     4.6    -      -       -      +
    142D  LEU      3.0    30.8    +      -       -      -
    169D  LEU*     3.9     1.8    -      -       -      -
    171D  ALA      3.1    12.1    -      -       -      -
    172D  ASN*     4.1     5.2    -      -       -      -
    173D  PRO*     5.2     2.9    -      -       -      -
    175D  PHE      5.6     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93D  GLY*     1.3    72.6    -      -       -      -
     95D  TYR*     1.3    53.1    +      -       -      +
    139D  THR*     3.8    18.4    -      -       +      -
    140D  TYR*     3.4    20.4    -      -       -      +
    141D  GLU*     4.0     7.9    -      -       +      +
    169D  LEU*     3.6     2.6    -      -       -      +
    170D  LEU*     2.6    64.7    +      -       +      -
    171D  ALA*     2.6    26.0    +      -       +      +
    173D  PRO*     5.0     6.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78D  CYS*     3.5    35.3    +      -       -      +
     79D  VAL*     4.6     6.1    -      -       +      -
     89D  ILE*     4.2     6.5    -      -       +      -
     91D  GLN*     2.7    32.5    +      -       -      +
     93D  GLY      3.4    26.0    -      -       -      -
     94D  LEU*     1.3    75.1    -      -       -      +
     96D  LEU*     1.3    60.1    +      -       -      +
     97D  ILE*     3.9     1.9    +      -       +      -
    138D  GLY      3.9     0.5    -      -       -      +
    139D  THR*     3.1     8.3    -      -       -      +
    140D  TYR*     2.7    38.3    +      -       -      +
    142D  LEU*     3.7    31.6    -      -       +      -
    167D  ILE*     3.7    31.9    -      -       +      -
    168D  ILE      3.3    11.9    -      -       -      +
    169D  LEU*     3.5    26.8    -      -       +      +
    170D  LEU*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  TYR*     1.3    71.9    -      -       -      +
     97D  ILE*     1.3    70.8    +      -       -      +
     98D  TYR*     4.0     6.9    +      -       +      -
    138D  GLY*     3.6    14.1    -      -       -      +
    139D  THR*     3.6    18.8    -      -       -      +
    167D  ILE*     3.2     3.2    -      -       -      +
    168D  ILE*     2.9    49.7    +      -       +      +
    170D  LEU*     4.2    27.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  TYR      5.0     1.8    -      -       -      +
     96D  LEU*     1.3    81.8    -      -       -      +
     98D  TYR*     1.4    68.4    +      -       -      +
    117D  LEU*     4.0    25.8    -      -       +      -
    124D  ILE*     4.4     1.8    -      -       +      -
    136D  VAL*     4.7     1.6    -      -       +      +
    137D  GLY*     3.1     9.8    -      -       -      -
    138D  GLY      2.9    34.1    +      -       -      +
    140D  TYR*     4.2    19.7    -      -       +      -
    142D  LEU*     4.7     3.8    -      -       +      -
    148D  ILE*     3.8    39.9    -      -       +      -
    165D  TRP*     3.8    17.3    -      -       +      -
    166D  GLY      3.4    11.9    -      -       -      +
    167D  ILE*     3.9    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59D  MET*     4.1    22.3    -      -       +      +
     60D  ALA      4.2     2.4    +      -       -      -
     61D  LYS*     4.2    15.5    -      -       +      +
     96D  LEU*     4.4    12.6    -      -       +      -
     97D  ILE*     1.4    77.9    -      -       -      +
     99D  GLY*     1.3    63.8    +      -       -      +
    136D  VAL*     3.1    13.9    -      -       -      -
    164D  TYR*     4.1    22.7    -      +       -      -
    165D  TRP*     3.3     4.3    -      -       -      +
    166D  GLY*     2.9    63.8    +      -       -      +
    167D  ILE*     3.6     8.5    -      -       -      -
    168D  ILE*     5.0     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98D  TYR*     1.3    88.1    -      -       -      +
    100D  GLN*     1.3    61.1    +      -       -      +
    135D  ASN*     3.6    13.9    +      -       -      -
    136D  VAL*     3.0    27.0    +      -       -      +
    164D  TYR*     3.0    20.6    -      -       -      -
    165D  TRP*     3.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  GLY*     1.3    74.6    -      -       -      +
    101D  VAL*     1.3    68.7    +      -       -      +
    102D  ALA*     4.5     0.4    -      -       +      +
    133D  ILE*     3.9    24.0    -      -       +      +
    134D  GLN      3.3     8.3    -      -       -      +
    135D  ASN*     5.1     5.0    -      -       -      +
    136D  VAL*     4.2     1.8    -      -       -      +
    162D  ASN*     3.3    41.3    +      -       -      +
    163D  THR*     3.2     2.8    -      -       -      +
    164D  TYR*     2.9    56.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 101 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100D  GLN*     1.3    79.2    -      -       -      +
    102D  ALA*     1.3    68.4    +      -       -      +
    103D  PRO*     3.2    14.5    -      -       +      +
    115D  VAL*     4.0    32.5    -      -       +      -
    127D  LEU*     3.6    26.9    -      -       +      -
    133D  ILE*     3.5     2.4    -      -       -      +
    134D  GLN*     2.7    32.7    +      -       +      +
    136D  VAL*     3.8    15.7    -      -       +      -
    150D  LEU*     4.1    15.7    -      -       +      -
    152D  PHE*     4.9     0.7    -      -       +      -
    158D  VAL*     4.7     9.2    -      -       +      -
    163D  THR*     3.9     9.2    -      -       +      +
----------------------------------------------------------
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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