Contacts of the strand formed by residues 93 - 101 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  GLN      3.6     1.2    +      -       -      -
     92B  ASN*     1.3    77.2    -      -       -      +
     94B  LEU*     1.3    61.8    +      -       -      -
     95B  TYR*     3.5    11.2    -      -       -      -
    141B  GLU*     3.4     7.5    -      -       -      +
    142B  LEU      2.9    31.0    +      -       -      +
    169B  LEU*     3.9     3.1    -      -       -      -
    171B  ALA      3.4    11.0    -      -       -      -
    172B  ASN*     4.1     5.6    -      -       -      -
    173B  PRO*     5.3     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  MET*     5.0     5.4    -      -       -      -
     98A  TYR*     3.7    44.6    -      -       +      +
    168A  ILE*     4.3    21.3    -      -       +      -
     93B  GLY*     1.3    73.1    -      -       -      -
     95B  TYR*     1.3    53.9    +      -       -      +
    139B  THR*     3.7    21.3    -      -       +      -
    140B  TYR      3.6    11.7    -      -       -      +
    141B  GLU*     4.2     6.5    -      -       +      +
    169B  LEU*     3.6     2.3    -      -       -      +
    170B  LEU*     2.7    63.2    +      -       +      +
    171B  ALA*     2.7    21.9    +      -       +      +
    172B  ASN*     4.7     0.2    -      -       -      +
    173B  PRO*     4.9     6.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  CYS*     3.6    33.3    +      -       -      +
     79B  VAL*     4.3     4.3    -      -       +      -
     89B  ILE*     3.8     6.2    -      -       +      +
     91B  GLN*     2.5    33.6    +      -       -      +
     93B  GLY      3.5    20.0    -      -       -      -
     94B  LEU*     1.3    75.1    -      -       -      +
     96B  LEU*     1.3    61.7    +      -       -      +
     97B  ILE*     3.9     1.5    +      -       +      -
    139B  THR*     3.6     3.3    -      -       -      +
    140B  TYR*     2.6    39.4    +      -       -      +
    142B  LEU*     3.7    34.1    -      -       +      -
    167B  ILE*     3.5    26.5    -      -       +      -
    168B  ILE      3.4     4.0    -      -       -      -
    169B  LEU*     3.4    40.7    -      -       +      +
    170B  LEU*     4.6     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  LEU*     3.8    17.7    -      -       +      -
     95B  TYR*     1.3    73.2    -      -       -      +
     97B  ILE*     1.3    76.4    +      -       -      +
     98B  TYR*     4.0     2.9    +      -       +      -
    138B  GLY*     3.8     6.5    -      -       -      +
    139B  THR*     3.4    21.1    -      -       -      +
    167B  ILE*     3.6     2.2    -      -       -      -
    168B  ILE*     2.7    53.3    +      -       +      +
    170B  LEU*     4.0    13.2    -      -       +      +
     96C  LEU*     4.6     8.3    -      -       +      -
    139C  THR*     3.5    40.8    -      -       +      +
    170C  LEU*     4.7     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  TYR      3.9     1.1    +      -       -      +
     96B  LEU*     1.3    83.5    -      -       -      +
     98B  TYR*     1.3    67.5    +      -       -      +
    117B  LEU*     4.0    16.2    -      -       +      -
    124B  ILE*     4.7     2.2    -      -       +      -
    135B  ASN*     5.5     0.5    +      -       -      -
    136B  VAL*     3.6     3.9    -      -       +      +
    137B  GLY*     3.3    17.8    -      -       -      +
    138B  GLY      2.7    38.3    +      -       -      +
    140B  TYR*     4.0    20.0    -      -       +      -
    142B  LEU*     4.6     7.6    -      -       +      -
    148B  ILE*     3.8    36.3    -      -       +      -
    165B  TRP*     4.2    11.0    -      -       +      -
    166B  GLY      3.5     9.2    -      -       -      +
    167B  ILE*     4.1    19.3    -      -       +      -
    139C  THR*     5.2     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  MET*     3.4    19.0    -      -       +      +
     60B  ALA      3.3    12.5    +      -       -      -
     61B  LYS*     3.7    13.0    -      -       +      +
     96B  LEU*     4.1    10.5    -      -       +      -
     97B  ILE*     1.3    74.6    -      -       -      +
     99B  GLY*     1.3    59.8    +      -       -      +
    135B  ASN*     5.0     0.4    -      -       -      +
    136B  VAL*     3.0    14.6    -      -       -      -
    164B  TYR*     4.0    21.8    -      +       -      -
    165B  TRP*     3.3     5.6    -      -       -      +
    166B  GLY*     2.6    50.5    +      -       -      +
    167B  ILE*     3.2    25.4    -      -       -      -
    168B  ILE      4.3     0.2    -      -       -      -
     94C  LEU*     4.1    38.4    -      -       +      -
    139C  THR*     3.6    29.4    -      -       -      +
    141C  GLU*     4.6    11.4    -      -       +      +
    175C  PHE*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  TYR*     1.3    78.1    -      -       -      +
    100B  GLN*     1.3    66.3    +      -       -      +
    135B  ASN*     3.2    12.5    +      -       -      +
    136B  VAL*     2.7    27.7    +      -       -      -
    164B  TYR*     3.1    30.3    -      -       -      -
    165B  TRP*     3.7     5.6    -      -       -      -
    139C  THR      4.4     1.0    +      -       -      -
    140C  TYR*     5.2     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  GLY*     1.3    77.9    -      -       -      +
    101B  VAL*     1.3    64.3    +      -       -      +
    102B  ALA*     5.3     1.2    -      -       -      +
    133B  ILE*     5.2    10.3    -      -       +      +
    134B  GLN      3.4    12.6    -      -       -      +
    135B  ASN*     4.9     1.3    -      -       -      +
    136B  VAL*     3.3     6.6    -      -       -      +
    162B  ASN*     2.9    31.7    -      -       -      +
    163B  THR*     3.1     5.7    -      -       -      +
    164B  TYR*     2.7    61.8    +      -       +      +
    119C  LYS*     5.2    15.8    -      -       -      +
    122C  ASP*     5.7     1.2    -      -       -      +
    124C  ILE*     4.9    13.5    -      -       -      +
    140C  TYR*     4.7    14.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  GLN*     1.3    75.9    -      -       -      +
    102B  ALA*     1.3    58.1    +      -       -      +
    103B  PRO*     2.8    22.4    -      -       +      +
    113B  PHE*     4.7     4.3    -      -       +      -
    115B  VAL*     3.7    34.5    -      -       +      -
    127B  LEU*     4.5     6.3    -      -       +      -
    133B  ILE*     3.4     3.8    -      -       -      +
    134B  GLN*     3.2    34.4    +      -       +      +
    136B  VAL*     3.7    19.7    -      -       +      -
    150B  LEU*     4.2    10.8    -      -       +      -
    159B  LEU*     3.1    34.5    -      -       +      -
    163B  THR*     3.6     2.9    -      -       +      -
----------------------------------------------------------
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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