Contacts of the strand formed by residues 98 - 104 (chain C) in PDB entry 4BC1


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 TYR 98 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  GLY*     3.6    11.4    -      -       -      -
     35C  ILE      3.2     7.4    -      -       -      +
     36C  PRO*     3.5    38.4    -      -       +      -
     37C  PHE*     3.5     5.6    -      -       -      -
     40C  PRO*     5.1     1.9    -      -       -      +
     60C  LEU*     6.3     0.2    -      -       +      -
     66C  GLN*     3.4    55.0    +      -       +      -
     95C  ASP*     2.9    42.1    +      -       -      -
     96C  CYS*     2.8    28.4    +      -       -      +
     97C  LEU*     1.3    75.8    -      -       -      +
     99C  LEU*     1.3    60.7    +      -       -      +
    100C  ASN*     5.3     1.4    +      -       -      +
    150C  ASN*     3.1    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  GLY      2.9     5.4    +      -       -      -
     35C  ILE*     2.8    54.0    +      -       +      +
     37C  PHE*     3.6    31.0    -      -       +      -
     98C  TYR*     1.3    73.9    -      -       -      +
    100C  ASN*     1.3    68.5    +      -       -      +
    101C  VAL*     4.2     7.4    -      -       +      -
    147C  VAL*     4.5     8.1    -      -       +      -
    148C  SER      3.2    15.3    -      -       -      +
    149C  MET*     3.9     8.3    -      -       +      -
    179C  ALA*     3.9    18.2    -      -       +      +
    182C  TRP*     3.5    44.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  PHE      3.4     6.5    -      -       -      +
     33C  LEU*     3.3     7.3    -      -       +      -
     34C  GLY*     2.9    27.2    +      -       -      -
     65C  PHE*     3.3    34.4    -      -       +      -
     66C  GLN      5.2     0.2    +      -       -      -
     98C  TYR      5.3     1.6    +      -       -      -
     99C  LEU*     1.3    76.2    -      -       -      +
    101C  VAL*     1.3    63.4    +      -       -      +
    102C  TRP*     4.2    11.0    -      -       +      -
    128C  ALA*     3.4    19.8    -      -       -      +
    146C  LEU      3.7     0.6    -      -       -      +
    147C  VAL*     3.2     8.3    -      -       -      +
    148C  SER*     2.8    51.6    +      -       -      +
    150C  ASN*     5.5     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30C  SER      3.7     1.0    -      -       -      +
     31C  ALA*     3.5     2.4    -      -       -      -
     32C  PHE*     2.8    47.4    +      -       +      +
     33C  LEU*     4.9     0.4    -      -       -      +
     35C  ILE*     4.1    21.8    -      -       +      -
     99C  LEU*     4.2     9.2    -      -       +      -
    100C  ASN*     1.3    78.8    -      -       -      +
    102C  TRP*     1.3    63.5    +      -       -      +
    103C  THR*     4.1    11.2    -      -       +      -
    145C  VAL*     4.0    19.3    -      -       +      -
    146C  LEU      3.3     8.1    -      -       -      +
    147C  VAL*     4.0    17.3    -      -       +      -
    182C  TRP*     4.4     9.0    -      -       +      -
    187C  ILE*     4.1     7.4    -      -       +      -
    190C  PHE*     4.3    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  LEU*     3.9    15.7    -      -       +      +
     29C  VAL*     4.5     3.4    -      -       +      -
     30C  SER      3.2     6.3    -      -       -      -
     31C  ALA*     3.9    18.5    -      -       +      +
     33C  LEU*     4.2     8.6    -      -       +      +
     65C  PHE*     4.0    28.5    -      +       -      -
    100C  ASN*     4.2     9.0    -      -       +      -
    101C  VAL*     1.3    75.5    -      -       -      +
    103C  THR*     1.3    63.2    +      -       -      +
    128C  ALA      4.7     3.1    -      -       -      -
    133C  TYR      3.8    10.8    -      -       -      -
    134C  ASP*     3.5    19.5    +      -       -      -
    135C  GLY*     3.5    44.0    -      -       -      +
    136C  ARG*     3.8    17.0    -      -       +      -
    139C  ALA*     4.0     5.6    -      -       +      +
    144C  ALA      3.5     2.8    -      -       -      +
    145C  VAL*     3.4     4.0    -      -       -      +
    146C  LEU*     2.8    64.4    +      -       +      +
    148C  SER*     3.7    23.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  VAL*     3.6     5.2    -      -       -      +
     30C  SER*     2.8    36.7    +      -       -      +
     32C  PHE*     4.6     4.9    -      -       +      -
    101C  VAL*     4.1     6.7    -      -       +      -
    102C  TRP*     1.3    77.1    -      -       -      +
    104C  PRO*     1.3    82.4    +      -       -      +
    107C  ARG*     3.3    16.4    -      -       +      +
    108C  PRO*     4.4     1.1    -      -       -      -
    139C  ALA*     4.0     5.2    -      -       -      -
    144C  ALA      3.9     1.1    -      -       -      -
    145C  VAL*     4.0    15.9    -      -       +      -
    190C  PHE*     3.7    37.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 104 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28C  PRO      5.0     0.4    -      -       -      +
     29C  VAL*     4.6     4.0    -      -       +      -
     30C  SER*     3.1     4.7    +      -       -      -
    103C  THR*     1.3   103.5    +      -       -      +
    105C  TYR*     1.3    58.7    +      -       -      +
    106C  PRO      3.2    20.3    -      -       -      +
    107C  ARG*     3.3     2.4    +      -       -      -
    108C  PRO*     4.1    19.7    -      -       +      -
    139C  ALA*     3.6    24.2    -      -       +      +
    140C  GLN*     5.5     2.2    -      -       -      +
    143C  GLY*     3.8    19.7    -      -       -      +
    144C  ALA      3.5    13.9    -      -       -      +
    145C  VAL*     4.8     1.1    -      -       +      -
----------------------------------------------------------
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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