Contacts of the strand formed by residues 230 - 237 (chain C) in PDB entry 6C3P


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 VAL 230 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  PRO*     3.2    24.6    -      -       +      +
    222C  LYS*     3.5    41.1    -      -       +      +
    223C  THR      3.2    13.0    -      -       -      +
    224C  THR*     3.2    24.7    -      -       +      +
    228C  GLY      3.3     3.7    +      -       -      +
    229C  GLU*     1.3    74.3    -      -       -      +
    231C  VAL*     1.3    63.7    +      -       -      +
    232C  PRO*     4.5     0.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  ARG*     5.3    11.4    -      -       -      +
    201B  ARG*     6.3     0.4    -      -       -      +
    256B  ILE*     5.2    15.3    -      -       +      -
    315B  PHE      5.6     2.7    -      -       -      +
    317B  PRO*     4.5    10.3    -      -       +      -
    222C  LYS*     3.4    15.9    -      -       -      -
    223C  THR*     3.3     6.6    +      -       +      +
    229C  GLU*     5.3    10.3    -      -       +      +
    230C  VAL*     1.3    83.1    -      -       -      +
    232C  PRO*     1.3    76.9    -      -       +      +
    233C  LEU      3.5     2.2    -      -       -      +
    234C  HIS*     3.4    41.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  PRO*     3.6    20.2    -      -       +      -
    319B  VAL*     3.0    51.6    -      -       +      +
    320B  ALA*     4.8     3.8    -      -       -      +
    321B  GLU      5.6     1.1    -      -       -      +
    326B  TYR*     6.2     0.9    -      -       +      -
    221C  ARG      3.2     2.6    -      -       -      +
    222C  LYS*     3.0    48.0    +      -       +      +
    230C  VAL*     4.5     0.7    -      -       +      +
    231C  VAL*     1.3    83.7    -      -       +      +
    233C  LEU*     1.3    66.3    +      -       +      +
    280C  ASP*     5.4     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  ALA*     4.6    13.0    -      -       +      +
    255B  LEU*     5.8     3.1    -      -       -      +
    319B  VAL*     4.2    17.6    -      -       +      +
    326B  TYR*     3.5    52.3    -      -       +      +
     35C  PHE*     3.4    44.2    -      -       +      -
     44C  VAL*     4.7     0.9    -      -       +      -
    220C  VAL*     5.2    10.3    -      -       +      -
    221C  ARG*     4.0     4.3    -      -       -      +
    231C  VAL*     4.6     3.4    -      -       -      +
    232C  PRO*     1.3    83.6    -      -       +      +
    234C  HIS*     1.3    65.5    +      -       -      +
    235C  GLN*     3.6    15.4    +      -       +      +
    282C  GLU*     5.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 234 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  ARG*     4.6    22.0    +      -       -      -
    258B  TYR*     5.4     7.6    +      +       -      -
    219C  VAL      4.5     0.2    -      -       -      -
    220C  VAL*     3.0    29.6    -      -       -      +
    221C  ARG*     2.8    22.3    +      -       +      +
    223C  THR*     3.3    28.7    -      -       +      +
    231C  VAL*     3.4    30.2    +      -       +      +
    232C  PRO      3.5     1.2    -      -       -      -
    233C  LEU*     1.3    74.8    -      -       -      +
    235C  GLN*     1.3    75.8    +      -       -      +
    236C  VAL*     3.3    30.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 235 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  PHE*     3.3    14.1    +      -       -      +
    253B  ALA*     4.6    11.1    +      -       -      +
    255B  LEU*     3.1    33.1    -      -       +      +
     35C  PHE*     3.8    29.7    -      -       -      -
    218C  GLN*     3.1    27.6    +      -       -      +
    219C  VAL      3.6     4.5    -      -       -      -
    220C  VAL*     3.6    13.2    -      -       +      -
    233C  LEU*     3.6    13.7    +      -       +      +
    234C  HIS*     1.3    92.5    +      -       -      +
    236C  VAL*     1.3    64.7    +      -       -      +
    237C  ASP*     4.2     1.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 236 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  GLY*     4.8    12.6    -      -       -      +
    218C  GLN*     3.4     2.8    -      -       -      +
    219C  VAL*     2.9    46.1    +      -       +      +
    234C  HIS*     3.3    33.2    -      -       +      +
    235C  GLN*     1.3    71.2    -      -       -      +
    237C  ASP*     1.3    68.8    +      -       -      +
    238C  ILE*     3.0     5.5    +      -       -      -
    266C  PRO*     3.7    31.4    -      -       +      -
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Residues in contact with ASP 237 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  MET*     5.8     0.2    -      -       -      +
    242B  ASN*     2.9    40.8    +      -       -      +
    243B  GLY*     4.0     5.1    -      -       -      +
    244B  VAL*     3.3    29.1    +      -       +      +
    248B  SER      3.5    12.0    -      -       -      +
    249B  ILE*     4.7     4.7    -      -       -      +
    216C  HIS*     5.5    11.9    -      -       +      +
    217C  MET      3.8     6.2    -      -       -      +
    218C  GLN*     3.0    34.9    +      -       -      +
    235C  GLN      4.3     0.4    +      -       -      -
    236C  VAL*     1.3    71.7    -      -       -      +
    238C  ILE*     1.3    63.8    +      -       -      +
    239C  PRO*     3.5     4.3    -      -       -      +
----------------------------------------------------------
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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