Contacts of the strand formed by residues 220 - 226 (chain C) in PDB entry 6H25


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 220 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199C  ALA*     3.6     5.4    -      -       -      +
    200C  VAL*     2.9    38.6    +      -       -      +
    215C  GLU*     6.1     0.3    -      -       -      +
    218C  ALA*     4.9     1.7    -      -       -      +
    219C  THR*     1.3    85.3    +      -       -      +
    221C  THR*     1.3    64.5    +      -       -      -
    237C  LYS*     6.3     1.3    -      -       -      -
    239C  GLY*     4.7    17.7    -      -       -      -
    240C  GLY      5.1     4.7    -      -       -      -
    241C  SER*     5.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 221 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197C  SER*     5.4     4.5    -      -       -      -
    198C  PHE      3.6     9.0    -      -       -      +
    199C  ALA*     5.5     1.0    -      -       +      -
    200C  VAL*     5.3     0.9    -      -       -      -
    215C  GLU*     3.8    29.4    +      -       +      +
    219C  THR      4.7     2.6    +      -       -      -
    220C  GLY*     1.3    76.4    +      -       -      -
    222C  LEU*     1.3    68.6    +      -       -      +
    223C  THR*     4.6     5.8    -      -       -      +
    236C  HIS*     4.8     3.1    -      -       +      +
    237C  LYS*     3.5    18.8    -      -       -      +
    238C  PRO*     3.2    30.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 222 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196C  THR      5.4     0.9    -      -       -      +
    197C  SER*     3.2     2.6    -      -       -      -
    198C  PHE*     2.9    47.6    +      -       +      +
    200C  VAL*     4.8    11.2    -      -       +      +
    206C  LEU*     5.9     0.9    -      -       +      -
    221C  THR*     1.3    74.1    -      -       -      +
    223C  THR*     1.3    82.8    +      -       -      +
    224C  ILE*     3.7    32.8    -      -       +      +
    235C  LEU*     5.3     4.0    -      -       +      -
    236C  HIS      3.6     4.3    -      -       -      -
    237C  LYS*     3.8    20.0    -      -       +      -
    243C  LEU*     3.7    31.0    -      -       +      -
    248C  LEU*     3.9    12.1    -      -       +      -
    251C  CYS*     4.3    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 223 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  PHE*     3.7    31.0    -      -       +      -
    149C  LEU*     4.0    12.5    -      -       +      +
    195C  ALA*     4.5    10.3    -      -       +      -
    196C  THR      3.6     6.1    -      -       -      +
    197C  SER*     2.9    25.8    +      -       -      +
    221C  THR*     4.6     6.8    -      -       -      +
    222C  LEU*     1.3    77.7    +      -       -      +
    224C  ILE*     1.3    67.7    +      -       -      +
    225C  VAL*     4.5     1.6    -      -       +      -
    234C  CYS      3.7     0.9    -      -       -      +
    235C  LEU*     3.5     6.1    -      -       -      +
    236C  HIS*     2.9    46.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 224 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194C  VAL      3.7     1.4    -      -       -      +
    195C  ALA*     3.2     1.1    -      -       -      -
    196C  THR*     2.9    42.2    +      -       -      +
    198C  PHE*     5.4     1.8    -      -       +      -
    222C  LEU*     3.7    16.6    -      -       +      -
    223C  THR*     1.3    78.1    -      -       -      +
    225C  VAL*     1.3    72.4    +      -       -      +
    226C  MET*     4.1    11.3    +      -       +      +
    232C  LEU*     4.6     8.7    -      -       +      -
    234C  CYS      3.8     4.0    -      -       -      +
    235C  LEU*     4.4    19.7    -      -       +      -
    248C  LEU*     5.0     3.6    -      -       +      +
    251C  CYS*     3.7    36.8    -      -       +      +
    252C  MET*     4.4    25.6    -      -       +      +
    255C  ALA*     4.7     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 225 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  PHE*     3.7    30.3    -      -       +      -
    112C  VAL*     4.2    12.1    -      -       +      -
    153C  THR*     5.2     2.5    -      -       +      +
    193C  PRO*     3.8    21.8    -      -       +      -
    194C  VAL      3.3    13.9    -      -       -      +
    195C  ALA*     3.7    12.6    -      -       +      +
    223C  THR*     4.5     1.3    -      -       +      -
    224C  ILE*     1.3    78.9    -      -       -      +
    226C  MET*     1.3    57.4    +      -       -      +
    232C  LEU*     3.6     4.3    -      -       -      -
    233C  CYS*     2.7    51.8    +      -       +      -
    234C  CYS*     3.3    20.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 226 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192C  HIS      3.5     1.7    -      -       -      +
    193C  PRO*     3.5     4.8    -      -       -      +
    194C  VAL      2.9    33.2    +      -       -      +
    224C  ILE*     4.7     6.3    -      -       +      +
    225C  VAL*     1.3    75.3    -      -       -      +
    227C  ASP*     1.3    74.2    +      -       -      +
    228C  GLU      5.9     0.7    -      -       -      +
    230C  GLY*     4.7    12.1    -      -       -      -
    231C  LYS      3.5     9.9    -      -       -      +
    232C  LEU*     4.8     1.1    -      -       +      +
    233C  CYS*     4.6     2.2    -      -       -      -
    252C  MET*     3.7    54.3    -      -       +      +
    255C  ALA*     3.7    21.5    -      -       +      +
    256C  VAL*     3.6    32.1    -      -       +      -
    259C  HIS*     3.9    10.0    +      -       +      -
----------------------------------------------------------
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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