Contacts of the strand formed by residues 224 - 231 (chain D) in PDB entry 2C10


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 ALA 224 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215D  PRO      4.5     0.3    -      -       -      +
    216D  ARG*     2.9    30.6    +      -       -      +
    217D  GLY*     3.2    10.6    +      -       -      -
    222D  ASP*     5.3     2.9    -      -       +      -
    223D  ARG*     1.3    73.5    -      -       -      +
    225D  THR*     1.3    61.7    +      -       -      +
    226D  TRP*     4.1     2.3    +      -       -      -
    248D  LEU*     3.7    15.8    -      -       +      +
    249D  VAL      3.2     8.1    -      -       -      +
    250D  ASN*     4.2     9.2    -      -       +      +
    262D  GLN*     3.5    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 225 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212D  THR*     3.5    12.3    -      -       -      +
    213D  THR*     3.5    12.1    -      -       -      +
    215D  PRO      5.4     0.9    -      -       -      +
    216D  ARG*     3.0    39.8    +      -       +      +
    224D  ALA*     1.3    72.6    -      -       -      +
    226D  TRP*     1.3    72.3    +      -       -      +
    227D  PHE*     3.4    27.4    +      -       +      -
    247D  LEU      3.2     3.3    -      -       -      +
    248D  LEU*     4.0     2.9    -      -       -      -
    249D  VAL      2.7    39.4    +      -       -      -
    251D  HIS*     2.7    22.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 226 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553C  TRP*     3.4    39.3    -      +       -      +
    213D  THR*     2.8    45.6    +      -       -      +
    224D  ALA      4.1     1.7    +      -       -      -
    225D  THR*     1.3    72.9    -      -       -      +
    227D  PHE*     1.3    60.9    -      -       -      +
    246D  GLU*     3.9    22.0    -      -       +      -
    247D  LEU      3.3    24.7    -      -       -      -
    248D  LEU*     3.7    39.9    -      -       +      +
    263D  LYS*     3.8    26.2    -      -       +      -
    264D  VAL      4.7     0.7    -      -       -      -
    265D  PHE*     4.3     4.5    -      -       +      -
    270D  TYR*     4.6     3.4    -      +       -      -
    377D  PRO*     3.5    37.2    -      -       +      -
    378D  ALA*     4.0    15.0    -      -       +      -
    381D  THR*     4.1    17.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 227 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176D  TYR*     4.3    13.7    -      +       -      -
    179D  ILE*     3.6    43.7    -      -       +      -
    180D  ASP*     5.5     0.7    -      -       -      -
    183D  ILE*     4.6     8.3    -      -       +      -
    210D  THR*     4.1    27.4    -      -       +      -
    211D  MET      3.7     4.7    -      -       -      +
    212D  THR*     3.7    37.7    -      -       -      -
    216D  ARG*     4.8     0.9    -      -       -      -
    225D  THR*     3.4    37.2    -      -       +      -
    226D  TRP*     1.3    73.6    -      -       -      +
    228D  GLY*     1.3    61.0    +      -       -      +
    229D  LEU*     4.2     4.3    +      -       +      +
    245D  LEU      4.1     0.2    -      -       -      +
    246D  GLU*     3.2     6.0    -      -       -      -
    247D  LEU*     2.7    41.0    +      -       +      +
    249D  VAL*     3.8    18.2    -      -       +      -
    378D  ALA*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 228 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210D  THR*     3.3     7.8    -      -       -      -
    211D  MET      3.2    30.9    +      -       -      -
    213D  THR*     5.6     0.6    -      -       -      +
    226D  TRP      4.2     1.0    +      -       -      -
    227D  PHE*     1.3    74.0    -      -       -      +
    229D  LEU*     1.3    62.9    +      -       -      +
    230D  TYR*     3.3    17.4    -      -       -      -
    242D  HIS*     4.1    11.0    -      -       -      -
    245D  LEU      3.6     6.5    -      -       -      -
    246D  GLU*     4.2     5.6    -      -       -      +
    378D  ALA*     5.1     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 229 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  ILE*     4.3     3.8    -      -       +      -
    184D  PHE*     4.2    10.3    -      -       +      -
    188D  LEU*     3.9    28.5    -      -       +      -
    208D  LEU*     4.4    13.5    -      -       +      -
    209D  VAL      3.4     2.2    -      -       -      +
    210D  THR*     3.8    22.7    -      -       +      -
    227D  PHE*     4.2     4.0    -      -       +      +
    228D  GLY*     1.3    76.6    -      -       -      +
    230D  TYR*     1.3    65.2    +      -       -      +
    242D  HIS*     3.7     4.9    +      -       -      -
    243D  VAL*     3.0    39.8    +      -       +      +
    245D  LEU*     3.0    35.2    +      -       +      +
    247D  LEU*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 230 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208D  LEU*     3.2     5.0    -      -       -      -
    209D  VAL*     2.8    37.9    +      -       +      +
    211D  MET*     3.7    35.2    +      -       +      +
    228D  GLY*     3.3    29.7    +      -       -      -
    229D  LEU*     1.3    73.6    -      -       -      +
    231D  TYR*     1.3    62.4    +      -       -      +
    238D  PHE*     3.4    49.1    -      +       +      +
    239D  PHE*     3.8    17.9    -      -       -      -
    241D  HIS      3.4     5.4    -      -       -      +
    242D  HIS*     3.5    46.1    +      +       +      -
    243D  VAL*     4.2     4.0    -      -       -      -
    496D  SER*     5.2     1.7    +      -       -      -
    497D  SER      4.0     7.2    +      -       -      -
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Residues in contact with TYR 231 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198D  CYS      3.3    15.6    +      -       -      -
    199D  CYS*     3.4    27.8    -      -       -      +
    200D  PHE*     3.6     3.2    -      +       -      -
    207D  ASN*     3.7    11.0    -      -       -      +
    208D  LEU*     3.7    12.6    -      -       +      -
    230D  TYR*     1.3    70.7    -      -       -      +
    232D  ASN*     1.3    60.0    +      -       -      +
    233D  ILE*     3.0    27.6    +      -       +      +
    238D  PHE*     3.3    22.2    -      -       -      +
    241D  HIS*     3.1    23.5    +      +       +      +
    243D  VAL*     3.8    24.1    -      -       +      +
    291D  ILE*     2.5    33.8    +      -       +      +
    292D  PRO      3.2    26.9    -      -       -      -
    293D  ASP*     3.6    25.8    -      -       +      -
----------------------------------------------------------
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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