Contacts of the strand formed by residues 224 - 231 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  PRO      4.6     0.5    -      -       -      +
    216B  ARG*     3.0    24.9    +      -       -      +
    217B  GLY*     3.2    10.7    +      -       -      -
    222B  ASP*     5.4     2.5    -      -       +      -
    223B  ARG*     1.3    76.0    -      -       -      +
    225B  THR*     1.3    60.8    +      -       -      +
    226B  TRP*     4.1     1.6    +      -       -      -
    248B  LEU*     3.6    15.9    -      -       +      +
    249B  VAL      3.0    10.8    -      -       -      +
    250B  ASN*     4.0     9.9    -      -       +      +
    262B  GLN*     3.7    27.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  THR*     3.4    25.1    -      -       -      +
    213B  THR*     3.6    11.2    -      -       -      +
    215B  PRO      5.3     0.7    -      -       -      -
    216B  ARG*     2.8    29.0    +      -       +      +
    224B  ALA*     1.3    72.3    -      -       -      +
    226B  TRP*     1.3    69.6    +      -       -      +
    227B  PHE*     3.5    22.6    +      -       +      -
    247B  LEU      3.3     2.8    -      -       -      +
    248B  LEU*     3.8     2.7    -      -       -      -
    249B  VAL      2.8    36.7    +      -       -      +
    251B  HIS*     2.7    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 226 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553A  TRP*     3.4    33.0    -      +       -      +
    213B  THR*     2.7    45.6    +      -       -      +
    215B  PRO      5.7     0.6    +      -       -      -
    224B  ALA      4.1     1.5    +      -       -      -
    225B  THR*     1.3    71.8    -      -       -      +
    227B  PHE*     1.3    60.9    +      -       -      +
    228B  GLY      4.1     0.3    +      -       -      -
    246B  GLU*     3.6    27.4    -      -       +      -
    247B  LEU      3.4    13.9    -      -       -      -
    248B  LEU*     3.3    61.2    -      -       +      +
    263B  LYS*     3.8    23.8    -      -       +      -
    264B  VAL      4.5     0.9    -      -       -      -
    265B  PHE*     4.3     7.0    -      -       +      -
    270B  TYR*     4.9     0.9    -      +       -      -
    377B  PRO*     3.5    33.2    -      -       +      -
    378B  ALA*     4.1    14.1    -      -       +      +
    381B  THR*     4.2    17.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 227 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  TYR*     4.2    14.6    -      +       +      -
    179B  ILE*     3.7    42.6    -      -       +      -
    180B  ASP*     5.5     0.4    -      -       -      -
    183B  ILE*     4.5     8.1    -      -       +      -
    210B  THR*     3.8    31.2    -      -       +      -
    211B  MET      3.6     4.7    -      -       -      -
    212B  THR*     3.6    36.3    -      -       -      -
    216B  ARG*     4.9     0.9    -      -       -      -
    225B  THR*     3.5    37.7    -      -       +      -
    226B  TRP*     1.3    71.4    -      -       -      +
    228B  GLY*     1.3    59.3    +      -       -      +
    229B  LEU*     4.4     2.9    -      -       +      +
    246B  GLU*     3.2     4.5    -      -       -      -
    247B  LEU*     2.7    43.5    +      -       +      +
    249B  VAL*     3.9    15.9    -      -       +      -
    251B  HIS*     4.7     0.2    -      -       -      -
    378B  ALA*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 228 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  THR*     3.2     7.3    -      -       -      -
    211B  MET      3.1    31.2    +      -       -      -
    213B  THR*     5.7     0.4    -      -       -      +
    226B  TRP      4.1     1.4    +      -       -      -
    227B  PHE*     1.3    74.4    -      -       -      +
    229B  LEU*     1.3    62.0    +      -       -      +
    230B  TYR*     3.4    15.9    +      -       -      -
    242B  HIS*     4.1     4.9    -      -       -      -
    245B  LEU      3.7     7.6    -      -       -      -
    246B  GLU*     4.1    12.5    -      -       -      +
    378B  ALA*     5.2     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 229 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  ILE*     4.6     1.8    -      -       +      -
    184B  PHE*     3.8    19.5    -      -       +      -
    188B  LEU*     3.9    14.8    -      -       +      -
    208B  LEU*     3.7    28.7    -      -       +      -
    209B  VAL      3.2     6.3    -      -       -      +
    210B  THR*     4.2    12.3    -      -       +      -
    227B  PHE*     4.4     3.1    -      -       +      +
    228B  GLY*     1.3    77.1    -      -       -      +
    230B  TYR*     1.3    62.3    -      -       -      +
    242B  HIS*     3.8     5.6    +      -       -      -
    243B  VAL*     3.1    38.9    +      -       +      +
    245B  LEU*     3.1    29.3    +      -       +      +
    247B  LEU*     3.7    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  LEU*     3.2     8.5    -      -       -      +
    209B  VAL*     2.7    42.4    +      -       +      +
    211B  MET*     3.7    34.7    +      -       +      +
    228B  GLY*     3.4    27.3    -      -       -      -
    229B  LEU*     1.3    76.4    -      -       -      +
    231B  TYR*     1.3    62.6    +      -       -      +
    238B  PHE*     3.5    46.2    -      +       +      +
    239B  PHE*     3.8    19.3    -      -       +      -
    241B  HIS      3.3     7.6    -      -       -      +
    242B  HIS*     3.4    46.9    +      +       +      -
    243B  VAL*     4.3     1.3    -      -       -      -
    496B  SER*     5.8     1.7    -      -       -      -
    497B  SER      4.0     6.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  CYS      3.2    17.2    +      -       -      -
    199B  CYS*     3.4    27.7    -      -       -      +
    200B  PHE*     3.7     2.6    -      +       -      -
    207B  ASN*     3.7    10.5    -      -       -      -
    208B  LEU*     3.9    11.0    -      -       +      -
    209B  VAL*     4.5     0.2    -      -       -      -
    230B  TYR*     1.3    73.1    -      -       -      +
    232B  ASN*     1.3    60.1    +      -       -      +
    233B  ILE*     2.8    29.0    +      -       +      +
    238B  PHE*     3.4    16.8    -      -       -      +
    241B  HIS*     3.2    22.9    +      +       +      -
    243B  VAL*     3.7    19.2    -      -       +      +
    291B  ILE*     2.6    37.5    +      -       +      +
    292B  PRO      3.3    27.1    -      -       -      -
    293B  ASP*     3.7    24.2    -      -       +      -
----------------------------------------------------------
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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