Contacts of the strand formed by residues 305 - 312 (chain B) in PDB entry 2A1H


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 305 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  VAL*     4.6     2.5    -      -       +      -
    246B  TYR      4.4     3.1    -      -       -      +
    247B  TRP*     4.0    11.7    -      -       +      -
    296B  LEU*     4.0    13.9    -      -       +      -
    299B  ALA*     3.6    32.2    +      -       +      -
    300B  LEU*     4.0    21.5    -      -       +      +
    303B  GLY*     3.5     6.5    -      -       -      +
    304B  ARG*     1.3    75.8    -      -       -      +
    306B  ARG*     1.3    63.5    +      -       -      +
    307B  GLU      4.2     6.3    -      -       -      +
    308B  VAL*     3.9    28.5    -      -       +      -
    332B  ILE*     4.3    12.1    -      -       +      -
    333B  PRO*     3.3    19.9    -      -       +      +
    337B  ASN*     4.0     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 306 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  TYR*     2.9    41.5    +      -       +      +
    247B  TRP*     4.7     3.1    -      -       -      +
    248B  THR*     4.8     7.9    +      -       -      -
    254B  LEU*     3.7    39.0    -      -       -      +
    303B  GLY      6.0     0.7    -      -       -      +
    304B  ARG      3.6     6.3    +      -       -      +
    305B  VAL*     1.3    77.5    -      -       -      +
    307B  GLU*     1.3    70.2    +      -       +      +
    333B  PRO      3.4    10.7    -      -       -      +
    334B  THR*     3.4     3.3    +      -       -      -
    337B  ASN*     2.9    36.2    +      -       +      +
    340B  GLU*     4.0    19.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 307 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  VAL*     3.5     2.1    -      -       -      +
    246B  TYR*     2.7    55.1    +      -       +      +
    305B  VAL*     4.5     0.4    -      -       -      +
    306B  ARG*     1.3    83.7    -      -       -      +
    308B  VAL*     1.3    64.6    +      -       -      +
    309B  PHE*     4.3     8.4    -      -       +      -
    334B  THR*     3.7    25.8    -      -       +      +
    337B  ASN*     4.1     6.6    -      -       +      +
    339B  PRO*     3.4    11.1    -      -       +      +
    340B  GLU*     3.4     8.6    +      -       -      +
    341B  LEU*     2.9    29.2    +      -       -      +
    342B  ILE*     3.0    36.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  LEU*     5.7     0.7    -      -       +      -
    235B  LEU*     5.8     1.1    -      -       +      -
    243B  ILE*     4.1    22.0    -      -       +      -
    244B  PHE      3.4    10.8    -      -       -      +
    245B  VAL*     4.0    17.9    -      -       +      -
    296B  LEU*     4.5    10.1    -      -       +      -
    305B  VAL*     3.9    13.0    -      -       +      -
    307B  GLU*     1.3    79.4    -      -       -      +
    309B  PHE*     1.3    66.5    +      -       -      +
    320B  VAL*     3.1    42.6    +      -       +      -
    323B  ILE*     5.2     7.0    -      -       +      -
    332B  ILE*     3.7    28.0    -      -       +      -
    334B  THR*     3.1    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  VAL*     5.0     0.7    -      -       -      -
    243B  ILE*     3.5     5.2    -      -       -      +
    244B  PHE*     2.8    68.0    +      +       +      +
    246B  TYR*     4.7     2.5    -      -       +      -
    256B  LEU*     3.9    14.6    -      -       +      -
    274B  LEU*     3.8    22.7    -      -       +      -
    307B  GLU*     4.4     9.0    -      -       +      -
    308B  VAL*     1.3    81.8    -      -       -      +
    310B  GLY*     1.3    71.3    +      -       -      +
    317B  VAL*     3.9    16.2    -      -       +      -
    318B  CYS      3.2    16.8    -      -       -      +
    320B  VAL*     4.3     6.1    -      -       -      -
    341B  LEU*     4.3     9.0    -      -       +      -
    342B  ILE*     3.7    33.7    -      -       +      -
    345B  PHE*     3.8    24.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  VAL*     4.4    11.4    -      -       -      -
    241B  MET*     4.3     9.9    -      -       -      -
    242B  ASN      3.1     9.9    -      -       -      -
    309B  PHE*     1.3    76.8    -      -       -      +
    311B  SER*     1.3    60.7    +      -       -      -
    315B  CYS*     4.3     4.9    -      -       -      -
    317B  VAL*     3.4     4.5    -      -       -      -
    318B  CYS*     2.8    40.1    +      -       -      -
    320B  VAL*     4.8     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  MET*     3.3    10.1    -      -       -      +
    242B  ASN*     2.8    40.0    +      -       -      +
    244B  PHE*     3.4    21.2    -      -       -      -
    270B  VAL*     4.0     5.6    -      -       -      -
    271B  ARG*     3.7    10.9    +      -       -      +
    274B  LEU*     3.9    23.8    -      -       -      -
    310B  GLY*     1.3    75.6    -      -       -      -
    312B  GLY*     1.3    57.9    +      -       -      +
    315B  CYS*     4.3     0.9    -      -       -      -
    316B  GLN      3.3    12.6    -      -       -      -
    400B  PLP      4.1     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  MET*     4.6     2.0    -      -       -      -
    270B  VAL*     3.6     9.1    -      -       -      +
    311B  SER*     1.3    76.4    -      -       -      +
    313B  THR*     1.3    59.7    +      -       -      -
    314B  ALA      3.3     2.7    -      -       -      -
    315B  CYS*     4.0     4.1    -      -       -      -
    316B  GLN*     2.7    35.3    +      -       -      -
    400B  PLP      3.7    17.0    -      -       -      -
    501B  GBN      3.6    14.1    -      -       -      -
----------------------------------------------------------
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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