Contacts of the strand formed by residues 305 - 312 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  VAL*     4.5     2.2    -      -       +      -
    246A  TYR      4.1     6.7    -      -       -      +
    247A  TRP*     3.9     9.9    -      -       +      -
    296A  LEU*     4.0    13.0    -      -       +      -
    299A  ALA*     3.7    28.4    +      -       +      -
    300A  LEU*     3.9    26.7    -      -       +      +
    303A  GLY*     3.5     5.8    -      -       -      +
    304A  ARG*     1.3    77.2    -      -       -      +
    306A  ARG*     1.3    64.8    -      -       -      +
    307A  GLU      4.1     4.3    -      -       -      +
    308A  VAL*     3.9    27.8    -      -       +      -
    332A  ILE*     4.2    12.8    -      -       +      -
    333A  PRO*     3.4    21.5    -      -       +      +
    337A  ASN*     3.9     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  TYR*     2.9    53.7    +      -       +      +
    247A  TRP*     5.0     0.7    -      -       -      -
    248A  THR*     5.4     2.7    -      -       -      +
    254A  LEU*     3.8    34.1    -      -       -      +
    304A  ARG      3.7     7.2    +      -       -      +
    305A  VAL*     1.3    76.8    -      -       -      +
    307A  GLU*     1.3    68.4    +      -       +      +
    333A  PRO      3.5     1.0    -      -       -      +
    334A  THR*     3.5    12.5    +      -       -      -
    337A  ASN*     3.0    39.9    +      -       +      +
    340A  GLU*     3.1    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  PHE      4.2     0.2    -      -       -      +
    246A  TYR*     2.7    54.0    +      -       +      +
    305A  VAL*     4.0     1.3    -      -       -      +
    306A  ARG*     1.3    88.3    +      -       -      +
    308A  VAL*     1.3    66.7    +      -       -      +
    309A  PHE*     4.5     5.5    -      -       +      -
    334A  THR*     3.7    26.9    -      -       +      +
    337A  ASN*     4.1     5.2    -      -       +      +
    339A  PRO*     3.5     4.4    -      -       -      +
    340A  GLU*     3.5    14.6    +      -       -      +
    341A  LEU*     2.9    30.2    +      -       -      +
    342A  ILE*     3.0    40.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  LEU*     5.7     0.2    -      -       +      -
    235A  LEU*     5.9     0.9    -      -       +      -
    243A  ILE*     4.1    22.7    -      -       +      -
    244A  PHE      3.4    11.0    -      -       -      +
    245A  VAL*     4.0    18.4    -      -       +      -
    296A  LEU*     4.6     8.7    -      -       +      -
    305A  VAL*     3.9    11.9    -      -       +      -
    307A  GLU*     1.3    78.8    -      -       -      +
    309A  PHE*     1.3    67.0    +      -       -      +
    319A  PRO*     3.8     1.6    -      -       -      +
    320A  VAL*     3.0    43.3    +      -       +      -
    323A  ILE*     5.2     6.3    -      -       +      -
    332A  ILE*     3.6    26.2    -      -       +      -
    334A  THR*     3.1    11.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 309 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  VAL*     5.0     0.4    -      -       -      -
    243A  ILE*     3.6     6.1    -      -       -      +
    244A  PHE*     2.8    64.9    +      +       +      +
    246A  TYR*     4.8     2.7    -      -       +      -
    256A  LEU*     3.9    10.5    -      -       +      -
    274A  LEU*     3.7    16.2    -      -       +      -
    307A  GLU*     4.5     6.7    -      -       +      -
    308A  VAL*     1.3    82.5    -      -       -      +
    310A  GLY*     1.3    63.4    +      -       -      +
    317A  VAL*     3.7    29.6    -      -       +      -
    318A  CYS      3.2    20.6    -      -       -      +
    320A  VAL*     4.3     6.5    -      -       -      -
    341A  LEU*     4.2    14.4    -      -       +      -
    342A  ILE*     3.7    28.0    -      -       +      -
    345A  PHE*     3.7    24.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  VAL*     4.4    11.9    -      -       -      -
    241A  MET*     4.0    20.1    -      -       -      +
    242A  ASN      3.1     9.2    -      -       -      -
    309A  PHE*     1.3    76.0    -      -       -      +
    311A  SER*     1.3    60.1    +      -       -      -
    317A  VAL*     3.5     4.3    -      -       -      -
    318A  CYS*     2.8    36.5    +      -       -      +
    320A  VAL*     4.7     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 311 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  MET*     3.3    10.7    -      -       -      +
    242A  ASN*     2.8    43.8    +      -       -      +
    244A  PHE*     3.4    20.3    -      -       -      -
    270A  VAL*     4.0     5.8    -      -       -      -
    271A  ARG*     3.8    10.2    +      -       -      -
    274A  LEU*     3.9    22.9    -      -       -      -
    309A  PHE*     5.2     0.2    -      -       -      -
    310A  GLY*     1.3    74.0    -      -       -      -
    312A  GLY*     1.3    58.9    +      -       -      +
    316A  GLN      3.3    14.4    -      -       -      -
    317A  VAL*     5.1     0.2    -      -       -      -
    400A  PLP      4.0     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  MET*     4.4     4.2    -      -       -      +
    270A  VAL*     3.6     9.8    -      -       -      +
    311A  SER*     1.3    76.5    -      -       -      +
    313A  THR*     1.3    60.7    +      -       -      -
    314A  ALA      3.4     2.5    -      -       -      -
    315A  CYS      4.2     0.9    -      -       -      -
    316A  GLN*     2.8    33.1    +      -       -      +
    400A  PLP      3.7    16.6    -      -       -      -
    502A  GBN      3.4    13.7    -      -       -      -
----------------------------------------------------------
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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