Contacts of the strand formed by residues 307 - 313 (chain B) in PDB entry 2F61


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 307 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278B  LEU      3.5     3.6    +      -       -      -
    279B  LEU*     3.2     8.6    -      -       -      +
    280B  MET*     2.8    25.5    +      -       -      +
    305B  VAL*     3.4     7.9    -      -       -      +
    306B  HIS*     1.3    81.7    -      -       -      +
    308B  ILE*     1.3    64.8    +      -       -      -
    334B  THR*     3.6     7.4    -      -       -      -
    335B  MET*     3.3    21.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279B  LEU*     5.1     0.2    -      -       -      -
    280B  MET*     3.9    17.0    -      -       +      -
    281B  LEU*     3.8    31.2    -      -       +      -
    288B  LEU*     4.0    16.6    -      -       +      -
    292B  ALA*     3.8    17.9    -      -       +      -
    296B  LEU*     4.0     7.6    -      -       +      -
    307B  GLY*     1.3    74.4    -      -       -      -
    309B  ALA*     1.3    59.7    +      -       -      +
    310B  VAL*     3.9     1.6    +      -       +      +
    327B  THR*     3.6    27.6    -      -       +      -
    331B  PHE*     5.2     1.3    -      -       +      -
    334B  THR*     3.7    23.6    -      -       +      +
    335B  MET*     2.8    11.6    +      -       -      +
    336B  LEU*     3.5    11.7    -      -       +      +
    337B  PHE*     2.9    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231B  THR*     4.5     2.9    -      -       +      -
    279B  LEU*     4.1    20.2    -      -       +      -
    280B  MET      3.0    11.0    +      -       -      +
    281B  LEU*     3.5     8.3    -      -       -      +
    282B  ASP*     2.7    41.5    +      -       +      +
    283B  ASP      3.4     2.3    +      -       -      -
    307B  GLY      4.1     1.2    -      -       -      -
    308B  ILE*     1.3    71.2    -      -       -      +
    310B  VAL*     1.3    60.0    +      -       -      +
    337B  PHE*     3.0     9.4    -      -       +      +
    339B  SER*     3.4    22.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281B  LEU*     4.1     7.2    -      -       +      -
    283B  ASP      2.9     6.7    -      -       -      +
    285B  ARG*     4.2    12.8    -      -       +      -
    288B  LEU*     3.9    26.9    -      -       +      -
    308B  ILE*     4.3     8.5    -      -       +      +
    309B  ALA*     1.3    79.5    -      -       -      +
    311B  HIS*     1.3    63.9    +      -       -      +
    312B  TRP*     3.9    19.7    -      -       -      +
    324B  LEU*     4.2    19.7    -      -       +      -
    336B  LEU*     4.8     1.8    -      -       +      -
    337B  PHE      2.8    17.3    +      -       -      +
    338B  ALA*     3.4    12.5    -      -       +      +
    339B  SER      3.0    23.7    +      -       -      -
    340B  GLU      3.8     0.7    +      -       -      -
    370B  ASN*     4.7     2.0    -      -       -      +
    375B  VAL*     5.4     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  ARG*     3.6     2.4    +      -       -      -
    234B  ASN*     3.0    25.6    -      -       -      -
    235B  GLU*     2.6    28.2    +      -       +      +
    282B  ASP*     2.7    44.0    +      -       -      -
    283B  ASP*     2.5    17.0    +      -       -      +
    284B  GLN*     3.5    20.4    -      -       -      +
    285B  ARG*     4.1     6.8    +      -       -      -
    310B  VAL*     1.3    75.6    -      -       -      +
    312B  TRP*     1.3    65.7    +      -       -      +
    313B  TYR*     4.5    10.1    -      -       +      -
    339B  SER*     3.3    17.9    +      -       -      -
    340B  GLU*     3.3    33.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  ARG*     2.9    56.1    -      -       -      -
    310B  VAL*     3.9    12.8    -      -       +      +
    311B  HIS*     1.3    78.5    -      -       -      +
    313B  TYR*     1.3    70.1    +      -       -      +
    314B  LEU*     3.7    13.5    -      -       +      -
    316B  PHE      5.6     4.9    -      -       -      -
    318B  ALA      5.1     3.4    -      -       -      -
    320B  ALA*     5.1     0.7    -      -       +      -
    324B  LEU*     3.8    11.2    -      -       +      -
    338B  ALA*     4.1    18.6    -      -       +      -
    340B  GLU      2.6    10.6    +      -       -      -
    341B  ALA*     3.0    35.6    -      -       +      -
    342B  CYS*     3.3     5.7    +      -       -      -
    366B  SER*     3.7    16.2    -      -       -      +
    369B  THR*     4.5    17.7    -      -       +      -
    370B  ASN*     2.7    42.1    +      -       -      -
    378B  TRP*     4.4     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235B  GLU*     3.2    34.9    +      -       -      -
    244B  TYR*     5.5     0.3    +      -       -      -
    246B  PHE*     6.0     1.4    -      -       -      -
    284B  GLN*     3.8    27.1    -      -       -      +
    311B  HIS*     4.5    11.2    -      -       +      -
    312B  TRP*     1.3    80.1    -      -       -      +
    314B  LEU*     1.3    53.4    +      -       -      +
    315B  ASP      2.7    17.8    +      -       -      +
    316B  PHE*     2.8    47.1    +      +       +      +
    340B  GLU*     4.0    11.2    +      -       -      -
    342B  CYS*     4.0    22.9    -      -       -      -
    345B  SER*     3.7    25.4    -      -       -      +
----------------------------------------------------------
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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