Contacts of the strand formed by residues 240 - 247 (chain B) in PDB entry 2P80


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 LYS 240 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  THR*     3.1    37.3    +      -       -      +
    172B  TYR*     4.4     0.2    -      -       -      -
    173B  ASP*     2.9    53.6    +      -       -      +
    174B  LYS      3.3     3.5    +      -       -      -
    238B  GLY      4.3     6.1    -      -       -      +
    239B  GLU*     1.3    74.1    -      -       -      +
    241B  VAL*     1.3    65.3    +      -       -      +
    292B  PHE*     2.7    32.8    -      -       +      -
    293B  TYR      3.8     2.5    -      -       -      -
    294B  THR*     3.9    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172B  TYR*     4.6     1.8    -      -       -      -
    174B  LYS*     2.9    47.8    -      -       +      +
    176B  TYR*     4.2    11.7    -      -       +      -
    235B  ALA*     4.2    13.7    -      -       +      -
    239B  GLU*     4.0    11.2    -      -       +      +
    240B  LYS*     1.3    78.2    -      -       -      +
    242B  LEU*     1.3    67.2    +      -       -      +
    243B  ILE*     3.8    24.4    +      -       +      +
    291B  ALA      3.6     1.4    -      -       -      +
    292B  PHE*     3.5     3.2    -      -       -      -
    293B  TYR*     3.2    33.4    +      -       -      +
    295B  PHE*     4.4    11.7    -      -       +      -
    320B  PHE*     5.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 242 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  MET*     4.1    11.9    -      -       -      -
    162B  LEU*     4.4    16.6    -      -       +      -
    172B  TYR*     4.0    23.0    -      -       +      +
    174B  LYS      3.1     6.9    +      -       -      -
    175B  ILE*     3.2    31.9    -      -       +      +
    176B  TYR      3.1    22.7    +      -       -      -
    241B  VAL*     1.3    73.7    -      -       -      +
    243B  ILE*     1.3    59.6    +      -       -      +
    244B  VAL*     3.9    15.5    -      -       +      -
    265B  TRP*     3.8    29.6    -      -       +      -
    270B  PHE*     5.7     0.4    -      -       +      -
    290B  ALA*     4.1    10.1    -      -       +      -
    291B  ALA      3.3    15.5    -      -       -      +
    292B  PHE*     3.8    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 243 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  TYR*     3.4    12.6    -      -       +      +
    178B  VAL*     4.4    17.9    -      -       +      -
    241B  VAL*     4.0    22.0    -      -       +      +
    242B  LEU*     1.3    74.3    -      -       -      +
    244B  VAL*     1.3    69.6    +      -       -      +
    245B  HIS*     3.7     3.6    +      -       -      +
    256B  LEU*     5.6     8.7    -      -       +      -
    290B  ALA*     3.7     1.1    -      -       -      -
    291B  ALA*     2.9    38.2    +      -       +      +
    293B  TYR*     6.2     3.4    -      -       +      -
    295B  PHE*     5.6     7.4    -      -       +      -
    303B  TYR*     4.6    34.8    +      -       +      +
    320B  PHE*     4.3    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  LEU*     4.5    10.8    -      -       +      -
    131B  VAL*     3.6    33.7    -      -       +      -
    153B  ALA*     5.2     0.2    -      -       +      -
    155B  MET*     4.2     7.0    -      -       -      -
    175B  ILE*     4.2    10.1    -      -       +      -
    176B  TYR      3.0     9.6    +      -       -      +
    177B  TYR*     3.4    20.4    -      -       +      -
    178B  VAL      2.8    25.6    +      -       -      -
    242B  LEU*     3.9    24.7    -      -       +      -
    243B  ILE*     1.3    75.9    -      -       -      +
    245B  HIS*     1.3    67.3    +      -       -      +
    288B  ALA*     4.7     3.1    -      -       +      -
    289B  GLY      3.4    14.6    -      -       -      +
    290B  ALA*     4.2     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  TYR*     4.4     1.1    -      -       -      -
    178B  VAL*     3.2    20.4    +      -       +      +
    180B  GLU*     2.9    31.5    +      -       +      +
    220B  PHE*     3.5    31.2    -      +       -      -
    243B  ILE*     3.7     4.2    +      -       +      +
    244B  VAL*     1.3    78.3    -      -       -      +
    246B  SER*     1.3    89.8    +      -       -      +
    252B  THR*     4.3    15.4    -      -       +      +
    254B  PRO*     4.6     3.1    -      -       +      +
    283B  ILE*     3.7    17.1    -      -       +      +
    288B  ALA*     3.2     3.2    -      -       -      +
    289B  GLY      2.9    29.6    +      -       -      -
    303B  TYR*     3.0    34.1    +      +       +      +
----------------------------------------------------------
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Residues in contact with SER 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL*     3.0    31.1    -      -       -      +
    151B  ASN*     5.3     2.8    +      -       -      +
    152B  GLY      3.9     0.5    +      -       -      -
    153B  ALA*     3.8     4.5    -      -       -      -
    177B  TYR*     2.4    32.3    +      -       -      -
    178B  VAL      3.4     3.0    +      -       -      -
    179B  GLY*     3.8     1.9    -      -       -      -
    180B  GLU      3.0    26.7    +      -       -      +
    245B  HIS*     1.3    83.6    -      -       -      +
    247B  GLN*     1.3    60.0    +      -       -      +
    248B  ALA      4.2     0.4    -      -       -      -
    283B  ILE*     5.3     0.4    -      -       -      -
    287B  ALA      3.9     0.4    -      -       -      -
    288B  ALA*     3.4    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL*     4.7     0.9    -      -       -      -
    180B  GLU*     3.7    44.8    +      -       +      +
    181B  GLN*     5.0     1.0    +      -       -      -
    182B  ASP*     2.9    35.8    +      -       -      +
    246B  SER*     1.3    72.6    -      -       -      +
    248B  ALA*     1.3    63.0    +      -       -      +
    249B  ASN*     3.2     9.0    +      -       -      +
    250B  ARG*     3.0    41.3    -      -       +      +
    252B  THR*     4.2    15.5    -      -       +      -
    283B  ILE*     5.0     2.5    -      -       +      +
    285B  GLY*     3.6     1.6    -      -       -      -
    286B  GLY      2.7    23.2    +      -       -      -
    287B  ALA      3.3    15.7    +      -       -      +
----------------------------------------------------------
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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