Contacts of the strand formed by residues 956 - 962 (chain B) in PDB entry 2PDA


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 SER 956 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    828B  PHE*     4.5     6.1    -      -       -      -
    831B  ARG*     2.6    24.1    +      -       -      +
    832B  MET*     3.0    11.7    -      -       -      +
    833B  PHE      2.8    23.5    +      -       -      -
    954B  LYS*     4.6     0.4    -      -       -      +
    955B  LYS*     1.3    71.9    -      -       -      +
    957B  VAL*     1.3    59.4    +      -       -      +
    958B  TRP*     2.6    33.0    +      -       -      -
    985B  ASN*     3.5     1.2    +      -       -      -
   1057B  GLU*     2.7    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 957 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    833B  PHE*     3.9    29.8    -      -       +      -
    876B  GLY*     3.2    32.1    -      -       -      +
    879B  MET*     4.6     3.8    -      -       +      -
    880B  ASN*     4.4    24.5    -      -       -      +
    883B  MET*     5.1     6.7    -      -       +      -
    954B  LYS*     5.2     2.1    -      -       -      +
    955B  LYS      3.9     6.6    +      -       -      +
    956B  SER*     1.3    72.7    +      -       -      +
    958B  TRP*     1.3    68.4    +      -       -      +
    959B  ILE*     5.2     0.4    -      -       +      -
    983B  ASP*     4.6     5.6    +      -       -      +
    984B  VAL*     3.6    14.7    -      -       +      +
    985B  ASN*     2.9    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 958 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    824B  ILE*     4.1     8.5    -      -       +      -
    828B  PHE*     3.3    34.9    -      +       -      -
    832B  MET*     3.5    28.4    -      -       +      +
    833B  PHE      2.7    17.5    +      -       -      +
    834B  ILE*     4.4     1.8    -      -       +      -
    835B  ALA*     3.0    24.8    +      -       -      +
    956B  SER*     2.6    37.3    +      -       -      -
    957B  VAL*     1.3    77.1    -      -       -      +
    959B  ILE*     1.3    65.1    +      -       -      +
    960B  PHE*     3.9    22.9    -      +       +      -
    985B  ASN*     3.2    33.2    -      -       +      -
    986B  VAL      4.9     1.1    -      -       -      -
    987B  PHE*     3.9    22.0    -      +       +      -
   1053B  LEU*     3.8    26.7    -      -       +      -
   1056B  ALA*     5.2     7.6    -      -       +      -
   1057B  GLU*     3.8    11.4    -      -       +      -
   1065B  VAL*     5.4     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 959 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    835B  ALA      3.5     5.2    -      -       -      +
    872B  ALA*     3.5    12.6    -      -       +      +
    873B  ALA*     3.4    51.6    -      -       +      +
    876B  GLY*     4.2    14.6    -      -       -      +
    957B  VAL*     5.0     0.4    -      -       +      +
    958B  TRP*     1.3    78.3    -      -       -      +
    960B  PHE*     1.3    60.9    +      -       -      +
    965B  TRP*     3.9    16.6    -      -       +      -
    977B  VAL*     4.3     3.1    -      -       +      -
    984B  VAL*     4.3    22.4    -      -       +      -
    985B  ASN      2.8    14.0    +      -       -      +
    986B  VAL*     3.4    21.5    -      -       +      +
    987B  PHE      2.9    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 960 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    821B  VAL*     4.0    21.1    -      -       +      -
    824B  ILE*     4.2    16.8    -      -       +      -
    825B  THR*     5.7     0.4    -      -       +      -
    832B  MET*     4.0     9.6    -      -       +      -
    834B  ILE*     3.4    42.0    -      -       +      -
    835B  ALA      2.9     7.8    +      -       -      +
    836B  ASN*     3.3    26.6    -      -       -      +
    837B  ALA*     2.7    34.0    +      -       -      +
    841B  SER*     5.1     2.2    -      -       -      +
    844B  TRP*     5.8     0.7    -      +       -      -
    853B  TYR*     3.6    11.4    -      +       -      -
    872B  ALA*     4.4     0.9    -      -       -      +
    958B  TRP*     3.9    21.7    -      +       +      -
    959B  ILE*     1.3    80.6    -      -       -      +
    961B  GLY*     1.3    53.8    +      -       -      +
    965B  TRP*     4.7     2.5    -      -       -      -
    987B  PHE*     3.7    30.3    -      +       +      +
    989B  MET*     5.3     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 961 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    836B  ASN*     4.7     0.2    -      -       -      -
    837B  ALA*     3.8    10.5    -      -       -      -
    838B  THR      5.6     0.4    -      -       -      -
    841B  SER*     4.2    12.2    +      -       -      -
    960B  PHE*     1.3    76.2    -      -       -      +
    962B  GLY*     1.3    62.0    -      -       -      -
    965B  TRP*     3.6    17.9    -      -       -      -
    987B  PHE      3.2     4.7    +      -       -      +
    988B  VAL*     3.0    11.3    -      -       -      -
    989B  MET*     3.0    22.1    +      -       -      +
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Residues in contact with GLY 962 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    838B  THR      5.4     1.4    +      -       -      -
    841B  SER*     4.5     2.2    +      -       -      -
    961B  GLY*     1.3    75.5    -      -       -      -
    963B  ASP*     1.3    59.2    +      -       -      -
    965B  TRP*     3.5     2.6    +      -       -      +
    966B  ALA*     3.1    27.7    +      -       -      +
    988B  VAL*     3.6     4.3    -      -       -      -
    989B  MET*     3.1    18.8    -      -       -      -
   1243B  TPP      3.2    31.1    +      -       -      -
----------------------------------------------------------
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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