Contacts of the strand formed by residues 10 - 16 (chain B) in PDB entry 2PPB


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 10 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  ASN*     5.2     2.9    -      -       -      +
    229A  GLN*     4.5    23.6    -      -       +      +
      8B  ALA      2.9    13.6    +      -       -      +
      9B  PRO*     1.3    68.9    -      -       -      +
     11B  PHE*     1.3    65.7    +      -       -      +
     12B  THR*     3.2    26.3    +      -       +      +
     24B  VAL      3.3     6.4    -      -       -      +
     25B  LEU*     3.7     2.8    -      -       -      -
     26B  GLU*     2.8    37.3    +      -       -      +
     27B  PRO*     5.1     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  TYR      3.7    12.3    -      -       -      +
    225A  PHE*     3.0    66.2    -      +       +      -
    226A  SER      4.9     2.2    -      -       -      -
    227A  ASN*     2.9    36.6    +      -       -      +
    228A  PRO*     3.3     6.5    -      -       +      -
    229A  GLN*     3.1    16.6    +      -       -      +
      9B  PRO      3.2     5.3    +      -       -      -
     10B  VAL*     1.3    71.5    -      -       -      +
     12B  THR*     1.3    59.3    +      -       -      +
     13B  VAL*     4.6    15.0    -      -       +      -
     23B  PHE*     4.1    21.8    -      +       +      -
     24B  VAL      3.5    14.8    -      -       -      -
     25B  LEU*     3.8    14.8    -      -       +      +
    208B  LEU*     4.8     3.4    -      -       +      -
    211B  LEU*     3.4    27.6    -      -       +      -
    212B  ASN*     5.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  GLN*     3.9    15.0    -      -       +      -
     10B  VAL*     3.2    31.4    -      -       +      +
     11B  PHE*     1.3    76.7    -      -       -      +
     13B  VAL*     1.3    65.5    +      -       -      +
     14B  ARG*     3.5    13.6    +      -       -      -
     22B  GLU      4.2     0.2    -      -       -      +
     23B  PHE*     3.7     3.3    -      -       -      +
     24B  VAL*     2.9    48.8    +      -       +      +
     26B  GLU*     4.4     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  PRO*     3.8    33.0    -      -       +      -
    229A  GLN      3.3    22.0    +      -       -      +
     11B  PHE*     4.6    10.8    -      -       +      -
     12B  THR*     1.3    78.5    -      -       -      +
     14B  ARG*     1.3    73.8    +      -       -      +
     15B  THR*     5.3     8.7    -      -       +      +
     22B  GLU      3.9     2.9    -      -       -      -
     23B  PHE*     4.0    21.1    -      -       +      -
    208B  LEU*     4.2    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  THR*     3.5    26.5    +      -       -      -
     13B  VAL*     1.3    80.7    -      -       -      +
     15B  THR*     1.3    59.4    +      -       -      +
     16B  GLN*     4.3     9.9    +      -       -      +
     20B  TYR*     5.3     3.6    -      -       -      -
     21B  GLY*     3.5     1.0    -      -       -      -
     22B  GLU*     2.9    64.8    +      -       +      +
     24B  VAL*     3.4    25.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  VAL*     5.5     8.3    -      -       +      -
     14B  ARG*     1.3    76.1    -      -       -      +
     16B  GLN*     1.3    68.6    +      -       -      +
     17B  GLY      3.3    14.8    +      -       -      +
     20B  TYR      3.0    18.2    +      -       -      -
     21B  GLY*     4.0     7.2    -      -       -      -
     23B  PHE*     5.3     7.6    -      -       +      -
    206B  THR*     4.6     2.6    +      -       -      +
    207B  PRO*     4.5     8.0    -      -       -      +
    208B  LEU*     5.6    11.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ARG*     4.9     7.3    -      -       -      +
     15B  THR*     1.3    83.1    +      -       -      +
     17B  GLY*     1.3    67.0    +      -       -      +
     19B  GLU*     3.9     2.3    -      -       -      +
     20B  TYR*     3.2    40.5    +      -       +      +
----------------------------------------------------------
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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