Contacts of the strand formed by residues 799 - 806 (chain M) 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 ILE 799 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63K  HIS*     5.4     3.1    -      -       +      -
     64K  GLU*     5.9     2.9    -      -       +      +
     65K  PHE*     3.4    37.7    -      -       +      -
    154K  GLU*     6.2     0.4    -      -       -      +
    165K  ILE*     6.2     5.8    -      -       +      -
    746M  GLY*     3.8    17.3    -      -       -      +
    747M  ALA      3.1    25.4    -      -       -      -
    748M  GLU*     3.3    14.1    -      -       +      +
    798M  GLY*     1.3    79.3    -      -       -      -
    800M  VAL*     1.3    62.8    +      -       -      +
    801M  VAL*     3.2     4.2    +      -       -      +
    827M  VAL*     3.2     3.9    -      -       -      +
    828M  ALA      2.7    31.0    +      -       -      +
    829M  GLN*     5.1     3.8    -      -       +      -
    830M  LYS      5.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 800 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    743M  VAL*     3.5    39.5    -      -       +      +
    744M  ARG      3.8    11.4    -      -       -      +
    745M  ILE*     3.2     8.9    -      -       +      +
    746M  GLY*     2.7    29.2    +      -       -      -
    747M  ALA      3.0     8.6    +      -       -      +
    749M  VAL*     3.6    29.4    -      -       +      -
    755M  LEU*     4.4     7.0    -      -       +      -
    799M  ILE*     1.3    70.9    -      -       -      +
    801M  VAL*     1.3    58.1    +      -       -      +
    802M  ARG      3.9     2.2    -      -       -      +
    803M  THR*     3.7    22.2    -      -       +      -
    825M  VAL*     3.9     4.3    -      -       +      -
    826M  TYR      3.6    11.9    -      -       -      +
    827M  VAL*     4.4     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 801 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63K  HIS*     3.6    27.3    +      -       +      +
     65K  PHE*     3.3    42.2    -      -       +      -
    705M  ILE*     4.8     8.3    -      -       +      -
    745M  ILE*     3.2    16.0    -      -       -      +
    799M  ILE      3.2     7.6    +      -       -      +
    800M  VAL*     1.3    73.7    -      -       -      +
    802M  ARG*     1.3    83.8    +      -       +      +
    826M  TYR*     3.0    24.9    +      -       +      +
    827M  VAL      4.7     0.2    -      -       -      +
    828M  ALA*     3.8    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 802 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63K  HIS*     5.6     0.9    -      -       -      +
     85M  GLU*     5.2    10.7    +      -       -      +
    627M  ARG*     5.7     5.7    -      -       -      +
    628M  PHE      5.1    11.0    -      -       -      -
    745M  ILE*     3.8     7.0    -      -       -      -
    800M  VAL*     3.7     0.5    -      -       -      +
    801M  VAL*     1.3   102.1    -      -       +      +
    803M  THR*     1.3    78.7    +      -       -      +
    804M  VAL*     4.2    14.6    -      -       -      +
    825M  VAL      3.8     0.2    -      -       -      -
    826M  TYR*     2.9    55.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 803 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    739M  GLU*     5.2     4.0    +      -       -      -
    742M  VAL*     3.8    32.3    -      -       +      +
    743M  VAL*     3.9     4.7    -      -       +      +
    745M  ILE*     4.2    14.6    -      -       +      +
    800M  VAL*     3.7    21.1    -      -       +      -
    802M  ARG*     1.3    89.8    +      -       -      +
    804M  VAL*     1.3    67.6    +      -       -      +
    805M  ARG      4.5     0.2    +      -       -      -
    823M  VAL*     6.0     0.7    -      -       -      -
    824M  ARG      3.3    11.7    -      -       -      +
    825M  VAL*     4.3     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 804 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85M  GLU*     4.0    25.6    -      -       +      +
    742M  VAL*     6.5     0.2    -      -       -      -
    802M  ARG*     4.2    20.6    -      -       -      +
    803M  THR*     1.3    80.1    -      -       -      +
    805M  ARG*     1.3    59.7    +      -       -      +
    806M  LEU*     3.4    26.4    -      -       +      +
    822M  VAL*     3.8     1.0    -      -       -      +
    823M  VAL*     3.2     7.9    -      -       -      +
    824M  ARG*     2.8    71.2    +      -       +      +
    826M  TYR*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 805 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722M  ILE*     4.0    32.3    +      -       -      +
    740M  GLU      4.1    17.8    +      -       -      -
    742M  VAL*     4.8    16.9    -      -       +      +
    803M  THR      4.4     0.2    -      -       -      -
    804M  VAL*     1.3    75.4    -      -       -      +
    806M  LEU*     1.3    67.7    +      -       -      +
    807M  ARG*     3.9    42.1    +      -       +      +
    821M  GLU*     3.7    19.0    +      -       -      +
    822M  VAL      3.7     4.3    -      -       -      +
    823M  VAL*     4.7     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 806 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85M  GLU*     4.8     6.1    -      -       -      +
     86M  LYS*     4.8    11.2    -      -       +      -
    804M  VAL*     3.4    27.8    -      -       +      -
    805M  ARG*     1.3    78.8    -      -       -      +
    807M  ARG*     1.3    63.7    +      -       -      +
    810M  ASP*     4.0    10.9    -      -       -      +
    811M  PRO*     6.5     0.4    -      -       +      -
    813M  VAL*     4.3    26.7    -      -       +      -
    815M  LEU*     4.4     4.2    -      -       +      +
    821M  GLU*     2.9    27.8    -      -       -      +
    822M  VAL*     3.2    36.5    +      -       +      -
    824M  ARG*     4.3    13.0    -      -       -      +
----------------------------------------------------------
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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