Contacts of the strand formed by residues 197 - 202 (chain E) in PDB entry 1PPF


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 197 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  MET*     3.3    19.2    -      -       -      +
     40E  HIS*     5.7     0.2    -      -       -      -
     43E  GLY*     3.5    10.9    -      -       -      -
     44E  ALA      4.4     0.2    -      -       -      +
    139E  MET      3.0    26.6    +      -       -      -
    140E  GLY*     4.0     1.6    -      -       -      -
    193E  GLY      4.5     0.3    +      -       -      -
    194E  ASP*     2.9    24.1    +      -       -      -
    195E  SER      3.0     1.6    +      -       -      -
    196E  GLY*     1.4    76.7    -      -       -      +
    198E  PRO*     1.3    72.1    -      -       -      +
    212E  ILE*     3.6     1.4    -      -       -      -
    213E  ALA*     2.9    27.4    +      -       -      +
    228E  PHE*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 198 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29E  PHE*     3.9    22.9    -      -       +      -
     30E  MET*     3.5    18.2    -      -       -      -
     44E  ALA      4.5     0.7    -      -       -      +
     45E  THR*     3.3    25.5    -      -       -      +
    137E  LEU      4.1     0.9    -      -       -      +
    138E  ALA*     3.9     3.5    -      -       -      +
    139E  MET*     3.8    33.7    +      -       +      +
    196E  GLY      4.4     0.2    -      -       -      +
    197E  SER*     1.3    91.7    -      -       -      +
    199E  LEU*     1.3    60.1    -      -       -      +
    200E  VAL*     4.0     2.2    -      -       +      -
    209E  ILE*     3.7    25.4    -      -       +      -
    211E  GLY      3.4     6.5    -      -       -      +
    212E  ILE*     4.9     0.7    -      -       +      -
    228E  PHE*     4.7     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 199 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  CYS*     3.7    11.0    -      -       +      -
    137E  LEU      3.7     9.0    -      -       -      +
    138E  ALA*     4.4     1.1    -      -       +      -
    160E  VAL*     3.6    31.2    -      -       +      -
    181E  VAL*     3.9    26.7    -      -       +      -
    183E  THR*     4.0    14.4    -      -       +      -
    198E  PRO*     1.3    74.5    -      -       -      +
    200E  VAL*     1.3    61.2    +      -       -      +
    201E  CYS*     3.9    20.1    +      -       -      -
    209E  ILE*     3.7     3.1    -      -       -      -
    210E  HIS*     2.9    25.7    +      -       +      -
    211E  GLY*     3.0    24.1    +      -       -      +
    228E  PHE*     3.6    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 200 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  FUC      3.2    38.8    -      -       +      +
     27E  TRP*     5.0     3.6    -      -       +      -
     29E  PHE*     4.4     8.1    -      -       +      -
    136E  CYS*     3.2     2.6    -      -       -      +
    137E  LEU*     3.0    32.9    +      -       +      +
    139E  MET*     3.6    30.5    -      -       +      -
    198E  PRO*     4.4     4.3    -      -       +      -
    199E  LEU*     1.3    77.9    -      -       -      +
    201E  CYS*     1.3    62.0    +      -       -      +
    207E  GLY*     4.4    10.8    -      -       -      +
    208E  LEU      3.4     9.0    -      -       -      +
    209E  ILE*     4.1    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 201 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  FUC      3.5     5.4    -      -       -      +
    130E  LEU*     3.5    29.4    -      -       +      -
    134E  VAL*     4.5     5.2    -      -       +      -
    136E  CYS*     2.0    45.1    -      -       -      -
    199E  LEU*     3.9    15.7    -      -       -      -
    200E  VAL*     1.3    74.9    -      -       -      +
    202E  ASN*     1.3    67.0    +      -       -      +
    207E  GLY      3.2     0.2    -      -       -      -
    208E  LEU*     2.9    25.2    +      -       -      +
    210E  HIS*     3.5    23.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 202 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  FUC      2.9    22.8    +      -       -      -
    130E  LEU*     4.9     6.1    -      -       -      +
    134E  VAL*     4.2    19.5    -      -       -      +
    135E  GLN      5.0     1.7    -      -       -      +
    201E  CYS*     1.3    73.7    +      -       -      +
    207E  GLY*     1.3    58.6    +      -       -      +
    208E  LEU*     3.2    22.3    +      -       +      +
    210E  HIS*     5.7     0.6    +      -       -      -
----------------------------------------------------------
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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