Contacts of the strand formed by residues 37 - 41 (chain S) in PDB entry 1O19


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 37 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32S  PHE*     3.8    23.4    -      -       -      -
     33S  ASP*     2.4    38.5    +      -       -      +
     34S  ALA*     3.4    10.6    -      -       -      +
     36S  SER*     1.4    72.2    -      -       -      +
     38S  VAL*     1.3    71.4    +      -       -      +
     50S  GLY      4.0     5.4    -      -       -      -
     51S  THR*     4.7     5.6    -      -       -      +
     79S  SER*     4.6     0.9    -      -       -      -
     80S  MET*     3.9    22.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 38 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34S  ALA      5.1     1.6    -      -       -      +
     35S  MLY      5.5     0.9    -      -       -      +
     36S  SER      4.0     1.1    -      -       -      +
     37S  SER*     1.3    85.0    -      -       -      +
     39S  PHE*     1.3    78.2    +      -       -      +
     40S  VAL*     4.6     3.8    -      -       +      -
     49S  MLY      3.7     5.4    -      -       -      +
     50S  GLY      2.7    41.3    +      -       -      +
     52S  ILE*     3.3    37.5    -      -       +      -
     62S  VAL*     5.2     1.8    -      -       +      -
     77S  VAL*     4.0    23.6    -      -       +      -
     78S  PHE      3.5    12.8    -      -       -      +
     79S  SER*     4.4     7.0    -      -       -      +
     80S  MET*     4.1    11.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 39 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38S  VAL*     1.3    85.9    -      -       -      +
     40S  VAL*     1.3    62.1    +      -       -      +
     47S  PHE*     5.3     0.9    -      -       +      -
     48S  VAL      3.9     3.1    -      -       -      -
     49S  MLY      3.7    39.9    -      -       +      -
     78S  PHE*     2.5    34.4    +      -       +      +
     79S  SER      3.2    21.1    -      -       -      -
     80S  MET*     4.0    21.8    -      -       +      -
     81S  ASN*     5.0     2.2    -      -       -      -
     98S  HIS*     4.4     2.9    -      +       -      -
    100S  PRO*     3.7    28.7    -      -       +      -
    101S  ALA*     3.9    20.9    -      -       +      -
    104S  TYR*     3.5    48.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 40 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38S  VAL*     4.6     4.7    -      -       +      +
     39S  PHE*     1.3    75.7    -      -       -      +
     41S  VAL*     1.3    74.2    +      -       -      +
     42S  HIS*     5.1     0.2    -      -       +      -
     47S  PHE*     3.1    12.4    -      -       -      -
     48S  VAL*     2.9    49.0    +      -       +      +
     49S  MLY      5.5     2.9    -      -       -      -
     50S  GLY      5.9     0.2    -      -       -      +
     62S  VAL*     5.0    18.4    -      -       +      -
     63S  MLY      6.0     0.7    -      -       -      +
     70S  LEU*     5.9     6.5    -      -       +      -
     72S  VAL*     3.5    24.9    -      -       +      -
     76S  GLN      2.8    23.8    -      -       -      +
     77S  VAL*     3.9     9.9    -      -       +      -
     78S  PHE*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40S  VAL*     1.3    92.3    -      -       +      +
     42S  HIS*     1.3    77.1    +      -       -      +
     43S  PRO*     4.3     6.3    -      -       +      +
     46S  SER      3.9     5.6    -      -       -      +
     47S  PHE*     4.0    18.1    -      -       +      -
     70S  LEU*     4.9     6.1    -      -       -      +
     72S  VAL*     4.1    13.2    -      -       +      -
     76S  GLN*     2.9    47.8    +      -       +      +
     78S  PHE*     4.7     1.8    -      -       +      -
----------------------------------------------------------
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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