Contacts of the strand formed by residues 37 - 41 (chain A) in PDB entry 1O18


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PHE*     3.8    24.1    -      -       -      -
     33A  ASP*     2.4    39.2    +      -       -      +
     34A  ALA*     3.4    10.2    -      -       -      +
     36A  SER*     1.4    72.1    +      -       -      +
     38A  VAL*     1.3    72.0    +      -       -      +
     50A  GLY      4.0     5.2    -      -       -      -
     51A  THR*     4.7     6.5    -      -       -      +
     79A  SER*     4.6     1.2    +      -       -      -
     80A  MET*     3.9    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ALA      5.1     1.3    -      -       -      +
     35A  MLY      5.5     1.3    -      -       -      +
     36A  SER      4.0     1.3    -      -       -      +
     37A  SER*     1.3    85.3    -      -       -      +
     39A  PHE*     1.3    79.4    +      -       -      +
     40A  VAL*     4.6     3.4    -      -       +      -
     49A  MLY      3.7     5.4    -      -       -      +
     50A  GLY      2.7    41.0    +      -       -      +
     52A  ILE*     3.3    36.8    -      -       +      -
     62A  VAL*     5.2     1.3    -      -       +      -
     77A  VAL*     4.0    24.0    -      -       +      -
     78A  PHE      3.5    13.2    -      -       -      +
     79A  SER*     4.4     6.1    -      -       -      +
     80A  MET*     4.1     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     1.3    86.6    -      -       -      +
     40A  VAL*     1.3    63.2    +      -       -      +
     47A  PHE*     5.4     0.2    -      -       +      -
     48A  VAL      3.9     2.9    -      -       -      -
     49A  MLY      3.7    39.3    -      -       +      -
     77A  VAL*     3.7     0.2    -      -       -      -
     78A  PHE*     2.5    34.0    +      -       +      +
     79A  SER      3.2    21.1    -      -       -      -
     80A  MET*     4.0    22.2    -      -       +      -
     81A  ASN*     5.0     2.0    -      -       -      -
     98A  HIS*     4.4     2.0    -      +       -      -
    100A  PRO*     3.7    28.9    -      -       +      -
    101A  ALA*     3.9    21.1    -      -       +      -
    104A  TYR*     3.5    48.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     4.6     4.3    -      -       +      -
     39A  PHE*     1.3    77.2    -      -       -      +
     41A  VAL*     1.3    74.0    +      -       -      +
     42A  HIS*     6.0     0.2    -      -       +      -
     47A  PHE*     3.1    12.2    -      -       -      -
     48A  VAL*     2.9    50.3    +      -       +      +
     49A  MLY      5.5     2.9    -      -       -      -
     50A  GLY      5.9     0.4    -      -       -      +
     62A  VAL*     5.0    17.7    -      -       +      -
     63A  MLY      6.0     0.4    -      -       -      +
     70A  LEU*     5.9     6.7    -      -       +      -
     72A  VAL*     3.5    24.2    -      -       +      -
     76A  GLN      2.8    23.8    -      -       -      +
     77A  VAL*     3.9    10.3    -      -       +      -
     78A  PHE*     4.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     1.3    90.1    -      -       +      +
     42A  HIS*     1.3    75.6    +      -       -      +
     43A  PRO*     4.4     6.8    -      -       +      +
     46A  SER      3.9     6.3    -      -       -      +
     47A  PHE*     4.0    18.1    -      -       +      -
     70A  LEU*     4.9     6.4    -      -       -      +
     72A  VAL*     4.1    12.7    -      -       +      +
     76A  GLN*     2.9    48.0    +      -       +      +
     78A  PHE*     4.7     2.0    -      -       +      -
----------------------------------------------------------
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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