Contacts of the strand formed by residues 103 - 107 (chain 7) 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 THR 103 (chain 7).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      87  LEU*     3.9    18.8    -      -       +      +
     107  CYS*     4.9     4.3    -      -       +      -
     907  PHE*     4.4    18.1    -      -       +      -
    1017  HIS      3.4     9.2    +      -       -      -
    1027  PRO*     1.3    73.9    +      -       -      +
    1047  LEU*     1.4    60.8    +      -       -      +
    1057  LEU*     3.7    27.6    +      -       +      +
    1237  MET*     4.6     6.7    -      -       -      -
    1297  VAL*     3.4    19.3    -      -       -      +
    1317  ALA      2.9    11.8    +      -       -      -
    1327  MET*     3.2    28.2    -      -       -      +
    1337  TYR      3.3     2.1    +      -       -      -
    3567  TRP*     3.8     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 104 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      87  LEU      2.9    14.2    +      -       -      +
      97  VAL*     3.3    22.0    -      -       +      -
     107  CYS*     2.9    26.0    +      -       -      +
    1037  THR*     1.4    69.2    -      -       -      +
    1057  LEU*     1.3    78.5    +      -       -      +
    1067  THR*     4.1     9.2    -      -       +      -
    1337  TYR*     3.5    32.1    -      -       +      +
    1357  ALA*     4.2     7.2    -      -       +      -
    1407  LEU*     4.4     0.2    -      -       +      -
    3437  GLY*     4.3    10.5    -      -       -      +
    3467  LEU*     4.2    16.8    -      -       +      -
    3477  ALA*     4.2    13.0    -      -       +      -
    3527  PHE*     4.1    12.1    -      -       +      -
    3567  TRP*     3.9    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     107  CYS*     3.5    34.3    -      -       +      +
     127  ASN*     4.3     7.9    -      -       -      +
     867  TRP*     4.4     9.4    -      -       +      +
     907  PHE*     6.1     0.4    -      -       +      -
    1037  THR*     3.9    18.6    -      -       +      +
    1047  LEU*     1.3    80.8    -      -       -      +
    1067  THR*     1.3    64.7    +      -       -      +
    1197  MET*     3.7    28.5    -      -       +      -
    1237  MET*     3.7    35.4    -      -       +      -
    1327  MET*     3.7    14.8    -      -       +      -
    1337  TYR      2.8    10.0    +      -       -      +
    1347  VAL*     3.4     3.1    -      -       +      -
    1357  ALA      2.9    23.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 106 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      97  VAL*     5.4     2.2    -      -       +      -
     107  CYS      3.4    10.6    +      -       -      +
     117  ASP*     2.9    31.2    +      -       +      +
     127  ASN*     3.7    18.1    +      -       -      +
    1047  LEU*     4.1     6.1    -      -       +      -
    1057  LEU*     1.3    80.2    -      -       -      +
    1077  GLU*     1.3    61.7    +      -       -      +
    1197  MET*     4.1     8.3    -      -       -      +
    1347  VAL*     4.4     3.4    -      -       -      -
    1357  ALA      3.3     7.0    -      -       -      -
    1377  GLN*     3.8    16.7    +      -       -      +
    1407  LEU*     3.4    31.9    -      -       +      -
    3397  VAL*     4.2     9.2    -      -       +      -
    3407  TRP*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 107 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     747  GLY      5.8     0.2    -      -       -      -
    1067  THR*     1.3    74.0    -      -       -      +
    1087  ALA*     1.3    64.8    +      -       -      +
    1097  PRO      5.3     0.7    -      -       -      +
    1117  ASN*     2.9    42.9    +      -       -      +
    1167  ARG*     3.1    51.2    +      -       -      +
    1197  MET*     5.0     4.3    -      -       -      -
    1347  VAL*     3.6    13.1    -      -       +      +
    1357  ALA      3.0    12.7    +      -       -      +
    1367  ILE*     3.7    14.3    -      -       +      +
    1377  GLN*     3.0    36.7    +      -       -      +
----------------------------------------------------------
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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