Contacts of the strand formed by residues 8 - 12 (chain 4) 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 LEU 8 (chain 4).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      74  ALA*     1.3    76.1    -      -       -      +
      94  VAL*     1.3    66.6    +      -       -      +
     104  CYS*     4.1     1.6    -      -       +      -
     204  GLY      3.6     4.3    -      -       -      +
     214  PHE*     3.5    36.8    -      -       +      -
     904  PHE*     4.0    25.1    -      -       +      -
     944  LEU*     4.2    14.1    -      -       +      -
     964  VAL*     4.0    19.5    -      -       +      -
     984  PRO*     5.3     2.5    -      -       +      -
    1014  HIS*     3.7    35.2    -      -       +      +
    1024  PRO      2.8    10.5    +      -       -      +
    1034  THR*     4.2    13.9    -      -       +      +
    1044  LEU*     2.9    24.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      84  LEU*     1.3    79.1    -      -       -      +
     104  CYS*     1.3    64.9    +      -       -      +
     114  ASP*     5.4     0.2    -      -       +      -
     194  ALA*     3.2    12.7    -      -       -      -
     204  GLY      3.0    10.8    +      -       -      -
     224  ALA*     4.2    15.7    -      -       +      -
    1044  LEU*     3.3    27.1    -      -       +      +
    1064  THR*     5.4     3.1    -      -       +      -
    3394  VAL      5.7     0.2    -      -       -      +
    3404  TRP*     2.8    60.5    +      -       +      +
    3434  GLY*     3.9    25.6    -      -       -      +
    3444  SER*     3.9     9.2    -      -       -      +
    3474  ALA*     4.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 10 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      84  LEU*     4.1     2.0    -      -       +      -
      94  VAL*     1.3    75.6    -      -       -      +
     114  ASP*     1.3    58.8    +      -       -      +
     124  ASN*     3.5    24.1    +      -       -      -
     174  VAL*     4.1    17.0    -      -       -      -
     184  LYS      3.6     2.9    -      -       -      -
     194  ALA*     4.5     4.3    -      -       +      +
     864  TRP*     4.0    18.2    -      -       -      -
     894  THR*     4.7    11.2    -      -       +      -
     904  PHE*     5.8     5.8    -      -       +      -
    1034  THR*     4.9     6.7    -      -       +      -
    1044  LEU      2.9     7.3    +      -       -      +
    1054  LEU*     3.5    20.1    -      -       +      +
    1064  THR*     3.4    22.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 11 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      94  VAL*     4.0     1.0    -      -       +      -
     104  CYS*     1.3    73.0    -      -       -      +
     124  ASN*     1.3    67.1    +      -       -      +
     134  GLY*     5.3     0.3    -      -       -      -
     174  VAL*     3.5     5.6    -      -       -      -
     184  LYS*     2.8    58.8    +      -       +      +
    1064  THR*     2.9    27.7    +      -       +      +
    1374  GLN*     4.2     7.4    -      -       -      +
    3394  VAL*     3.4    34.0    -      -       +      +
    3404  TRP*     4.0    17.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 12 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     104  CYS*     3.5    19.4    +      -       -      -
     114  ASP*     1.3    78.7    +      -       -      +
     134  GLY*     1.3    59.0    +      -       -      +
     164  LEU      4.7     0.4    -      -       -      -
     174  VAL*     4.5     9.2    -      -       -      +
     714  ILE*     3.5    24.0    -      -       +      +
     744  GLY*     5.3     2.9    -      -       -      +
     764  ILE*     5.5     3.8    -      -       +      +
     824  MET*     3.5    12.0    -      -       +      +
     864  TRP*     2.9    39.3    +      -       -      +
    1054  LEU*     4.3     7.9    -      -       -      +
    1064  THR*     3.7    20.6    +      -       -      +
    1194  MET*     4.8     3.8    -      -       -      +
    1374  GLN*     4.1    14.7    +      -       -      +
----------------------------------------------------------
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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