Contacts of the strand formed by residues 16 - 21 (chain V) 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 LEU 16 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13V  GLY*     3.1    17.2    +      -       -      -
     15V  GLY*     1.3    82.3    -      -       -      +
     17V  VAL*     1.3    59.1    +      -       -      +
     18V  LYS*     2.7    38.7    +      -       +      +
     30V  VAL*     3.8    15.9    -      -       +      -
     31V  PHE*     3.5    28.5    -      -       -      +
     32V  PRO*     3.8     8.5    -      -       +      -
     33V  SER*     4.6     2.0    -      -       -      -
    157V  ASP*     5.2     5.3    -      -       +      +
    210V  ARG*     6.1     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 17 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10V  CYS*     4.1    23.6    -      -       -      -
     11V  ASP      3.5    11.2    -      -       -      +
     12V  ASN*     4.6     8.1    -      -       -      +
     13V  GLY      4.6     0.4    -      -       -      +
     16V  LEU*     1.3    74.2    -      -       -      +
     18V  LYS*     1.3    70.7    +      -       -      +
     29V  ALA      4.2     0.4    -      -       -      -
     30V  VAL*     3.2    23.9    -      -       -      +
     31V  PHE*     3.0    40.0    +      -       +      +
     33V  SER*     4.0    13.5    -      -       -      +
     82V  MET*     5.8     0.4    -      -       +      -
     85V  ILE*     3.7    28.3    -      -       +      -
     86V  TRP*     6.1     0.2    -      -       +      -
     89V  THR*     4.5     8.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 18 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10V  CYS*     3.6     0.3    -      -       -      -
     11V  ASP*     2.8    60.2    +      -       +      +
     13V  GLY*     4.3     7.9    -      -       -      -
     16V  LEU*     2.7    41.3    +      -       +      +
     17V  VAL*     1.3    76.4    -      -       -      +
     19V  ALA*     1.3    61.1    +      -       -      +
     27V  PRO*     4.0     7.0    -      -       +      -
     29V  ALA      3.3     5.2    -      -       -      -
     30V  VAL*     4.2     6.7    -      -       +      -
    336V  LYS      5.1     4.7    -      -       -      +
    337V  TYR*     3.8    33.7    -      -       +      -
    340V  TRP*     3.4    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 19 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9V  VAL      3.2    11.4    -      -       -      +
     10V  CYS*     4.6     5.6    -      -       +      -
     17V  VAL*     4.7     3.6    -      -       +      -
     18V  LYS*     1.3    75.2    -      -       -      +
     20V  GLY*     1.3    51.8    +      -       -      +
     27V  PRO*     3.2     4.0    -      -       -      +
     28V  ARG      2.6    30.7    +      -       -      -
     29V  ALA*     2.7    25.7    +      -       +      +
     31V  PHE*     5.2     0.2    -      -       +      -
     89V  THR*     3.6    31.2    -      -       +      -
     94V  LEU*     4.0     7.0    -      -       +      -
    340V  TRP*     3.6     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 20 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8V  LEU*     3.6     7.1    -      -       -      +
      9V  VAL      3.0    24.5    +      -       -      -
     19V  ALA*     1.3    79.0    -      -       -      +
     21V  PHE*     1.3    66.8    +      -       -      -
     24V  ASP*     4.4     0.2    -      -       -      -
     28V  ARG*     3.7    18.4    -      -       -      -
     94V  LEU*     3.6    13.3    -      -       -      +
    340V  TRP*     3.6    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 21 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641G  LYS      5.1     0.2    -      -       -      +
    642G  LYS*     2.2    46.6    -      -       -      +
      5V  THR      3.8    22.9    -      -       -      +
      7V  ALA      3.5     2.5    -      -       -      -
      8V  LEU*     3.5    28.0    -      -       +      -
     20V  GLY*     1.3    74.1    -      -       -      -
     22V  ALA*     1.3    54.1    -      -       -      +
     24V  ASP*     3.0     9.7    +      -       -      +
     28V  ARG*     3.5    38.1    -      -       +      -
     94V  LEU*     4.3    28.7    -      -       +      -
     96V  VAL*     3.7    26.5    -      -       +      -
    101V  HIS*     4.6     7.2    -      +       -      -
    340V  TRP*     3.5     1.7    -      -       -      -
----------------------------------------------------------
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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