Contacts of the helix formed by residues 196 - 201 (chain B) in PDB entry 3VF1
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.
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 GLY 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA* 3.0 15.3 + - - -
194B ASN 3.3 0.8 - - - -
195B LEU* 1.3 80.2 - - - +
197B LEU* 1.3 65.4 + - - +
198B SER* 3.7 2.2 - - - -
199B HIS* 3.6 12.9 + - - -
218B THR* 4.6 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 2.9 18.8 + - - +
195B LEU* 3.7 24.2 - - + +
196B GLY* 1.3 85.7 - - - +
198B SER* 1.3 57.1 + - - +
199B HIS* 3.1 22.7 - - + +
200B LEU* 3.0 34.8 + - + +
215B GLN* 3.9 19.7 - - + +
216B LEU* 3.9 39.5 - - + +
218B THR* 3.9 7.2 - - + -
604B VAL* 4.2 22.0 - - + -
607B VAL* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 3.9 18.5 - - - +
192B PHE* 3.5 12.9 + - - -
193B ALA* 3.8 28.9 - - - +
196B GLY 3.7 1.4 - - - -
197B LEU* 1.3 77.8 - - - +
199B HIS* 1.3 61.1 + - - +
200B LEU 3.0 2.2 + - - -
201B PHE* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLY 3.6 24.0 + - - -
197B LEU* 3.9 15.5 - - + +
198B SER* 1.3 80.7 + - - +
200B LEU* 1.3 84.2 + - + +
201B PHE 3.4 1.1 - - - +
203B ILE* 3.6 15.9 - - - +
215B GLN* 5.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 4.1 2.7 - - - -
197B LEU* 3.0 20.1 + - + +
199B HIS* 1.3 110.7 - - + +
201B PHE* 1.3 61.8 + - - +
202B GLY 3.4 0.9 + - - -
203B ILE* 3.3 24.1 + - + +
207B TRP* 3.8 24.2 - - + -
215B GLN* 5.2 6.1 - - + +
216B LEU* 4.3 5.4 - - + -
600B LYS* 3.8 31.6 - - + +
601B HIS* 3.9 13.2 - - - -
604B VAL* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL 4.2 4.5 - - - -
188B GLY* 3.8 8.3 - - - -
189B LEU* 3.5 50.7 - - + -
192B PHE* 3.6 37.6 - + + -
198B SER 3.1 17.9 + - - +
199B HIS 3.4 0.9 - - - +
200B LEU* 1.3 76.9 - - - +
202B GLY* 1.3 67.2 + - - +
203B ILE* 3.2 9.1 + - - +
601B HIS* 3.8 18.8 - + - -
----------------------------------------------------------
Back to top of page
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