Contacts of the helix formed by residues 196 - 208 (chain A) in PDB entry 3VLN
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 THR 196 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 6.1 1.1 - - + -
150A PHE* 3.9 31.0 - - + +
151A THR* 4.0 13.9 - - + +
154A GLU* 3.2 24.5 - - + -
192A CYS 4.1 4.0 + - - +
193A VAL* 2.9 33.4 + - - +
194A ASP 3.4 0.6 - - - -
195A HIS* 1.3 86.5 - - + +
197A PRO* 1.3 66.9 - - - +
199A LEU* 3.2 13.5 + - - +
200A LYS 3.1 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 3.2 13.2 - - + +
193A VAL 4.9 0.4 - - - +
194A ASP 5.3 2.0 - - - +
195A HIS* 3.5 9.0 - - - +
196A THR* 1.3 89.9 - - - +
198A LYS* 1.3 66.4 + - + +
200A LYS* 3.4 9.7 + - + +
201A LEU* 3.1 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 2.9 22.9 + - - +
157A LEU* 3.7 36.0 - - + +
158A THR* 3.8 33.8 + - - +
161A LYS* 5.5 13.7 - - - +
162A THR 6.2 0.2 - - - +
197A PRO* 1.3 78.5 - - + +
199A LEU* 1.3 57.9 + - - +
201A LEU* 3.3 14.3 + - + +
202A TRP* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE* 3.6 47.8 - - + +
153A LEU* 4.4 5.6 - - + -
154A GLU* 2.8 21.7 + - - +
157A LEU* 3.9 6.7 - - + +
165A PHE* 3.8 28.5 - - + -
181A PHE* 4.0 25.1 - - + -
193A VAL* 4.2 5.8 - - + -
196A THR* 3.6 13.7 - - - +
198A LYS* 1.3 70.9 - - - +
200A LYS* 1.3 65.9 + - - +
202A TRP* 3.3 18.5 + - + +
203A MET* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASN* 4.2 21.1 - - - +
193A VAL* 4.1 21.5 + - + +
194A ASP* 4.5 16.3 + - - +
196A THR* 3.1 13.2 + - - +
197A PRO* 3.6 11.2 - - + +
198A LYS 3.3 0.2 - - - -
199A LEU* 1.3 77.1 - - - +
201A LEU* 1.3 65.8 + - + +
203A MET* 3.2 23.0 + - - +
204A ALA* 3.3 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 3.1 17.6 + - + +
198A LYS* 3.6 16.2 - - + +
200A LYS* 1.3 77.0 - - + +
202A TRP* 1.3 57.3 + - - +
204A ALA* 3.2 11.0 + - + +
205A ALA* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.1 11.0 - - + -
163A THR 3.6 22.9 - - - +
164A PHE* 3.9 10.1 - + - -
165A PHE* 3.5 18.7 - + - -
174A ASP* 2.9 30.7 + - - -
177A ILE* 3.7 32.8 - - + -
178A TRP* 3.9 24.0 - + - -
181A PHE* 3.7 31.4 - + - -
198A LYS 2.9 13.8 + - - +
199A LEU* 3.4 19.1 - - + +
201A LEU* 1.3 75.8 - - - +
203A MET* 1.3 79.9 + - + +
205A ALA* 3.2 7.3 + - - +
206A MET* 2.8 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TRP* 4.1 12.9 - - + -
181A PHE* 3.9 31.2 - - + +
184A LEU* 5.0 4.9 - - + -
185A GLU* 3.8 25.6 - - - +
190A ASN* 4.3 12.3 - - - +
193A VAL* 4.2 27.4 - - - -
199A LEU 3.1 17.3 + - - +
200A LYS* 3.2 10.1 + - - +
202A TRP* 1.3 98.0 - - + +
204A ALA* 1.3 60.7 - - - +
206A MET* 3.3 3.1 + - - +
207A LYS* 3.1 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS 3.3 7.6 + - - +
201A LEU* 3.2 15.9 + - + +
203A MET* 1.3 77.0 - - - +
205A ALA* 1.3 61.7 + - - +
207A LYS* 3.3 18.7 + - - +
208A GLU* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 4.2 15.0 - - + -
164A PHE* 3.9 29.6 - - + -
201A LEU 3.0 13.0 + - - +
202A TRP* 3.5 11.0 - - - +
204A ALA* 1.3 73.8 - - - +
206A MET* 1.3 65.6 + - - +
208A GLU* 3.2 26.0 + - - +
209A ASP* 3.5 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 3.7 15.3 - - + -
170A ILE* 3.6 28.3 - - + -
174A ASP* 3.4 42.2 - - + +
175A TYR* 4.3 1.8 - - + +
178A TRP* 3.6 35.0 - - + -
202A TRP* 2.8 43.8 + - + +
203A MET 3.3 6.0 + - - +
205A ALA* 1.3 71.8 - - - +
207A LYS* 1.3 58.7 + - - +
209A ASP* 3.0 18.9 + - - +
212A VAL* 3.2 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TRP* 3.7 23.5 - - + -
185A GLU* 3.7 22.4 + - - +
203A MET* 3.1 23.4 + - - +
204A ALA* 3.6 11.9 - - - +
205A ALA 3.3 0.6 - - - -
206A MET* 1.3 76.2 - - - +
208A GLU* 1.3 59.4 + - + +
209A ASP 3.3 0.8 + - - -
212A VAL* 4.4 5.4 - - - -
213A SER* 3.9 20.2 + - - -
216A LEU* 3.6 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 3.5 19.3 - - - +
205A ALA* 3.2 17.5 + - - +
206A MET 3.1 0.4 - - - -
207A LYS* 1.3 78.2 - - + +
209A ASP* 1.3 62.9 + - - +
210A PRO* 3.5 8.3 - - - +
213A SER* 5.1 1.9 - - - -
----------------------------------------------------------
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