Contacts of the helix formed by residues 201 - 214 (chain D) in PDB entry 2VM8
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 ASN 201 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 3.3 24.6 + - - +
238B ARG* 4.0 4.6 - - - +
168D MET 4.0 1.3 - - - -
175D GLN* 5.3 0.9 + - - -
200D GLU* 1.3 69.3 - - - +
202D GLY* 1.3 60.7 + - - +
203D ASP* 3.0 22.7 + - - +
204D ILE* 3.2 38.2 + - + +
205D ILE* 3.1 25.9 + - - +
231D VAL* 3.0 18.1 + - + +
234D GLU* 2.9 28.7 + - - +
235D ALA* 3.5 0.6 - - - +
238D ARG* 4.0 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D MET 2.9 17.4 + - - -
169D ALA* 3.8 11.9 - - - -
170D PHE 4.4 4.3 - - - -
171D LYS* 4.2 3.2 - - - +
175D GLN* 3.6 17.2 - - - -
200D GLU 3.2 1.6 + - - -
201D ASN* 1.3 69.6 + - - +
203D ASP* 1.3 61.0 + - - +
204D ILE 3.4 0.2 - - - -
205D ILE* 3.8 9.1 - - - +
206D ALA* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 5.0 3.6 - - - -
178B ASP* 3.3 34.1 + - + +
179B CYS* 3.9 16.3 + - - +
182B TYR* 6.3 0.4 - - - -
171D LYS* 3.2 35.0 + - - +
175D GLN* 3.8 20.3 + - - +
201D ASN* 3.0 9.8 + - - +
202D GLY* 1.3 79.1 - - - +
204D ILE* 1.3 65.3 + - - +
206D ALA* 3.5 1.9 + - - +
207D GLU* 3.4 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 5.6 2.2 - - + +
182B TYR* 4.5 15.8 - - + -
241B THR* 3.7 29.6 - - + -
242B ILE* 3.7 29.4 - - + +
245B GLN* 4.0 20.2 - - + -
201D ASN* 3.2 38.4 + - + +
203D ASP* 1.3 76.6 - - + +
205D ILE* 1.3 58.7 + - - +
207D GLU* 3.3 5.0 + - - +
208D GLU* 2.9 36.1 + - + +
226D SER 5.6 0.7 - - - +
228D PRO* 6.1 0.2 - - + -
231D VAL* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ALA* 4.8 0.9 - - + -
200D GLU* 3.7 26.2 - - + +
201D ASN 3.1 25.5 + - - +
202D GLY* 3.8 7.9 - - - +
203D ASP 3.2 0.4 - - - -
204D ILE* 1.3 71.3 - - - +
206D ALA* 1.3 59.9 + - - +
207D GLU 3.0 1.3 - - - -
208D GLU 2.9 1.6 + - - -
209D GLN* 2.7 49.3 + - + +
226D SER 3.8 21.5 - - - +
227D ARG* 3.5 40.6 - - + +
231D VAL* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D LYS* 3.8 31.0 - - + -
202D GLY 2.8 22.0 + - - +
203D ASP 4.0 2.0 - - - +
205D ILE* 1.3 74.5 - - - +
207D GLU* 1.3 66.0 + - - +
209D GLN* 3.7 16.9 - - - +
210D GLN* 3.6 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B CYS* 3.5 28.2 - - - -
182B TYR* 3.6 49.2 + - + -
183B GLU* 4.5 10.2 - - - +
171D LYS* 4.5 4.2 + - - -
203D ASP 3.4 13.1 + - - +
204D ILE 3.3 6.9 + - - +
205D ILE 3.0 0.8 - - - -
206D ALA* 1.3 80.4 - - - +
208D GLU* 1.3 61.0 + - - +
210D GLN* 3.3 7.6 + - - +
211D ARG* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 2.6 33.2 + - + +
245B GLN* 3.5 28.7 - - + +
490B GLU* 5.1 0.2 - - - +
204D ILE* 2.9 29.2 + - + +
205D ILE 2.9 2.0 + - - -
207D GLU* 1.3 73.6 - - - +
209D GLN* 1.3 69.3 + - - +
211D ARG* 2.8 34.9 + - - +
212D ILE* 3.0 35.2 + - + +
225D LEU 4.7 3.2 - - - +
226D SER* 3.8 22.9 - - - +
228D PRO* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ILE* 2.7 31.4 + - + +
206D ALA* 3.7 15.6 - - - +
208D GLU* 1.3 72.5 - - - +
210D GLN* 1.3 59.8 + - - +
212D ILE* 3.1 2.1 + - - +
213D LEU* 2.8 34.9 + - + +
226D SER* 3.8 20.2 - - - +
227D ARG* 3.6 24.5 - - - +
348D PHE* 4.1 6.2 - - + -
349D THR* 4.3 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ALA 3.6 10.0 + - - +
207D GLU* 3.3 9.6 + - - +
208D GLU 3.3 0.4 - - - -
209D GLN* 1.3 82.8 - - - +
211D ARG* 1.3 61.5 + - - +
213D LEU* 3.4 18.1 + - - +
214D ASP* 3.1 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 4.0 11.0 + - - +
245B GLN 5.1 3.4 + - - -
490B GLU* 2.8 39.2 + - - -
207D GLU 2.9 17.0 + - - +
208D GLU* 2.8 40.6 + - - +
210D GLN* 1.3 77.0 - - - +
212D ILE* 1.3 63.8 + - - +
214D ASP* 3.5 9.6 + - - +
215D LEU* 3.2 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLU* 4.2 13.2 - - - +
208D GLU* 3.0 32.2 + - - +
209D GLN 3.8 2.0 - - - +
211D ARG* 1.3 93.4 - - - +
213D LEU* 1.3 65.2 + - - +
215D LEU* 3.4 9.5 + - + +
217D ILE* 2.9 56.1 + - + +
222D GLY* 4.3 10.8 - - - -
225D LEU* 3.7 29.6 - - + +
226D SER* 3.9 12.8 - - - -
348D PHE* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D GLN* 2.8 19.3 + - + +
210D GLN* 3.4 22.4 + - - +
212D ILE* 1.3 74.3 - - - +
214D ASP* 1.3 60.1 + - - +
216D GLY* 2.8 29.5 + - - -
217D ILE 3.6 5.1 - - - +
218D THR* 4.1 15.1 - - + +
347D ASN* 3.1 44.9 - - - +
348D PHE* 3.5 26.0 - - + -
349D THR* 3.9 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D GLN* 3.1 43.6 + - - +
211D ARG* 3.5 9.6 - - - +
212D ILE 3.3 0.2 - - - -
213D LEU* 1.3 73.5 - - - +
215D LEU* 1.3 62.9 + - - +
216D GLY 3.3 0.4 - - - -
----------------------------------------------------------
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