Contacts of the helix formed by residues 213 - 224 (chain J) in PDB entry 3MQT
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 ASP 213 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211J TRP* 4.2 1.7 - - - +
212J THR* 1.3 80.7 + - - +
214J TRP* 1.3 65.4 + - - +
215J GLN* 2.9 24.3 + - - +
216J LYS* 3.1 24.2 + - + +
217J ALA* 3.3 8.8 + - - +
236J LEU* 3.8 5.3 - - - +
230M TYR* 4.2 1.4 + - - -
254M ARG* 2.8 27.6 + - - -
303M ASN* 4.0 10.1 + - - +
305M GLN* 3.2 31.1 - - + +
329M ILE 5.7 1.8 - - - +
331M GLU* 4.9 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 214 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212J THR 3.7 1.0 + - - -
213J ASP* 1.3 72.5 + - - +
215J GLN* 1.3 88.3 + - + +
217J ALA* 3.4 3.8 + - - +
218J ARG* 2.9 67.5 + - + +
236J LEU* 3.8 17.4 - - + +
243J GLY* 3.6 18.8 - - - +
246J LYS* 3.6 52.2 - - + +
247J LEU* 3.7 18.8 - - + +
250J ALA* 4.0 8.1 - - + -
275M GLY 6.2 0.7 - - - -
277M SER* 4.2 8.5 + - - -
303M ASN* 2.8 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213J ASP* 2.9 12.5 + - - +
214J TRP* 1.3 111.7 - - + +
216J LYS* 1.3 60.6 + - - +
218J ARG* 3.2 30.7 + - - +
219J TRP* 3.3 21.3 + - - +
253M THR* 3.6 27.4 + - - +
254M ARG* 3.6 35.9 + - + +
255M LEU 5.2 0.2 - - - +
277M SER* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASP* 3.1 29.1 - - - +
211J TRP* 3.8 10.8 - - + -
213J ASP* 3.1 26.4 + - + +
215J GLN* 1.3 76.9 - - - +
217J ALA* 1.3 64.7 + - - +
218J ARG 3.4 0.3 + - - -
219J TRP* 3.4 8.7 + - + +
220J THR* 3.4 20.1 + - - -
202M ASP* 5.5 1.9 + - - -
230M TYR* 5.9 2.5 - - - -
254M ARG* 3.7 8.5 - - - +
331M GLU* 2.7 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211J TRP* 3.8 27.2 - - + +
213J ASP 3.3 5.8 + - - +
214J TRP 3.4 7.6 + - - +
216J LYS* 1.3 78.3 - - - +
218J ARG* 1.3 63.0 + - - +
220J THR* 3.1 10.7 + - - -
221J PHE* 3.1 21.1 + - + -
235J CYS* 3.5 32.1 - - - -
236J LEU* 4.5 2.7 - - + -
247J LEU* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214J TRP* 2.9 42.5 + - + +
215J GLN* 3.2 35.2 + - - +
216J LYS 3.3 0.2 - - - -
217J ALA* 1.3 77.4 - - - +
219J TRP* 1.3 63.2 + - - +
221J PHE* 3.9 0.5 - - - +
222J ARG* 3.0 43.0 + - + +
247J LEU* 3.7 14.8 - - + +
250J ALA* 3.8 26.0 + - + +
251J ILE* 5.2 4.1 - - + +
248M ALA 5.5 2.0 + - - -
249M ALA 5.8 0.4 + - - -
251M ILE 3.5 19.0 + - - -
252M ASN* 3.5 29.5 + - - +
253M THR 4.0 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 219 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASP* 4.1 10.8 - - + -
184J LYS* 3.4 58.8 - - + -
187J VAL* 4.2 4.5 - - + -
215J GLN 3.3 10.9 + - - +
216J LYS* 3.6 11.2 - - + +
218J ARG* 1.3 79.6 - - - +
220J THR* 1.3 76.1 + - - +
222J ARG* 3.5 20.5 + - - +
223J GLN* 3.0 62.2 + - + +
228M ASP* 2.9 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASP* 3.3 34.4 + - - +
186J ILE* 4.6 8.3 - - + -
187J VAL* 3.7 16.5 - - + +
211J TRP* 3.6 26.2 - - + -
216J LYS 3.4 4.2 + - - -
217J ALA 3.1 9.6 + - - -
219J TRP* 1.3 88.4 - - - +
221J PHE* 1.3 63.2 + - + +
223J GLN* 3.3 17.2 + - - +
224J LEU* 3.3 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J ILE* 5.3 0.4 - - + -
190J LEU* 4.5 8.3 - - + -
205J VAL* 5.3 2.9 - - + -
207J CYS* 3.8 5.8 - - - -
211J TRP* 3.6 39.3 - + - -
217J ALA 3.1 27.3 + - - +
218J ARG 4.6 0.2 - - - +
220J THR* 1.3 75.8 - - + +
222J ARG* 1.3 64.9 + - - +
224J LEU* 3.1 29.5 + - + -
225J GLU* 3.2 17.7 + - - +
229J LEU* 3.8 18.6 - - + -
232J ILE* 3.6 48.7 - - + -
235J CYS* 3.9 16.4 - - - -
247J LEU* 5.3 3.8 - - + -
251J ILE* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218J ARG* 3.0 46.3 + - + +
219J TRP* 3.6 33.2 - - - +
221J PHE* 1.3 74.5 - - - +
223J GLN* 1.3 73.7 + - - +
224J LEU 3.2 0.9 + - - -
225J GLU* 3.4 34.6 + - - +
251J ILE* 5.7 0.8 - - - +
225M GLU 5.9 1.2 + - - -
228M ASP* 4.3 5.9 + - - -
252M ASN* 3.3 54.3 + - - +
253M THR* 5.4 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184J LYS* 4.3 7.0 + - - +
187J VAL* 3.9 18.4 - - + -
191J ARG* 3.1 29.7 + - - +
219J TRP* 3.0 72.6 + - + +
220J THR 3.3 8.0 + - - +
222J ARG* 1.3 89.8 - - - +
224J LEU* 1.3 57.5 + - - +
225J GLU 3.3 1.4 + - - -
226J ASP* 3.4 5.2 + - - +
228M ASP* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J VAL* 3.7 38.6 - - + +
190J LEU* 3.5 31.9 - - + -
191J ARG* 3.9 10.8 - - + -
220J THR* 3.3 24.4 + - + +
221J PHE* 3.1 26.1 + - + +
222J ARG 3.1 1.6 - - - -
223J GLN* 1.3 76.9 - - - +
225J GLU* 1.3 63.9 + - - +
226J ASP* 3.1 5.3 + - - -
227J ILE* 3.2 38.5 + - + +
228J ASP 3.9 1.9 + - - -
229J LEU* 4.4 13.6 + - + +
----------------------------------------------------------
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