Contacts of the helix formed by residues 213 - 234 (chain F) in PDB entry 5MGX
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 213 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211F MET 3.8 1.2 + - - -
212F LEU* 1.3 75.0 - - - +
214F GLY* 1.3 53.6 + - - +
215F GLN* 3.6 21.7 + - + +
216F GLU* 3.0 46.9 + - + +
217F ARG* 2.8 33.7 + - - +
257F VAL* 4.5 7.7 - - - +
259F MET* 4.9 0.2 - - - -
263F GLU* 5.3 1.6 + - - -
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Residues in contact with GLY 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F THR* 1.3 73.8 + - - +
215F GLN* 1.4 55.1 + - - +
217F ARG* 3.3 4.7 + - - +
218F VAL* 3.0 36.0 + - - +
257F VAL* 5.0 0.4 - - - +
259F MET* 3.8 33.9 - - - +
263F GLU* 3.8 22.8 + - - -
267F LEU* 4.3 1.8 - - - +
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Residues in contact with GLN 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F THR* 3.3 16.6 + - + +
214F GLY* 1.4 75.6 - - - +
216F GLU* 1.3 57.2 + - + +
218F VAL* 3.5 9.1 + - - +
219F ALA* 3.2 25.6 + - - +
263F GLU* 3.8 15.0 + - - +
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Residues in contact with GLU 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F MET 4.7 1.7 - - - +
212F LEU* 3.8 26.1 - - + +
213F THR* 3.0 39.2 + - + +
215F GLN* 1.3 76.9 - - + +
217F ARG* 1.4 54.7 - - - +
219F ALA* 3.4 7.2 + - - +
220F LEU* 2.9 35.7 + - - +
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Residues in contact with ARG 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F LEU 2.8 25.3 + - - -
210F GLU 4.2 5.1 + - - -
212F LEU* 3.0 42.3 + - + +
213F THR 2.8 13.1 + - - +
214F GLY* 3.4 7.4 - - - +
216F GLU* 1.4 74.5 - - - +
218F VAL* 1.4 57.6 + - - +
220F LEU* 4.2 1.4 - - - +
221F ALA* 3.1 31.7 + - - +
250F ALA* 2.8 47.4 + - - +
251F ILE 3.6 13.9 - - - -
253F SER* 2.8 28.8 + - - -
254F SER* 4.0 15.0 - - - +
257F VAL* 4.3 4.2 - - - +
259F MET* 4.0 10.6 - - - -
267F LEU* 3.9 24.8 - - + +
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Residues in contact with VAL 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F GLY 3.0 20.9 + - - +
215F GLN* 3.6 8.7 - - - +
217F ARG* 1.4 75.3 - - - +
219F ALA* 1.3 58.7 + - + +
222F ASN* 2.9 49.8 + - - +
263F GLU* 5.0 2.7 - - + +
266F GLN* 3.8 40.6 - - + +
267F LEU* 3.9 25.4 - - + +
270F LEU* 3.9 8.2 - - + +
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F GLN 3.2 17.3 + - - +
216F GLU* 3.4 8.3 + - - +
218F VAL* 1.3 75.4 - - - +
220F LEU* 1.3 63.3 + - - +
222F ASN* 3.8 4.9 + - - +
223F ARG* 3.2 23.0 + - - +
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Residues in contact with LEU 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F THR* 5.4 4.9 - - - +
207F PRO* 4.6 18.6 - - + -
209F LEU* 4.8 8.1 - - + -
212F LEU* 3.9 24.9 - - + -
216F GLU 2.9 20.6 + - - +
217F ARG 4.2 2.9 - - - +
219F ALA* 1.3 69.6 - - - +
221F ALA* 1.3 61.5 + - - +
223F ARG* 3.2 10.6 + - + +
224F LYS* 3.0 54.9 + - + +
250F ALA* 3.9 19.1 - - + -
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Residues in contact with ALA 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F ARG 3.1 19.1 + - - +
220F LEU* 1.3 74.2 - - - +
222F ASN* 1.3 57.1 + - - +
224F LYS 3.5 0.7 + - - -
225F ARG* 3.0 29.2 + - - +
247F ALA* 3.7 22.0 - - - +
250F ALA* 4.7 5.1 - - + +
251F ILE* 3.6 31.9 - - + -
270F LEU* 3.7 14.8 - - + -
274F CYS* 4.8 0.3 - - - -
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Residues in contact with ASN 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F VAL* 2.9 35.9 + - - +
219F ALA* 4.1 4.9 - - - +
221F ALA* 1.3 73.0 - - - +
223F ARG* 1.3 60.9 + - - +
225F ARG* 2.9 38.6 + - - +
226F GLU* 2.9 41.0 + - - +
266F GLN* 5.9 0.2 - - - +
270F LEU* 3.5 23.6 - - - +
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Residues in contact with ARG 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 4.3 17.0 - - - +
144F VAL 3.7 24.7 + - - +
151F ASP* 5.1 5.9 + - - +
152F VAL* 4.5 8.9 - - - +
219F ALA 3.2 18.5 + - - +
220F LEU* 3.2 13.1 + - + +
222F ASN* 1.3 73.9 - - - +
224F LYS* 1.3 65.1 + - + +
226F GLU* 3.3 23.3 + - - +
227F CYS* 3.0 57.8 + - - +
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Residues in contact with LYS 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F THR* 3.4 11.8 + - - -
149F ASP* 2.8 29.3 + - - -
151F ASP* 2.8 39.1 + - - +
220F LEU* 3.0 42.3 + - + +
223F ARG* 1.3 76.0 - - + +
225F ARG* 1.4 56.0 + - - +
227F CYS* 3.2 6.7 + - + +
228F GLY* 2.9 29.5 + - - -
243F SER* 3.4 27.0 - - - +
246F LEU* 4.4 15.9 - - + +
247F ALA* 3.7 21.1 - - + +
250F ALA* 5.7 0.2 - - + -
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Residues in contact with ARG 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A ASP* 3.1 42.1 + - - +
221F ALA 3.0 18.2 + - - +
222F ASN* 2.9 29.7 + - - +
224F LYS* 1.4 75.2 - - - +
226F GLU* 1.4 82.9 + - - +
228F GLY 3.5 0.5 + - - -
229F ASN* 2.9 50.4 + - - +
244F TYR* 3.6 10.7 - - + -
247F ALA* 4.1 2.8 - - - +
270F LEU* 4.1 11.1 - - - +
273F LYS* 4.6 11.4 - - - +
274F CYS* 3.9 24.9 - - - -
277F ASN* 4.1 9.2 - - - +
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Residues in contact with GLU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ASN* 2.9 29.1 + - - +
223F ARG* 3.3 23.1 + - - +
225F ARG* 1.4 93.8 + - - +
227F CYS* 1.4 64.3 + - - +
229F ASN* 3.6 9.8 + - - +
230F ALA* 3.2 22.5 + - - +
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Residues in contact with CYS 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ASP* 3.3 45.8 - - - +
223F ARG* 3.0 51.4 + - - -
224F LYS* 3.4 11.2 - - - +
226F GLU* 1.4 72.8 - - - +
228F GLY* 1.3 64.8 + - - +
230F ALA* 3.0 18.8 + - - +
231F HIS* 3.1 19.5 + - - -
243F SER* 4.0 9.6 - - - +
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Residues in contact with GLY 228 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224F LYS 2.9 10.5 + - - -
225F ARG 3.5 0.2 + - - -
227F CYS* 1.3 73.8 - - - +
229F ASN* 1.4 55.2 + - - +
231F HIS* 3.2 2.0 + - - -
232F TYR 2.9 24.1 + - - -
240F ALA* 3.4 15.4 - - - +
243F SER* 3.4 20.3 - - - -
244F TYR* 3.2 26.2 + - - -
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Residues in contact with ASN 229 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708A VAL* 3.2 17.3 + - + +
709A ASP 3.0 21.0 + - - +
225F ARG* 2.9 36.1 + - - +
226F GLU* 3.7 8.7 - - - +
227F CYS 3.2 0.2 - - - -
228F GLY* 1.4 75.5 - - - +
230F ALA* 1.4 55.8 + - - +
232F TYR* 3.3 2.6 + - - +
233F GLN* 3.0 42.0 + - - +
244F TYR* 2.7 26.3 + - - -
277F ASN* 3.1 17.2 + - - -
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Residues in contact with ALA 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ASP 6.0 0.7 - - - +
226F GLU 3.2 12.2 + - - +
227F CYS* 3.0 12.4 + - - +
229F ASN* 1.4 75.4 - - - +
231F HIS* 1.4 61.8 + - + +
233F GLN* 3.7 13.1 + - - +
234F ARG* 3.4 31.0 + - - +
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Residues in contact with HIS 231 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F CYS 2.9 24.2 + - - -
151F ASP 3.3 11.6 + - - -
152F VAL 3.1 26.9 - - - -
227F CYS 3.1 24.0 + - - -
228F GLY 3.5 4.0 - - - +
230F ALA* 1.4 73.1 - - + +
232F TYR* 1.3 58.0 + - - +
234F ARG* 2.9 29.5 + - - +
235F ALA 3.5 2.9 + - - -
236F ASP* 2.8 37.9 + - - +
239F LEU* 3.5 27.0 - - + +
240F ALA 3.5 18.6 - - - +
243F SER* 3.4 19.2 + - - -
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Residues in contact with TYR 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A GLU* 2.7 37.9 + - + +
707A GLU* 5.0 0.4 - - - -
708A VAL* 4.0 24.9 - - + -
228F GLY 2.9 16.7 + - - +
229F ASN* 3.3 5.6 + - - +
231F HIS* 1.3 75.5 - - - +
233F GLN* 1.4 67.3 + - - +
235F ALA* 3.0 20.6 + - - -
236F ASP 4.4 0.9 - - - -
237F PHE* 3.5 33.3 - + - -
240F ALA* 3.7 6.0 - - + +
244F TYR* 3.8 7.0 - - - +
280F ALA* 3.8 38.3 + - + +
281F SER* 3.5 18.2 - - - -
284F LYS* 4.4 11.0 + - - -
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Residues in contact with GLN 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A GLU* 6.1 1.4 - - - +
708A VAL* 3.5 26.4 + - - +
185F SER* 6.2 4.9 - - - -
229F ASN* 3.0 33.6 + - - +
230F ALA* 3.9 9.2 - - - +
231F HIS 3.5 0.2 - - - -
232F TYR* 1.4 80.1 - - - +
234F ARG* 1.3 60.3 + - + +
235F ALA* 3.6 1.2 + - - +
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Residues in contact with ARG 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F VAL 3.9 9.7 + - - -
153F ILE* 4.8 0.4 - - - +
178F CYS 4.4 8.9 + - - -
179F TYR* 3.3 51.5 + - - +
182F GLN* 3.3 23.9 - - - +
183F GLY 3.6 22.0 - - - +
184F ARG* 3.8 11.4 - - + +
185F SER 5.5 0.4 - - - +
230F ALA* 3.4 28.4 + - - +
231F HIS* 2.9 43.9 + - - +
232F TYR 3.2 0.6 - - - -
233F GLN* 1.3 75.5 - - + +
235F ALA* 1.4 67.0 + - - +
236F ASP* 3.8 22.4 + - + +
239F LEU* 4.3 2.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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