Contacts of the helix formed by residues 211 - 227 (chain F) in PDB entry 6MZL
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 PRO 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210F ASP* 1.3 90.5 - - - +
212F THR* 1.3 64.0 + - + +
214F TYR* 3.2 16.3 + - + +
215F GLU* 2.9 31.0 + - - +
247F MET* 5.3 1.4 - - + +
250F GLU* 6.0 1.8 - - + +
251F LEU* 3.7 24.2 - - + +
254F ASN* 4.3 17.3 - - - +
256F HIS* 4.2 29.4 - - + +
259F GLU* 6.2 1.3 - - + -
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Residues in contact with THR 212 (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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210F ASP* 2.9 23.3 + - - +
211F PRO* 1.3 78.1 - - + +
213F MET* 1.3 63.2 + - - +
215F GLU* 3.0 21.6 + - - +
216F GLU* 2.8 37.5 + - - +
259F GLU* 4.1 28.5 - - + -
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Residues in contact with MET 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F ASP* 3.3 33.8 + - + +
212F THR* 1.3 81.2 + - - +
214F TYR* 1.3 58.8 + - + +
216F GLU* 3.4 16.0 + - + +
217F TYR* 2.9 67.8 + - + +
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Residues in contact with TYR 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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210F ASP 3.4 25.1 + - - -
211F PRO* 3.2 15.8 + - + +
213F MET* 1.3 76.8 - - + +
215F GLU* 1.3 60.5 + - - +
217F TYR* 3.5 29.6 - + - +
218F TYR* 2.9 27.4 + - - +
247F MET* 3.6 24.5 - - + +
250F GLU* 3.9 19.5 - - - -
326F ASN* 2.8 33.3 + - + +
327F ASN* 5.0 0.4 - - - -
328F GLN* 3.6 32.9 + - + +
329F ILE* 5.3 5.0 - - + +
331F ASN* 5.9 0.2 + - - -
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F PRO 2.9 19.3 + - - +
212F THR* 3.0 23.6 + - - +
214F TYR* 1.3 75.5 - - - +
216F GLU* 1.3 60.0 + - - +
218F TYR* 3.2 4.6 + - - +
219F SER* 3.0 29.3 + - - -
247F MET* 5.8 2.9 - - + -
251F LEU* 3.4 32.9 - - + +
259F GLU* 3.5 14.8 - - - +
263F PHE* 3.4 50.4 - - + +
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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
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212F THR* 2.8 36.5 + - - +
213F MET* 3.8 19.1 + - + +
215F GLU* 1.3 74.6 - - - +
217F TYR* 1.3 64.7 + - + +
219F SER* 3.3 10.5 + - - +
220F GLY* 2.9 24.4 + - - -
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Residues in contact with TYR 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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213F MET* 2.9 49.4 + - + +
214F TYR* 3.5 36.1 - + + +
215F GLU 3.2 0.2 - - - -
216F GLU* 1.3 77.7 - - + +
218F TYR* 1.3 59.7 + - - +
220F GLY* 3.4 1.6 + - - +
221F LEU* 2.9 24.6 + - - +
324F LYS* 3.1 48.0 + - + +
325F GLN 4.8 16.0 + - - -
327F ASN* 5.1 5.8 - - - -
329F ILE* 4.4 8.7 - - + -
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Residues in contact with TYR 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 TYR 2.9 14.0 + - - +
215F GLU* 3.6 7.2 - - - +
217F TYR* 1.3 73.4 - - - +
219F SER* 1.3 63.7 + - - +
221F LEU* 3.8 3.8 - - + -
222F LYS* 2.8 54.7 + - + +
240F PHE* 3.1 26.0 + + - -
243F LEU* 3.6 40.6 - - + -
244F PHE* 3.3 35.5 - + + +
247F MET* 5.0 10.5 - - + -
263F PHE* 3.5 25.8 - + + -
267F PHE* 4.3 11.3 + + + -
271F GLN* 4.0 7.6 + - - -
329F ILE* 4.5 6.6 - - + +
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Residues in contact with SER 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 GLU 3.0 15.3 + - - -
216F GLU* 3.5 15.7 - - - +
217F TYR 3.3 0.2 - - - -
218F TYR* 1.3 77.3 - - - +
220F GLY* 1.3 56.9 + - - +
222F LYS* 3.4 6.2 + - - +
223F HIS* 3.0 28.6 + - - +
263F PHE* 4.7 0.2 - - - -
266F LYS* 5.3 2.5 + - - -
267F PHE* 3.2 34.6 - - - -
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Residues in contact with GLY 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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216F GLU 2.9 14.0 + - - -
217F TYR* 3.8 2.5 - - - -
218F TYR 3.3 0.2 - - - -
219F SER* 1.3 76.5 - - - +
221F LEU* 1.3 57.1 + - - +
223F HIS* 3.4 5.8 + - - +
224F PHE* 2.9 28.6 + - - +
320F HIS* 4.6 6.0 + - - -
324F LYS* 5.2 1.1 - - - -
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Residues in contact with LEU 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 TYR 2.9 18.1 + - - +
218F TYR* 3.9 4.7 - - + +
220F GLY* 1.3 74.1 - - - +
222F LYS* 1.3 60.2 + - - +
224F PHE* 4.2 5.6 - - + -
225F ILE* 2.9 59.0 + - + +
243F LEU* 3.7 28.9 - - + -
317F LEU* 5.0 11.7 - - + -
320F HIS* 3.5 28.7 - - + -
321F LEU* 4.7 5.8 - - + -
324F LYS* 3.8 7.5 - - - +
329F ILE* 3.8 28.5 - - + -
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Residues in contact with LYS 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 TYR* 2.8 39.5 + - + +
219F SER 3.6 5.2 - - - +
221F LEU* 1.3 77.0 - - - +
223F HIS* 1.3 56.6 + - - +
225F ILE* 3.4 1.4 + - - -
226F GLU* 2.8 63.0 + - - +
240F PHE* 3.6 31.1 - - + -
267F PHE* 3.7 25.1 - - + -
270F ASP* 3.3 43.0 + - - +
271F GLN* 5.4 0.2 - - - +
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Residues in contact with HIS 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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219F SER 3.0 16.7 + - - +
220F GLY* 3.9 6.5 - - - +
222F LYS* 1.3 77.4 - - - +
224F PHE* 1.3 58.3 + - - +
226F GLU* 3.4 18.7 + - + +
227F CYS* 2.9 50.2 + - - -
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Residues in contact with PHE 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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220F GLY 2.9 18.4 + - - +
221F LEU* 3.6 9.2 - - + +
222F LYS 3.2 0.2 - - - -
223F HIS* 1.3 76.1 - - - +
225F ILE* 1.3 66.5 + - + +
227F CYS* 3.1 27.4 + - + +
228F SER* 3.3 14.4 + - - -
316F LEU* 4.4 25.8 - - + -
319F ARG 6.0 0.4 - - - -
320F HIS* 3.6 54.7 - + + +
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Residues in contact with ILE 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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221F LEU* 2.9 46.5 + - + +
222F LYS* 5.1 0.2 - - - -
224F PHE* 1.3 79.3 - - + +
226F GLU* 1.3 62.6 + - - +
228F SER* 3.3 22.7 + - - +
233F ARG* 4.2 13.9 - - - +
236F LEU* 3.8 39.0 - - + -
239F LEU* 5.0 15.3 - - + -
240F PHE* 3.6 34.5 - - + -
243F LEU* 5.7 4.3 - - + -
317F LEU* 6.1 2.9 - - + -
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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 LYS* 2.8 51.9 + - - +
223F HIS* 3.6 22.4 + - + +
224F PHE 3.3 0.2 - - - -
225F ILE* 1.3 77.5 - - - +
227F CYS* 1.3 56.6 + - - +
228F SER 3.2 6.4 + - - +
233F ARG* 4.3 40.4 + - - +
240F PHE* 4.0 13.7 - - + -
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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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223F HIS* 2.9 51.5 + - - +
224F PHE* 3.1 19.5 + - + +
226F GLU* 1.3 76.8 - - - +
228F SER* 1.3 59.1 + - - +
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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