Contacts of the helix formed by residues 231 - 247 (chain F) in PDB entry 1MK9
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 SER 231 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230F VAL* 1.3 77.7 - - - +
232F PHE* 1.3 67.0 + - - +
233F ASP* 4.0 13.8 + - - +
234F LYS* 3.0 33.6 + - - +
235F ALA* 2.9 20.1 + - - +
270F TYR* 3.6 2.9 - - - -
305F LEU* 5.3 0.8 - - - +
343F LYS 5.1 0.4 - - - -
344F THR* 3.9 22.7 - - - -
345F LYS* 4.1 4.2 - - - +
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Residues in contact with PHE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F SER* 1.3 72.5 - - - +
233F ASP* 1.3 70.9 + - - +
235F ALA* 3.4 2.4 + - - +
236F CYS* 3.2 34.3 + - - -
266F LEU* 5.2 1.3 - - + -
270F TYR* 3.2 53.4 + + + -
273F GLN* 3.6 31.2 - - - +
274F LYS 4.6 0.2 - - - -
275F GLY* 3.3 31.6 - - - -
278F LYS* 3.4 24.9 - - + -
343F LYS 5.2 1.0 + - - -
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Residues in contact with ASP 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F SER* 4.0 15.1 - - - +
232F PHE* 1.3 79.3 + - - +
234F LYS* 1.3 69.1 + - + +
236F CYS* 2.7 16.3 + - - +
237F GLU* 3.0 20.6 + - - +
278F LYS* 3.5 29.6 + - - +
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Residues in contact with LYS 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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230F VAL* 4.0 6.7 - - + -
231F SER* 3.0 26.8 + - - +
233F ASP* 1.3 80.0 - - + +
235F ALA* 1.3 55.9 + - - +
237F GLU* 2.6 49.2 + - - +
238F PHE* 2.8 27.0 + - + -
301F LEU* 4.1 29.0 - - + +
304F SER* 5.2 2.5 - - - -
305F LEU* 4.2 28.5 - - + -
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Residues in contact with ALA 235 (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 ILE* 5.6 0.9 - - - -
230F VAL* 3.8 7.7 - - + +
231F SER 2.9 8.0 + - - +
232F PHE 3.5 9.9 - - - +
234F LYS* 1.3 75.7 - - - +
236F CYS* 1.3 57.0 + - - +
238F PHE* 3.6 12.6 + - - +
239F ALA* 3.2 20.4 + - - +
265F PHE 4.1 1.4 - - - +
266F LEU* 3.4 18.1 - - + +
267F PRO* 3.7 19.1 - - + -
270F TYR* 3.7 25.8 - - + -
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Residues in contact with CYS 236 (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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232F PHE* 3.2 32.8 - - - -
233F ASP 2.7 15.1 + - - +
235F ALA* 1.3 72.1 - - - +
237F GLU* 1.3 60.3 + - + +
239F ALA 4.0 0.2 - - - -
240F GLY* 3.1 20.3 + - - -
266F LEU* 4.4 2.7 - - - -
275F GLY 3.5 9.6 - - - -
278F LYS* 3.6 30.3 - - + +
279F ILE* 3.5 35.2 - - + -
282F ALA* 3.6 11.8 - - + +
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Residues in contact with GLU 237 (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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324D LYS* 5.2 14.1 - - + -
233F ASP* 3.0 17.5 + - - +
234F LYS* 2.6 42.2 + - - +
236F CYS* 1.3 73.6 - - + +
238F PHE* 1.3 61.6 + - - +
240F GLY* 3.1 9.5 + - - -
241F TYR* 3.2 26.8 + - + -
282F ALA* 4.2 13.8 - - + +
301F LEU* 4.0 19.6 - - + +
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Residues in contact with PHE 238 (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 ILE* 3.4 31.6 - - + -
228F HIS* 5.4 0.7 - + - -
230F VAL* 3.9 18.6 - - + -
234F LYS* 2.8 39.1 + - + -
235F ALA* 3.8 10.5 - - - +
237F GLU* 1.3 74.0 - - - +
239F ALA* 1.3 54.8 + - - +
241F TYR* 3.0 3.7 + - - -
242F GLN* 2.7 30.6 + - - +
298F TYR* 2.9 65.8 - + - +
301F LEU* 3.6 25.6 - - + -
302F ALA* 3.9 8.1 - - - -
305F LEU* 4.1 18.2 - - + -
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Residues in contact with ALA 239 (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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235F ALA 3.2 8.4 + - - +
237F GLU 3.4 0.2 - - - -
238F PHE* 1.3 78.4 - - - +
240F GLY* 1.3 54.2 + - - +
242F GLN* 3.3 12.3 + - - +
243F CYS* 2.7 37.4 + - - +
265F PHE* 3.2 35.2 + - + +
279F ILE* 3.5 30.5 - - + -
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Residues in contact with GLY 240 (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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236F CYS 3.1 15.3 + - - -
237F GLU 3.4 5.8 - - - -
238F PHE 3.0 1.2 - - - -
239F ALA* 1.3 78.6 - - - +
241F TYR* 1.3 59.7 + - - +
243F CYS* 3.5 3.5 + - - +
244F GLN* 3.2 20.1 + - - +
279F ILE* 3.8 19.7 - - - +
282F ALA* 4.0 3.1 - - - -
283F HIS* 3.8 17.6 - - - -
286F CYS* 4.1 3.9 - - - -
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Residues in contact with TYR 241 (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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237F GLU* 3.2 30.2 + - + -
238F PHE* 3.0 2.7 + - - -
240F GLY* 1.3 72.6 - - - +
242F GLN* 1.3 67.8 - - - +
244F GLN* 3.0 6.6 + - - +
245F ILE* 2.8 29.0 + - + +
286F CYS* 3.9 22.4 - - - -
289F MET* 4.2 17.9 - - + -
294F ALA* 4.0 18.2 - - + +
297F ARG* 3.8 32.1 + - + +
298F TYR* 3.5 34.8 - + + -
301F LEU* 4.6 15.1 - - + +
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Residues in contact with GLN 242 (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 TYR* 3.4 22.7 - - - +
220F ARG* 3.4 19.0 - - - +
224F LEU* 3.8 12.9 - - - +
238F PHE* 2.7 12.7 + - - +
239F ALA* 3.3 14.6 - - - +
241F TYR* 1.3 75.9 - - - +
243F CYS* 1.3 63.4 + - - +
245F ILE* 3.0 6.0 + - - +
246F GLN* 3.0 38.1 + - - +
264F ASP 2.8 28.9 + - - -
265F PHE* 3.6 26.4 - - + +
298F TYR* 3.3 22.4 + - + -
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Residues in contact with CYS 243 (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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239F ALA 2.7 24.2 + - - +
240F GLY 3.6 4.0 - - - +
241F TYR 3.2 0.2 - - - -
242F GLN* 1.3 73.5 - - - +
244F GLN* 1.3 55.5 + - - +
247F PHE* 2.7 52.2 + - + +
248F GLY 3.5 0.3 + - - -
260F LEU* 3.7 11.7 - - - -
265F PHE* 3.6 17.7 - - - -
279F ILE* 3.6 22.9 - - - -
280F PHE* 3.7 12.3 - - - -
283F HIS* 3.4 22.7 - - + +
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Residues in contact with GLN 244 (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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240F GLY 3.2 10.8 + - - +
241F TYR* 3.0 11.6 + - - +
243F CYS* 1.3 79.4 - - - +
245F ILE* 1.3 60.5 + - - +
248F GLY* 3.3 22.5 + - - -
249F PRO* 3.0 38.5 - - - +
250F HIS 3.9 0.2 + - - -
283F HIS* 3.1 19.6 + - - +
286F CYS* 3.1 35.7 - - + +
287F GLY 3.8 5.2 + - - +
289F MET* 3.0 30.1 + - + +
290F SER 5.1 0.2 - - - +
291F GLU* 4.6 7.3 + - - -
294F ALA* 4.2 13.9 - - + -
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Residues in contact with ILE 245 (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 TYR* 3.4 50.7 - - + +
241F TYR* 2.8 27.8 + - + +
242F GLN 3.2 6.3 - - - +
244F GLN* 1.3 81.1 - - - +
246F GLN* 1.3 66.8 + - + +
248F GLY* 4.8 0.9 + - - -
291F GLU* 3.9 24.9 - - + +
294F ALA* 3.5 20.2 - - + +
295F LYS* 3.8 34.1 - - + +
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Residues in contact with GLN 246 (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 TYR* 4.0 1.4 + - - -
220F ARG* 3.4 25.1 + - - +
242F GLN* 3.0 31.0 + - - +
243F CYS 4.4 0.4 - - - +
245F ILE* 1.3 87.8 - - + +
247F PHE* 1.3 76.9 + - + +
248F GLY 3.7 0.2 - - - -
265F PHE* 3.2 31.0 - - - -
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Residues in contact with PHE 247 (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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243F CYS* 2.7 43.4 + - + +
246F GLN* 1.3 90.3 - - + +
248F GLY* 1.3 60.2 + - - +
249F PRO* 4.6 0.7 - - - +
255F HIS* 3.8 28.6 + + + +
259F PHE* 4.3 24.7 - + - -
260F LEU* 3.9 11.9 - - + -
265F PHE* 3.4 42.6 - + - -
283F HIS* 4.6 2.9 - + + -
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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