Contacts of the helix formed by residues 231 - 248 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B VAL* 1.3 76.9 - - - +
232B PHE* 1.3 67.6 + - - +
233B ASP* 4.0 10.0 + - - +
234B LYS* 3.0 32.1 + - - +
235B ALA* 2.8 22.2 + - - +
270B TYR* 3.5 3.6 - - - -
305B LEU* 5.7 0.2 - - - +
343B LYS 5.1 0.9 - - - -
344B THR* 3.7 22.2 - - - -
345B LYS* 4.2 2.7 - - - +
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Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B SER* 1.3 73.8 - - - +
233B ASP* 1.3 73.8 + - - +
235B ALA* 3.2 3.1 + - - +
236B CYS* 3.1 31.9 + - - -
266B LEU* 5.5 0.7 - - + -
270B TYR* 3.3 44.7 + + + -
273B GLN* 3.2 64.6 - - + +
274B LYS 4.9 0.2 - - - -
275B GLY* 3.8 18.6 - - - -
278B LYS* 3.2 35.2 - - + -
343B LYS 5.4 0.8 + - - -
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B SER* 3.2 10.3 + - - +
232B PHE* 1.3 89.8 + - - +
234B LYS* 1.3 62.3 + - + +
236B CYS* 3.4 6.2 + - - +
237B GLU* 3.2 29.2 + - - +
278B LYS* 3.6 26.8 + - - +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B VAL* 4.1 2.7 - - + -
231B SER* 3.0 32.7 + - - +
233B ASP* 1.3 75.2 - - + +
235B ALA* 1.3 59.5 - - - +
237B GLU* 2.7 47.6 + - - +
238B PHE* 2.8 30.6 + - + -
301B LEU* 4.1 25.1 - - + +
304B SER* 5.3 1.4 + - - -
305B LEU* 4.3 27.7 - - + +
323H ASN* 6.2 1.6 - - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ILE* 5.3 1.1 - - - -
230B VAL* 3.7 14.7 - - + +
231B SER 2.8 11.5 + - - +
232B PHE 3.4 9.2 - - - +
234B LYS* 1.3 77.3 - - - +
236B CYS* 1.3 55.7 + - - +
238B PHE* 3.4 14.0 + - - +
239B ALA* 2.9 27.2 + - - +
265B PHE 4.1 1.7 - - - +
266B LEU* 3.7 11.4 - - + +
267B PRO* 3.8 25.1 - - + +
270B TYR* 4.0 8.3 - - + -
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Residues in contact with CYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B PHE* 3.1 29.9 + - - -
233B ASP* 3.7 8.5 - - - +
234B LYS 3.1 0.4 - - - -
235B ALA* 1.3 75.0 - - - +
237B GLU* 1.3 60.6 + - - +
239B ALA* 3.9 7.7 - - - +
240B GLY 3.0 21.3 + - - -
266B LEU* 4.4 8.5 - - - -
275B GLY* 4.3 11.9 - - - -
278B LYS* 3.8 46.7 - - + +
279B ILE* 3.9 9.3 - - - +
282B ALA* 3.6 10.1 - - - +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASP* 3.2 21.3 + - - +
234B LYS* 2.7 39.7 + - - +
236B CYS* 1.3 72.3 - - - +
238B PHE* 1.3 65.1 + - - +
240B GLY* 3.1 10.0 + - - -
241B TYR* 3.2 27.1 + - + -
282B ALA* 4.2 12.7 - - + +
301B LEU* 4.0 23.1 - - + +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ILE* 3.5 31.0 - - + -
230B VAL* 4.0 8.1 - - + -
234B LYS* 2.8 42.9 + - + -
235B ALA* 3.4 12.3 - - - +
237B GLU* 1.3 75.4 - - - +
239B ALA* 1.3 65.8 + - - +
241B TYR* 3.2 5.0 + - - +
242B GLN* 2.8 18.6 + - - +
265B PHE 5.8 0.2 - - - +
298B TYR* 3.3 58.0 - + - +
301B LEU* 3.5 30.7 - - + -
302B ALA* 3.7 24.9 - - - -
305B LEU* 4.2 6.7 - - + -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ALA 2.9 13.0 + - - +
236B CYS* 3.9 0.7 - - - +
238B PHE* 1.3 71.4 - - - +
240B GLY* 1.3 73.1 + - - +
242B GLN* 2.8 12.5 + - - +
243B CYS* 2.6 20.8 + - - +
265B PHE* 3.3 34.0 + - + +
266B LEU* 4.5 0.4 - - + -
279B ILE* 3.3 32.5 - - + -
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B CYS 3.0 15.4 + - - -
237B GLU 3.1 5.4 + - - -
238B PHE 3.1 0.6 - - - -
239B ALA* 1.3 80.8 - - - +
241B TYR* 1.3 53.2 + - - +
243B CYS* 2.6 20.1 + - - +
244B GLN* 3.0 10.2 + - - +
279B ILE* 4.0 8.4 - - - +
282B ALA* 3.7 18.2 - - - -
283B HIS* 3.8 15.4 - - - -
286B CYS* 4.7 1.6 - - - -
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLU* 3.2 31.3 + - + -
238B PHE* 3.2 9.7 + - - +
240B GLY* 1.3 71.8 - - - +
242B GLN* 1.3 52.7 + - - +
244B GLN* 2.8 12.2 + - - +
245B ILE* 2.7 37.7 + - + +
286B CYS* 4.2 18.0 - - - -
289B MET* 4.2 16.4 - - + -
294B ALA* 3.5 27.8 - - + +
297B ARG* 3.9 34.4 + - + +
298B TYR* 3.6 20.0 - + + -
301B LEU* 4.5 18.3 - - + +
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Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TYR* 3.4 21.8 - - - +
220B ARG* 3.8 22.7 - - - +
224B LEU* 4.2 6.9 - - - +
238B PHE 2.8 12.9 + - - +
239B ALA* 2.8 15.6 + - - +
241B TYR* 1.3 72.5 - - - +
243B CYS* 1.3 57.8 + - - +
245B ILE* 3.9 1.7 - - - +
246B GLN* 2.9 58.0 + - - +
264B ASP* 3.1 22.1 + - - +
265B PHE* 3.3 38.9 - - + +
298B TYR* 4.3 7.5 + - + -
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Residues in contact with CYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ALA 2.6 10.9 + - - -
240B GLY 2.6 11.0 + - - +
242B GLN* 1.3 69.8 - - - +
244B GLN* 1.3 58.1 + - - +
247B PHE* 2.8 45.0 + - + +
248B GLY 3.6 0.5 + - - +
260B LEU* 3.7 17.0 - - - -
265B PHE* 3.4 24.5 - - - -
279B ILE* 3.5 27.4 - - - -
280B PHE* 4.9 2.7 - - - -
283B HIS* 3.5 26.0 - - + +
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLY 3.0 8.2 + - - +
241B TYR* 2.8 14.8 + - - +
243B CYS* 1.3 78.6 - - - +
245B ILE* 1.3 56.6 + - - +
248B GLY* 3.1 29.8 + - - -
249B PRO* 3.1 30.5 - - - +
250B HIS 3.9 2.1 + - - -
283B HIS* 2.8 32.5 + - + +
286B CYS* 3.1 30.0 - - + +
287B GLY 3.1 11.6 + - - +
289B MET* 3.5 27.5 + - + +
290B SER 5.4 0.4 - - - +
291B GLU* 4.9 6.1 + - - +
294B ALA* 4.3 15.0 - - + -
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TYR* 3.6 37.2 - - + +
241B TYR 2.7 19.4 + - - +
242B GLN 3.9 4.0 - - - +
244B GLN* 1.3 79.7 - - - +
246B GLN* 1.3 63.8 + - + +
248B GLY* 4.6 1.6 + - - -
291B GLU* 3.8 26.6 - - + +
294B ALA* 3.4 19.3 - - + +
295B LYS* 3.2 56.5 - - + +
298B TYR* 4.9 0.9 - - + -
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Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TYR* 4.5 7.0 + - - +
220B ARG* 4.6 6.6 + - - +
242B GLN* 2.9 52.9 + - + +
243B CYS 4.3 0.7 - - - +
245B ILE* 1.3 82.7 - - + +
247B PHE* 1.3 81.6 + - + +
265B PHE* 3.6 16.0 - - - -
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B CYS* 2.8 35.6 + - + +
246B GLN* 1.3 91.7 - - + +
248B GLY* 1.3 60.2 + - - +
249B PRO* 4.8 1.7 - - - +
254B LYS* 6.0 2.5 - - - -
255B HIS* 3.9 25.1 - + + +
259B PHE* 3.5 41.3 - + - -
260B LEU* 3.6 17.7 - - + -
265B PHE* 3.7 24.5 - + - -
280B PHE* 5.9 0.2 - + - -
283B HIS* 4.7 2.7 - + + -
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B CYS 3.6 0.2 + - - -
244B GLN* 3.1 24.8 + - - -
245B ILE 4.6 1.0 + - - -
246B GLN 3.8 0.6 - - - -
247B PHE* 1.3 80.6 - - - +
249B PRO* 1.3 79.8 - - - +
283B HIS* 2.9 19.4 + - - -
289B MET 5.9 0.2 - - - -
291B GLU* 6.2 2.7 - - - -
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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