Contacts of the helix formed by residues 213 - 226 (chain F) in PDB entry 1MKD
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 ARG 213 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210F SER* 3.0 26.9 + - - +
211F GLY 4.1 5.0 + - - +
212F ASN* 1.3 83.0 + - - +
214F PRO* 1.3 66.3 - - - +
215F LEU 3.2 2.2 - - - -
216F THR* 3.4 4.8 + - - -
217F VAL* 2.9 28.3 + - + +
244F MET* 3.1 63.7 + - + +
247F GLU* 3.4 27.3 - - - +
248F ASP* 2.8 27.7 + - - -
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Residues in contact with PRO 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F VAL* 4.5 5.4 - - + -
206F ILE* 4.5 5.4 - - + -
207F ALA* 3.9 28.0 - - + +
210F SER* 3.4 5.8 - - - +
212F ASN* 3.3 5.8 - - - +
213F ARG* 1.3 90.7 - - - +
215F LEU* 1.3 58.3 + - - +
217F VAL* 4.5 3.6 - - + -
218F ILE* 2.8 42.6 + - + +
247F GLU* 3.1 7.4 - - - +
259F ASN* 3.2 29.2 - - - +
260F ILE* 4.0 9.9 - - + -
263F ALA* 3.7 12.1 - - + -
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Residues in contact with LEU 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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214F PRO* 1.3 80.1 - - - +
216F THR* 1.3 57.0 + - - +
219F MET* 2.8 54.6 + - + +
243F LEU* 5.0 3.4 - - + +
246F LEU* 4.0 20.4 - - + -
247F GLU* 2.9 28.5 + - + +
250F TYR* 3.8 32.8 - - + -
259F ASN* 3.9 7.6 - - + +
262F ALA* 4.0 5.8 - - + -
263F ALA* 3.6 27.3 - - - +
266F VAL* 3.9 12.6 - - + -
295F ALA* 4.0 6.3 - - + +
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Residues in contact with THR 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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213F ARG* 3.4 9.6 + - - -
215F LEU* 1.3 73.2 - - - +
217F VAL* 1.3 65.1 + - + +
220F HIS* 3.0 26.3 + - + +
240F ILE* 4.6 13.2 - - + -
243F LEU* 3.4 44.0 + - + +
244F MET* 3.6 32.2 + - + -
247F GLU* 2.6 29.8 + - - -
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Residues in contact with VAL 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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189F LEU* 4.6 11.4 - - + -
193F LEU* 3.4 37.0 - - + -
206F ILE* 4.4 7.2 - - + -
210F SER* 3.7 20.2 - - - -
213F ARG* 2.9 27.6 + - + +
214F PRO* 3.9 4.5 - - + +
216F THR* 1.3 78.1 - - + +
218F ILE* 1.3 52.7 + - - +
220F HIS* 3.4 4.9 + - - +
221F THR* 2.7 36.8 + - + +
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Residues in contact with ILE 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F LEU* 4.2 16.6 - - + -
196F VAL* 4.8 4.0 - - + -
201F LEU* 4.1 16.6 - - + -
203F VAL* 4.0 18.6 - - + -
206F ILE* 4.3 12.3 - - + -
214F PRO 2.8 27.1 + - - +
215F LEU 4.2 0.9 - - - +
217F VAL* 1.3 70.0 - - - +
219F MET* 1.3 64.3 + - - +
221F THR* 3.0 7.6 + - - -
222F ILE* 3.0 43.9 + - + +
263F ALA* 3.9 26.5 - - + +
266F VAL* 4.7 2.7 - - + -
267F GLN* 4.1 17.9 - - + +
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Residues in contact with MET 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 LEU* 2.8 42.3 + - + +
218F ILE* 1.3 73.4 - - - +
220F HIS* 1.3 64.5 + - - +
222F ILE* 3.1 3.8 + - - -
223F PHE* 2.9 57.2 + - + -
239F LEU* 5.5 1.1 - - + -
242F TYR* 6.2 1.3 - - + -
243F LEU* 3.5 32.5 - - + -
246F LEU* 5.8 0.2 - - + -
266F VAL* 3.6 24.2 - - + -
291F ILE* 3.8 15.9 - - + +
292F PHE* 4.6 11.2 - - + -
295F ALA* 3.6 24.0 - - + -
345F ILE* 6.1 1.8 - - + -
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Residues in contact with HIS 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 THR* 3.0 20.2 + - + +
217F VAL* 3.7 4.5 + - - +
219F MET* 1.3 76.7 - - - +
221F THR* 1.3 64.2 + - + +
223F PHE* 3.2 7.2 + - - +
224F GLN* 3.0 68.3 + - + +
229F LEU* 4.7 0.9 - - + -
236F VAL* 4.0 14.4 - - + +
239F LEU* 4.2 12.3 - - + -
240F ILE* 3.4 28.8 - - + +
243F LEU* 3.9 9.5 - - + +
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Residues in contact with THR 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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193F LEU* 3.7 39.3 - - + +
196F VAL* 4.8 11.8 - - - +
217F VAL 2.7 23.3 + - - +
218F ILE* 3.0 15.9 + - - +
220F HIS* 1.3 80.9 - - - +
222F ILE* 1.3 57.0 + - - +
224F GLN* 3.6 9.5 - - + +
225F GLU* 2.9 28.4 + - - +
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Residues in contact with ILE 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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196F VAL* 3.6 19.5 - - + -
218F ILE* 3.0 38.5 + - + +
219F MET* 3.7 4.7 - - - +
221F THR* 1.3 73.3 - - - +
223F PHE* 1.3 63.2 + - + +
225F GLU* 3.5 6.0 - - - +
226F ARG* 2.8 29.6 + - - +
266F VAL* 3.8 18.2 - - + -
267F GLN* 4.0 5.6 - - - -
270F HIS* 3.4 46.2 - - + +
291F ILE* 4.0 25.1 - - + -
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Residues in contact with PHE 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 MET* 2.9 56.1 + - + +
220F HIS 3.2 8.5 + - - +
222F ILE* 1.3 76.0 - - + +
224F GLN* 1.3 59.0 + - - +
226F ARG 3.3 0.2 + - - -
227F ASP* 2.8 24.6 + - - -
228F LEU* 3.0 35.0 + - + -
229F LEU* 4.0 11.1 + - + -
234F ILE* 3.7 26.5 - - + -
239F LEU* 3.8 34.1 - - + -
288F LEU* 3.8 25.4 - - + -
291F ILE* 4.1 13.9 - - + -
292F PHE* 5.7 3.6 - - + -
345F ILE* 5.1 10.3 - - + -
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Residues in contact with GLN 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 HIS* 3.0 53.1 + - + +
221F THR* 3.6 11.2 - - + +
223F PHE* 1.3 76.9 - - - +
225F GLU* 1.3 57.2 + - - +
227F ASP* 2.8 23.6 + - - +
229F LEU* 3.2 23.7 - - - +
236F VAL* 4.9 4.9 - - - +
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Residues in contact with GLU 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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196F VAL* 4.4 10.2 - - + +
197F ASN* 3.4 36.9 + - - +
221F THR 2.9 20.0 + - - +
222F ILE* 3.5 8.5 - - - +
224F GLN* 1.3 78.9 - - - +
226F ARG* 1.3 60.1 + - + +
227F ASP* 5.0 1.4 - - - +
270F HIS* 4.1 13.5 - - + +
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Residues in contact with ARG 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 ILE* 2.8 21.1 + - - +
225F GLU* 1.3 74.6 - - + +
227F ASP* 1.3 71.0 + - - +
228F LEU* 3.0 22.0 + - + +
231F THR* 4.7 1.7 + - - -
270F HIS* 2.8 42.1 + - + -
273F LEU* 3.5 15.7 + - - +
274F SER* 2.9 28.4 + - - +
284F ASP* 5.6 1.9 - - - +
287F ILE* 3.9 32.2 - - + +
291F ILE* 3.5 25.6 - - - +
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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