Contacts of the helix formed by residues 209 - 225 (chain H) 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 PRO 209 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749G GLU* 2.4 26.8 - - + +
750G ALA* 1.3 75.0 - - - +
210H VAL* 1.3 74.8 + - + +
212H LEU* 4.4 1.3 - - + +
213H ASN* 3.3 19.2 + - - +
292H ILE* 5.7 14.1 - - + +
295H LYS* 5.5 0.5 + - - -
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Residues in contact with VAL 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750G ALA 3.4 0.2 - - - -
209H PRO* 1.3 85.3 - - + +
211H GLN* 1.3 69.5 + - + +
213H ASN* 3.1 16.3 + - - +
214H LEU* 3.1 36.2 + - + +
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Residues in contact with GLN 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745G PRO* 4.1 17.8 - - + +
750G ALA* 3.8 21.0 + - + +
210H VAL* 1.3 82.5 - - + +
212H LEU* 1.3 64.0 + - - +
214H LEU* 3.2 34.8 + - - +
215H LEU* 3.3 16.6 + - - +
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Residues in contact with LEU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745G PRO* 4.1 14.2 - - - +
746G LEU* 3.8 30.5 - - + +
750G ALA 3.2 19.6 + - - +
209H PRO 4.4 1.6 - - - +
211H GLN* 1.3 76.2 - - - +
213H ASN* 1.3 64.7 + - - +
215H LEU* 2.9 20.1 + - + +
216H TYR* 3.0 10.2 + - - +
292H ILE* 3.3 38.8 - - + +
295H LYS* 3.9 16.2 - - + -
296H VAL* 3.5 29.2 - - + +
299H VAL* 4.6 6.7 - - + -
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Residues in contact with ASN 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209H PRO 3.3 13.9 + - - +
210H VAL* 3.1 12.7 + - - +
212H LEU* 1.3 79.7 - - - +
214H LEU* 1.3 64.8 + - - +
216H TYR* 3.1 9.2 + - - +
217H VAL* 2.8 51.2 + - - +
295H LYS* 2.5 35.0 + - + +
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Residues in contact with LEU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H VAL* 3.1 32.9 + - + +
211H GLN* 3.5 37.9 - - - +
212H LEU 3.2 0.2 - - - -
213H ASN* 1.3 84.2 - - - +
215H LEU* 1.3 62.5 + - + +
217H VAL* 4.1 5.2 - - + +
218H GLN* 3.1 27.7 + - - +
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Residues in contact with LEU 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744G ASN* 5.5 0.2 - - - +
745G PRO* 4.2 21.8 - - + -
746G LEU* 3.8 27.8 - - + -
211H GLN* 3.3 16.6 + - - +
212H LEU* 2.9 9.9 + - - +
214H LEU* 1.3 78.6 - - - +
216H TYR* 1.3 57.9 + - - +
218H GLN* 3.7 4.5 - - - +
219H ALA* 3.1 28.6 + - - +
299H VAL* 3.9 15.5 - - + +
303H ARG* 3.8 22.7 - - - +
308H TYR* 6.0 2.5 - - - +
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Residues in contact with TYR 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H LEU 3.0 10.9 + - - +
213H ASN* 3.1 13.0 + - - +
215H LEU* 1.3 73.5 - - - +
217H VAL* 1.3 60.9 + - + +
218H GLN 3.1 1.1 - - - -
219H ALA* 3.0 2.6 + - - +
220H ARG* 2.6 73.6 + - + +
242H GLN* 3.7 19.6 - - - +
245H ILE* 3.3 45.6 - - + +
246H GLN* 6.1 0.3 - - - +
295H LYS* 3.7 36.3 - - + -
298H TYR* 3.7 32.8 - + + -
299H VAL* 3.8 10.3 - - + +
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Residues in contact with VAL 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H ASN* 2.8 45.1 + - - +
214H LEU* 4.1 6.1 - - + +
216H TYR* 1.3 73.1 - - + +
218H GLN* 1.3 60.0 + - - +
220H ARG* 3.3 37.4 + - - +
221H ASP* 2.9 47.3 + - - +
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Residues in contact with GLN 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H LEU 3.1 18.3 + - - +
215H LEU* 3.7 6.5 - - - +
217H VAL* 1.3 81.4 - - - +
219H ALA* 1.3 61.6 + - - +
221H ASP* 3.9 3.9 - - - +
222H ASP* 2.6 57.9 + - - +
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215H LEU 3.1 15.5 + - - +
216H TYR* 3.0 4.5 + - - +
218H GLN* 1.3 75.7 - - - +
220H ARG* 1.3 70.3 + - - +
222H ASP* 3.5 7.8 + - - +
223H ILE* 3.3 23.9 + - - +
228H HIS* 5.5 1.0 + - - -
298H TYR* 4.3 10.3 - - + -
299H VAL* 4.8 9.0 - - + -
302H ALA* 4.2 23.8 - - + -
308H TYR* 5.2 11.2 - - + +
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Residues in contact with ARG 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H TYR* 2.6 60.3 + - + +
217H VAL* 3.5 30.7 - - - +
219H ALA* 1.3 72.3 - - - +
221H ASP* 1.3 77.7 + - - +
223H ILE* 2.8 22.0 + - - +
224H LEU* 2.8 28.9 + - + +
242H GLN* 3.6 24.6 + - - +
298H TYR* 3.4 21.4 + - + +
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Residues in contact with ASP 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H VAL* 2.9 31.9 + - - +
218H GLN* 3.9 5.2 - - - +
220H ARG* 1.3 95.0 + - - +
222H ASP* 1.3 54.0 + - - +
223H ILE 2.8 4.7 - - - -
224H LEU* 4.2 10.5 - - - +
225H ASN* 2.6 48.5 + - + +
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Residues in contact with ASP 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H GLN* 2.6 49.1 + - - +
219H ALA* 3.7 9.0 - - - +
220H ARG 3.3 0.2 - - - -
221H ASP* 1.3 76.5 - - - +
223H ILE* 1.3 53.1 + - - +
225H ASN* 3.4 7.5 - - - +
227H SER* 2.7 21.1 + - - -
228H HIS* 2.6 44.6 + - + +
308H TYR* 6.0 1.4 - - - -
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Residues in contact with ILE 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H ALA 3.3 11.2 + - - +
220H ARG 2.8 8.9 + - - +
221H ASP 2.8 0.4 + - - -
222H ASP* 1.3 77.6 - - - +
224H LEU* 1.3 70.2 + - + +
225H ASN 3.1 1.8 - - - -
226H GLY* 2.9 15.9 + - - -
228H HIS* 4.1 28.6 - - + +
230H VAL* 4.1 15.5 - - + -
235H ALA* 5.5 1.6 - - - +
238H PHE* 3.5 46.2 - - + -
265H PHE 6.2 0.2 - - - +
267H PRO* 3.6 27.7 - - + +
298H TYR* 3.7 19.5 - - + +
302H ALA* 4.7 4.0 - - + -
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Residues in contact with LEU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H ARG* 2.8 38.3 + - + +
221H ASP* 3.9 9.9 - - - +
223H ILE* 1.3 76.4 - - + +
225H ASN* 1.3 58.9 + - + +
226H GLY 3.2 3.3 + - - -
242H GLN* 3.8 15.9 - - - +
263H LYS 4.9 1.9 - - - +
264H ASP* 3.0 36.1 - - + +
265H PHE* 3.4 25.6 - - - +
266H LEU* 3.6 9.6 - - - +
267H PRO* 3.7 16.0 - - - +
268H LYS 4.3 3.5 + - - -
298H TYR* 5.6 0.9 - - - +
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Residues in contact with ASN 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H ASP* 2.6 39.7 + - + +
222H ASP* 3.1 11.6 + - - +
224H LEU* 1.3 70.1 - - + +
226H GLY* 1.3 63.5 + - - +
227H SER* 2.7 25.8 + - - -
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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