Contacts of the helix formed by residues 209 - 225 (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 PRO 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A GLU* 3.4 17.5 - - + +
750A ALA* 1.3 91.6 - - - +
210B VAL* 1.3 69.3 + - + +
212B LEU* 4.1 4.9 - - + +
213B ASN* 3.2 23.4 + - - +
292B ILE* 5.2 17.9 - - + -
295B LYS* 5.4 1.6 + - - +
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Residues in contact with VAL 210 (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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750A ALA 3.1 0.8 - - - -
209B PRO* 1.3 85.5 - - + +
211B GLN* 1.3 60.3 + - - +
213B ASN* 3.9 7.6 + - + +
214B LEU* 3.5 19.4 + - - +
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Residues in contact with GLN 211 (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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745A PRO* 3.6 29.7 - - + +
750A ALA* 2.8 23.2 + - + -
210B VAL* 1.3 77.8 + - - +
212B LEU* 1.3 63.3 + - - +
213B ASN 3.1 1.3 - - - -
214B LEU* 3.0 40.3 + - - +
215B LEU* 3.2 25.3 + - + +
400D LEU* 5.9 2.6 - - - +
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Residues in contact with LEU 212 (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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745A PRO 3.9 20.6 + - - +
746A LEU* 4.3 8.3 - - + +
750A ALA* 2.6 22.2 + - - +
209B PRO* 4.1 4.5 - - + +
211B GLN* 1.3 73.5 - - - +
213B ASN* 1.3 57.8 + - - +
215B LEU* 3.2 15.1 + - + +
216B TYR* 3.0 24.1 + - - +
292B ILE* 3.4 42.8 - - + +
295B LYS* 3.9 17.7 - - + +
296B VAL* 3.5 34.1 - - + +
299B VAL* 5.2 4.3 - - + -
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Residues in contact with ASN 213 (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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209B PRO 3.2 17.7 + - - +
210B VAL* 3.9 10.0 + - - +
211B GLN 3.1 0.2 - - - -
212B LEU* 1.3 79.0 - - - +
214B LEU* 1.3 59.2 + - - +
216B TYR* 4.0 5.5 - - - -
217B VAL* 2.8 54.5 + - - +
295B LYS* 2.7 38.5 + - - +
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Residues in contact with LEU 214 (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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210B VAL 3.5 11.8 + - - +
211B GLN* 3.0 35.6 + - - +
213B ASN* 1.3 79.9 - - - +
215B LEU* 1.3 59.7 + - + +
217B VAL* 4.3 3.0 - - - +
218B GLN* 3.1 41.4 + - + +
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Residues in contact with LEU 215 (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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745A PRO* 4.1 24.7 - - + -
746A LEU* 4.8 7.4 - - + -
211B GLN* 3.2 25.3 + - - +
212B LEU* 3.5 14.8 - - + +
213B ASN 3.1 0.4 - - - -
214B LEU* 1.3 79.8 - - + +
216B TYR* 1.3 59.7 + - - +
218B GLN* 3.5 5.6 + - + +
219B ALA* 3.0 31.0 + - - +
299B VAL* 3.4 16.7 - - + +
303B ARG* 3.8 24.7 - - - +
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Residues in contact with TYR 216 (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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212B LEU 3.0 15.7 + - - +
213B ASN* 3.7 4.0 - - - +
215B LEU* 1.3 74.0 - - - +
217B VAL* 1.3 72.0 + - + +
219B ALA* 3.2 2.3 + - - +
220B ARG* 2.6 76.6 + - + +
242B GLN* 3.4 26.0 + - - +
245B ILE* 3.6 32.9 - - + +
246B GLN* 4.5 1.7 + - - +
295B LYS* 3.8 31.4 - - + -
298B TYR* 3.5 45.5 - + + -
299B VAL* 3.4 13.4 - - + +
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Residues in contact with VAL 217 (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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213B ASN* 2.8 43.8 + - - +
214B LEU* 4.3 4.3 - - + +
216B TYR* 1.3 81.3 - - + +
218B GLN* 1.3 61.6 + - - +
220B ARG* 3.3 32.1 - - - +
221B ASP* 2.8 43.6 + - - +
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Residues in contact with GLN 218 (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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214B LEU* 3.1 40.6 + - + +
215B LEU* 3.7 8.5 - - + +
217B VAL* 1.3 77.6 - - - +
219B ALA* 1.3 65.3 + - - +
221B ASP* 3.5 4.3 - - - +
222B ASP* 3.0 45.6 + - - +
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Residues in contact with ALA 219 (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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215B LEU 3.0 15.1 + - - +
216B TYR 3.7 2.5 - - - +
218B GLN* 1.3 80.5 - - - +
220B ARG* 1.3 63.3 + - - +
222B ASP* 3.2 16.0 + - - +
223B ILE* 3.2 18.4 + - - +
228B HIS* 5.5 0.7 + - - -
298B TYR* 4.6 6.3 - - + -
299B VAL* 4.2 14.8 - - + -
302B ALA* 4.3 21.5 - - + -
308B TYR* 5.4 11.2 - - + +
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Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B TYR* 2.6 70.9 + - + +
217B VAL* 3.3 33.6 - - - +
219B ALA* 1.3 72.9 - - - +
221B ASP* 1.3 68.3 + - - +
223B ILE* 3.3 3.3 + - - +
224B LEU* 3.0 43.2 + - + +
242B GLN* 3.8 20.4 - - - +
246B GLN* 4.6 10.9 + - - +
298B TYR* 3.6 25.6 + - + +
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Residues in contact with ASP 221 (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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217B VAL* 2.8 35.8 + - - +
218B GLN* 3.5 4.9 - - - +
220B ARG* 1.3 100.2 + - - +
222B ASP* 1.3 64.5 + - - +
224B LEU* 4.0 6.7 - - - +
225B ASN* 2.9 34.8 + - - +
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Residues in contact with ASP 222 (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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218B GLN* 3.0 32.6 + - - +
219B ALA* 3.2 10.4 + - - +
221B ASP* 1.3 76.9 - - - +
223B ILE* 1.3 58.8 + - - +
225B ASN* 2.9 11.1 + - - +
227B SER* 2.7 52.7 + - - -
228B HIS* 3.0 15.8 + - + +
308B TYR* 6.0 2.2 - - + -
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Residues in contact with ILE 223 (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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219B ALA 3.2 13.0 + - - +
220B ARG 3.7 6.3 - - - +
221B ASP 3.2 0.4 - - - -
222B ASP* 1.3 76.1 - - - +
224B LEU* 1.3 71.6 + - + +
226B GLY* 3.3 8.0 + - - -
228B HIS* 3.8 34.1 - - + +
230B VAL* 3.7 20.4 - - + -
235B ALA* 5.3 1.1 - - + -
238B PHE* 3.5 49.8 - - + -
267B PRO* 3.0 32.8 - - + +
298B TYR* 4.6 9.4 - - + +
302B ALA* 4.8 3.4 - - + -
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Residues in contact with LEU 224 (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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220B ARG* 3.0 44.6 + - + +
221B ASP* 4.0 7.6 - - - +
223B ILE* 1.3 86.6 - - + +
225B ASN* 1.3 57.7 + - - +
226B GLY 3.1 5.2 + - - -
242B GLN* 4.2 7.0 - - - +
264B ASP* 2.9 33.4 - - - +
265B PHE 4.0 19.5 - - - +
266B LEU* 4.1 9.3 - - - +
267B PRO* 3.6 17.4 - - + +
268B LYS* 4.1 5.2 + - - +
298B TYR* 5.1 2.9 - - - +
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Residues in contact with ASN 225 (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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221B ASP* 2.9 32.5 + - - +
222B ASP* 2.9 8.6 + - - +
224B LEU* 1.3 74.2 - - - +
226B GLY* 1.3 57.2 + - - +
227B SER* 2.6 35.4 + - - -
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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