Contacts of the helix formed by residues 235 - 249 (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 PRO 235 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233F LYS 3.4 9.4 - - - +
234F ILE* 1.3 85.0 - - + +
236F VAL* 1.3 56.7 + - - +
237F ASP* 3.1 15.0 - - - +
238F THR* 2.7 48.1 + - + +
239F LEU* 2.9 11.3 + - - +
345F ILE 5.0 0.2 - - - +
347F GLN* 3.8 30.5 - - + +
348F ASN* 4.6 2.0 - - - +
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Residues in contact with VAL 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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220F HIS* 4.0 14.8 - - + +
224F GLN* 4.9 3.6 - - - +
229F LEU* 4.3 28.3 - - + -
234F ILE 3.2 4.5 + - - +
235F PRO* 1.3 70.3 - - - +
237F ASP* 1.3 65.0 + - - +
239F LEU* 3.3 1.8 + - - +
240F ILE* 3.0 46.0 + - + +
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Residues in contact with ASP 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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235F PRO* 3.9 14.5 - - - +
236F VAL* 1.3 79.2 + - - +
238F THR* 1.3 66.8 + - - +
240F ILE* 3.5 4.8 + - - +
241F THR* 2.7 39.3 + - - +
342F ASN* 3.1 17.6 + - - +
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Residues in contact with THR 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F PRO* 2.7 39.6 + - + +
237F ASP* 1.3 72.9 + - - +
239F LEU* 1.3 61.8 + - - +
241F THR* 3.2 2.3 + - - -
242F TYR* 2.9 23.7 + - - +
342F ASN* 2.9 44.2 + - - +
343F CYS 4.0 0.4 - - - -
344F ASP 3.7 5.6 - - - +
345F ILE* 3.7 34.1 - - - +
347F GLN* 3.9 6.4 + - - +
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Residues in contact with LEU 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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219F MET* 5.5 0.2 - - + -
220F HIS* 4.2 21.8 - - + -
223F PHE* 3.8 37.9 - - + -
229F LEU* 3.5 24.9 - - + -
234F ILE* 4.3 12.1 - - + -
235F PRO 2.9 9.8 + - - +
236F VAL* 3.3 11.0 + - - +
238F THR* 1.3 76.4 - - - +
240F ILE* 1.3 58.6 + - + +
242F TYR* 3.2 3.4 + - + +
243F LEU* 2.9 52.9 + - + +
345F ILE* 3.5 18.3 - - + +
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Residues in contact with ILE 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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216F THR* 4.6 9.4 - - + -
220F HIS* 3.4 35.9 - - + +
236F VAL* 3.0 35.3 + - + +
237F ASP* 4.0 5.2 - - - +
239F LEU* 1.3 79.7 - - + +
241F THR* 1.3 67.5 + - - +
243F LEU* 3.9 6.4 - - + +
244F MET* 2.9 51.1 + - + +
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Residues in contact with THR 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 ASP* 2.7 26.7 + - - +
238F THR 3.5 4.3 - - - -
240F ILE* 1.3 78.1 - - - +
242F TYR* 1.3 61.2 + - - +
244F MET* 3.6 6.0 + - - +
245F THR* 2.9 28.3 + - - +
341F GLU* 3.6 13.5 - - + +
342F ASN* 3.8 16.6 + - - +
343F CYS* 3.6 22.0 - - - -
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Residues in contact with TYR 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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219F MET* 6.2 0.9 - - + -
238F THR 2.9 13.8 + - - +
239F LEU* 3.6 3.1 - - + +
241F THR* 1.3 74.5 - - - +
243F LEU* 1.3 67.1 + - + +
245F THR* 2.9 4.7 + - - -
246F LEU* 2.7 57.0 + - + +
292F PHE* 3.5 32.8 - + - -
296F ILE* 3.7 8.3 - - - +
334F GLY* 2.7 24.7 + - - -
337F LEU* 3.7 24.0 - - + -
338F LEU* 3.6 16.2 - - + -
343F CYS* 3.3 44.4 - - + +
345F ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 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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215F LEU* 5.0 4.1 - - + +
216F THR* 3.4 45.9 + - + +
219F MET* 3.5 45.3 - - + -
220F HIS* 3.9 9.2 - - + +
239F LEU* 2.9 46.3 + - + +
240F ILE* 3.9 2.7 - - + +
242F TYR* 1.3 80.0 - - + +
244F MET* 1.3 58.9 + - - +
246F LEU* 3.7 12.2 - - + +
247F GLU* 2.8 33.6 + - - +
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Residues in contact with MET 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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213F ARG* 3.1 49.0 + - + +
216F THR* 3.6 23.8 - - + +
240F ILE* 2.9 41.2 + - + +
241F THR* 3.6 7.4 - - - +
243F LEU* 1.3 77.8 - - - +
245F THR* 1.3 58.2 + - - +
248F ASP* 2.9 32.9 + - - +
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Residues in contact with THR 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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241F THR* 2.9 16.1 + - - +
242F TYR* 2.9 8.8 + - - -
244F MET* 1.3 73.8 - - - +
246F LEU* 1.3 63.3 + - - +
248F ASP* 3.1 10.2 + - + +
249F HIS* 2.7 54.0 + - + -
337F LEU* 3.8 13.7 - - + -
340F GLU* 3.4 22.2 + - - +
343F CYS* 3.9 12.5 - - - -
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Residues in contact with LEU 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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215F LEU* 4.0 16.6 - - + -
242F TYR* 2.7 44.4 + - + +
243F LEU* 3.7 9.4 - - + +
245F THR* 1.3 73.0 - - - +
247F GLU* 1.3 59.2 + - - +
249F HIS* 2.8 24.9 + - - +
250F TYR* 3.6 9.1 - - + -
295F ALA* 3.7 26.0 - - + +
296F ILE* 3.7 29.6 - - + -
299F VAL* 3.7 27.6 - - + -
334F GLY* 4.7 1.8 - - - -
337F LEU* 3.7 14.5 - - + +
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Residues in contact with GLU 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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212F ASN* 4.4 2.2 - - - +
213F ARG* 3.4 31.9 - - - +
214F PRO* 3.1 2.9 - - - +
215F LEU* 2.9 40.8 + - + +
216F THR* 2.6 36.6 + - - -
243F LEU 2.8 20.8 + - - +
246F LEU* 1.3 73.4 - - - +
248F ASP* 1.3 62.2 + - - +
250F TYR* 3.1 23.3 + - - +
259F ASN* 2.8 35.7 + - + +
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Residues in contact with ASP 248 (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* 2.8 28.0 + - - -
244F MET* 2.9 28.4 + - - +
245F THR* 3.3 13.7 - - - +
246F LEU 3.1 0.2 - - - -
247F GLU* 1.3 75.6 - - - +
249F HIS* 1.3 64.6 + - + +
250F TYR 3.2 10.0 + - - +
251F HIS* 5.5 0.2 - - - -
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Residues in contact with HIS 249 (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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245F THR* 2.7 33.2 + - + -
246F LEU 2.8 12.1 + - - +
248F ASP* 1.3 79.9 - - + +
250F TYR* 1.3 60.8 + - - +
251F HIS* 3.7 5.9 + - - -
299F VAL* 3.6 14.6 - - + -
300F ASP* 2.9 36.7 + - + +
333F VAL* 4.5 11.9 - - + -
337F LEU* 3.6 33.4 - - + +
340F GLU* 5.5 1.3 - - - -
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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