Contacts of the helix formed by residues 235 - 249 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C LYS 3.4 10.1 - - - +
234C ILE* 1.3 85.4 - - + +
236C VAL* 1.3 56.6 + - - +
237C ASP* 3.1 14.1 - - - +
238C THR* 2.7 49.6 + - + +
239C LEU* 2.9 10.4 + - - +
345C ILE 5.0 0.4 - - - +
347C GLN* 3.8 31.0 - - + +
348C ASN* 4.6 1.8 - - - +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C HIS* 4.0 15.3 - - + +
224C GLN* 4.9 3.8 - - - +
229C LEU* 4.2 28.3 - - + -
234C ILE 3.1 4.7 + - - +
235C PRO* 1.3 70.1 - - - +
237C ASP* 1.3 64.8 + - - +
239C LEU* 3.3 1.8 + - - +
240C ILE* 2.9 46.6 + - + +
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Residues in contact with ASP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C PRO* 3.9 14.4 - - - +
236C VAL* 1.3 79.8 + - - +
238C THR* 1.3 68.5 + - - +
240C ILE* 3.6 5.1 + - - +
241C THR* 2.7 38.6 + - - +
342C ASN* 3.1 18.1 + - - +
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Residues in contact with THR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C PRO* 2.7 38.5 + - + +
237C ASP* 1.3 73.5 + - - +
239C LEU* 1.3 62.4 + - - +
241C THR* 3.2 2.3 + - - -
242C TYR* 2.9 23.0 + - - +
342C ASN* 2.9 44.5 + - - +
343C CYS 4.0 0.2 - - - -
344C ASP 3.7 5.8 - - - +
345C ILE* 3.7 34.8 - - + +
347C GLN* 3.9 6.7 + - - +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C MET* 5.5 0.2 - - + -
220C HIS* 4.2 21.3 - - + -
223C PHE* 3.8 40.2 - - + -
229C LEU* 3.5 26.2 - - + -
234C ILE* 4.3 12.1 - - + -
235C PRO 2.9 9.9 + - - +
236C VAL* 3.3 10.5 + - - +
238C THR* 1.3 78.1 - - - +
240C ILE* 1.3 58.5 + - + +
242C TYR* 3.6 1.5 - - + +
243C LEU* 2.9 58.3 + - + +
345C ILE* 3.5 18.6 - - + +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C THR* 4.6 9.6 - - + -
220C HIS* 3.5 35.9 - - + +
236C VAL* 2.9 34.4 + - + +
237C ASP* 4.1 4.9 - - - +
239C LEU* 1.3 83.2 - - + +
241C THR* 1.3 64.5 + - - +
243C LEU* 3.9 6.7 - - + +
244C MET* 2.9 50.1 + - + +
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Residues in contact with THR 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ASP* 2.7 25.3 + - - +
238C THR 3.2 5.1 + - - -
240C ILE* 1.3 78.4 - - - +
242C TYR* 1.3 61.3 + - - +
244C MET* 3.6 6.0 - - - +
245C THR* 2.9 29.1 + - - +
341C GLU* 3.6 26.5 - - + +
342C ASN* 3.8 14.9 + - - +
343C CYS* 3.7 9.2 - - - -
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Residues in contact with TYR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C MET* 6.2 0.9 - - + -
238C THR 2.9 13.2 + - - +
239C LEU* 3.6 3.6 - - + +
241C THR* 1.3 74.7 - - - +
243C LEU* 1.3 66.0 + - + +
245C THR* 3.0 7.9 + - - -
246C LEU* 2.8 57.7 + - + +
292C PHE* 3.5 32.7 - + - -
296C ILE* 3.6 8.3 - - - +
334C GLY* 2.8 23.5 + - - -
337C LEU* 3.7 24.5 - - + -
338C LEU* 3.6 16.2 - - + -
343C CYS* 3.3 41.1 - - + +
345C ILE* 3.8 17.7 - - + -
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 5.0 3.2 - - + +
216C THR* 3.4 47.4 + - + +
219C MET* 3.5 45.8 - - + -
220C HIS* 3.9 10.1 - - + +
239C LEU* 2.9 45.9 + - + +
240C ILE* 3.9 3.1 - - - +
242C TYR* 1.3 80.8 - - + +
244C MET* 1.3 57.3 + - - +
246C LEU* 3.7 10.8 - - + +
247C GLU* 2.8 33.3 + - - +
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Residues in contact with MET 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ARG* 3.0 47.7 + - + +
216C THR* 3.6 24.0 - - + -
240C ILE* 2.9 41.2 + - + +
241C THR* 3.6 7.2 - - - +
243C LEU* 1.3 76.7 - - - +
245C THR* 1.3 57.3 + - - +
248C ASP* 2.9 32.9 + - - +
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Residues in contact with THR 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C THR* 2.9 16.0 + - - +
242C TYR* 3.0 8.1 + - - -
244C MET* 1.3 73.8 - - - +
246C LEU* 1.3 63.4 + - - +
248C ASP* 3.1 10.7 + - + +
249C HIS* 2.7 51.8 + - + -
337C LEU* 3.7 13.5 - - + -
340C GLU* 3.4 22.5 + - - +
343C CYS* 3.8 12.4 - - - -
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 4.0 15.7 - - + -
219C MET* 5.7 0.2 - - + -
242C TYR* 2.8 43.9 + - + +
243C LEU* 3.7 9.9 - - + +
245C THR* 1.3 72.9 - - - +
247C GLU* 1.3 58.0 + - - +
249C HIS* 2.8 24.9 + - - +
250C TYR* 3.6 9.1 - - + -
295C ALA* 3.7 26.9 - - + +
296C ILE* 3.8 28.5 - - + -
299C VAL* 3.8 27.6 - - + -
334C GLY* 4.7 2.2 - - - -
337C LEU* 3.7 14.8 - - + +
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Residues in contact with GLU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ASN* 4.4 2.0 - - - +
213C ARG* 3.4 30.2 - - - +
214C PRO* 3.1 2.8 - - - +
215C LEU* 2.9 40.4 + - + +
216C THR* 2.6 37.4 + - - -
243C LEU 2.8 16.2 + - - +
246C LEU* 1.3 77.2 - - - +
248C ASP* 1.3 62.2 + - - +
250C TYR* 3.1 23.6 + - - +
259C ASN* 2.7 37.2 + - + +
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Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ARG* 2.8 28.4 + - - -
244C MET* 2.9 27.7 + - - +
245C THR* 3.3 13.9 - - + +
246C LEU 3.1 0.2 - - - -
247C GLU* 1.3 76.6 - - - +
249C HIS* 1.3 64.3 + - + +
250C TYR 3.2 9.8 + - - +
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Residues in contact with HIS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C THR* 2.7 33.0 + - + -
246C LEU 2.8 13.3 + - - +
248C ASP* 1.3 80.9 - - + +
250C TYR* 1.3 59.5 + - - +
251C HIS* 3.7 5.3 + - - -
299C VAL* 3.6 14.6 - - + -
300C ASP* 2.9 35.3 + - + +
333C VAL* 4.5 11.9 - - + -
337C LEU* 3.6 33.3 - - + +
340C GLU* 5.5 1.1 - - - -
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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