Contacts of the helix formed by residues 235 - 249 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233L LYS 3.4 9.4 - - - +
234L ILE* 1.3 85.7 - - + +
236L VAL* 1.3 58.4 + - - +
237L ASP* 3.1 14.8 - - - +
238L THR* 2.7 47.2 + - + +
239L LEU* 2.9 10.9 + - - +
345L ILE 4.9 0.2 - - - +
347L GLN* 3.8 31.9 - - + +
348L ASN* 4.6 2.0 - - - +
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Residues in contact with VAL 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L HIS* 4.0 15.3 - - + +
224L GLN* 4.9 3.6 - - - +
229L LEU* 4.2 28.3 - - + -
234L ILE 3.1 4.9 + - - +
235L PRO* 1.3 70.4 - - - +
237L ASP* 1.3 64.1 + - - +
239L LEU* 3.3 1.0 + - - +
240L ILE* 2.9 47.8 + - + +
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Residues in contact with ASP 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L PRO* 3.9 14.0 - - - +
236L VAL* 1.3 80.7 + - - +
238L THR* 1.3 68.2 + - - +
240L ILE* 3.5 5.1 + - - +
241L THR* 2.7 39.7 + - - +
342L ASN* 3.1 16.8 + - - +
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Residues in contact with THR 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L PRO* 2.7 38.9 + - + +
237L ASP* 1.3 73.2 + - - +
239L LEU* 1.3 57.2 + - - +
241L THR* 3.2 2.4 + - - -
242L TYR* 2.9 29.1 + - - +
342L ASN* 2.9 45.7 + - - +
343L CYS 4.0 0.2 - - - -
344L ASP 3.7 5.2 - - - +
345L ILE* 3.6 34.5 - - + +
347L GLN* 3.9 6.9 + - - +
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Residues in contact with LEU 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L MET* 5.5 0.2 - - + -
220L HIS* 4.1 22.7 - - + -
223L PHE* 3.9 39.5 - - + -
229L LEU* 3.5 25.8 - - + -
234L ILE* 4.3 11.4 - - + -
235L PRO 2.9 10.7 + - - +
236L VAL* 3.5 10.1 - - - +
238L THR* 1.3 77.3 - - - +
240L ILE* 1.3 57.1 + - + +
242L TYR* 3.3 3.3 + - + +
243L LEU* 2.9 52.6 + - + +
345L ILE* 3.5 19.2 - - + +
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Residues in contact with ILE 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L THR* 4.6 9.9 - - + -
220L HIS* 3.4 36.1 - - + +
236L VAL* 2.9 37.7 + - + +
237L ASP* 4.0 4.5 - - - +
239L LEU* 1.3 80.3 - - + +
241L THR* 1.3 67.5 + - - +
243L LEU* 4.3 6.1 - - + -
244L MET* 2.9 57.5 + - + +
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Residues in contact with THR 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237L ASP* 2.7 27.4 + - - +
238L THR 3.5 5.8 - - - -
240L ILE* 1.3 80.0 - - - +
242L TYR* 1.3 59.2 + - - +
244L MET* 3.5 6.3 + - - +
245L THR* 2.8 28.7 + - - +
341L GLU* 3.6 26.7 - - + +
342L ASN* 3.8 15.6 + - - +
343L CYS* 3.6 10.1 - - - -
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Residues in contact with TYR 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L MET* 6.2 0.4 - - + -
238L THR 2.9 14.7 + - - +
239L LEU* 3.6 3.6 - - + +
241L THR* 1.3 73.8 - - - +
243L LEU* 1.3 66.2 + - + +
245L THR* 2.9 7.7 + - - -
246L LEU* 2.7 57.9 + - + +
292L PHE* 3.4 32.3 - + - -
296L ILE* 3.6 8.1 - - - +
334L GLY* 2.7 24.4 + - - -
337L LEU* 3.7 24.6 - - + +
338L LEU* 3.6 16.2 - - + -
343L CYS* 3.3 41.5 - - + +
345L ILE* 3.8 17.7 - - + -
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Residues in contact with LEU 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L LEU* 5.0 4.0 - - + +
216L THR* 3.4 48.4 + - + +
219L MET* 3.5 44.6 - - + -
220L HIS* 3.9 9.6 - - + +
239L LEU* 2.9 46.5 + - + +
240L ILE* 3.9 3.1 - - + +
242L TYR* 1.3 80.5 - - + +
244L MET* 1.3 58.0 + - - +
246L LEU* 3.7 12.1 - - + +
247L GLU* 2.8 33.6 + - - +
345L ILE* 6.3 0.2 - - + -
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Residues in contact with MET 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L ARG* 3.0 48.0 + - + +
216L THR* 3.5 25.3 + - + -
240L ILE* 2.9 41.4 + - + +
241L THR* 3.6 7.6 - - - +
243L LEU* 1.3 75.4 - - - +
245L THR* 1.3 58.2 + - - +
248L ASP* 2.9 32.6 + - - +
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Residues in contact with THR 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241L THR* 2.8 15.4 + - - +
242L TYR* 2.9 8.4 + - - -
244L MET* 1.3 75.1 - - - +
246L LEU* 1.3 63.5 + - - +
248L ASP* 3.1 9.8 + - + +
249L HIS* 2.7 53.0 + - + -
337L LEU* 3.8 13.2 - - + -
340L GLU* 3.4 21.6 + - - +
343L CYS* 3.9 12.7 - - - -
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Residues in contact with LEU 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L LEU* 4.0 15.7 - - + -
219L MET* 5.8 0.2 - - + -
242L TYR* 2.7 43.9 + - + +
243L LEU* 3.7 10.3 - - + +
245L THR* 1.3 71.6 - - - +
247L GLU* 1.3 57.9 + - - +
249L HIS* 2.8 25.1 + - - +
250L TYR* 3.5 12.2 - - + -
295L ALA* 3.8 21.8 - - + +
296L ILE* 3.8 34.3 - - + -
299L VAL* 3.7 28.0 - - + -
334L GLY* 4.7 1.6 - - - -
337L LEU* 3.7 15.4 - - + +
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Residues in contact with GLU 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L ASN* 4.4 2.5 - - - +
213L ARG* 3.4 32.1 - - - +
214L PRO* 3.1 3.1 - - - +
215L LEU* 2.9 40.5 + - + +
216L THR* 2.6 37.2 + - - -
243L LEU 2.8 19.5 + - - +
246L LEU* 1.3 73.0 - - - +
248L ASP* 1.3 62.9 + - - +
250L TYR* 3.1 22.7 + - - +
259L ASN* 2.8 35.2 + - + +
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Residues in contact with ASP 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L ARG* 2.8 26.4 + - - -
244L MET* 2.9 28.4 + - - +
245L THR* 3.3 13.4 - - - +
246L LEU 3.1 0.2 - - - -
247L GLU* 1.3 76.9 - - - +
249L HIS* 1.3 64.1 + - + +
250L TYR 3.3 10.2 + - - +
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Residues in contact with HIS 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245L THR* 2.7 36.0 + - + -
246L LEU 2.8 12.8 + - - +
248L ASP* 1.3 79.3 - - + +
250L TYR* 1.3 58.9 + - - +
251L HIS* 3.7 6.0 + - - -
299L VAL* 3.6 15.9 - - + -
300L ASP* 2.9 36.4 + - + +
333L VAL* 4.4 11.2 - - + -
337L LEU* 3.6 32.1 - - + +
340L GLU* 5.5 1.6 - - - -
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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