Contacts of the helix formed by residues 213 - 226 (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 ARG 213 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210L SER* 2.9 29.0 + - - +
211L GLY 4.0 5.3 + - - +
212L ASN* 1.3 81.4 + - - +
214L PRO* 1.3 65.5 - - - +
215L LEU 3.3 2.6 + - - -
216L THR* 3.4 4.6 + - - -
217L VAL* 3.0 28.7 + - + +
244L MET* 3.0 64.9 + - + +
247L GLU* 3.3 27.7 - - - +
248L ASP* 2.8 26.8 + - - -
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Residues in contact with PRO 214 (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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203L VAL* 4.5 6.1 - - + -
206L ILE* 4.5 3.8 - - + -
207L ALA* 3.9 28.3 - - + +
210L SER* 3.3 5.8 - - - +
212L ASN* 3.2 5.2 - - - +
213L ARG* 1.3 91.5 - - - +
215L LEU* 1.3 58.0 + - - +
217L VAL* 4.5 3.6 - - + -
218L ILE* 2.8 44.2 + - + +
247L GLU* 3.1 7.4 - - - +
259L ASN* 3.1 29.4 - - - +
260L ILE* 4.0 10.5 - - + -
263L ALA* 3.7 11.2 - - + -
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Residues in contact with LEU 215 (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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214L PRO* 1.3 76.2 - - - +
216L THR* 1.3 60.4 + - - +
218L ILE* 4.9 0.2 - - - -
219L MET* 2.8 54.8 + - + +
243L LEU* 5.0 3.6 - - + +
246L LEU* 4.0 19.3 - - + -
247L GLU* 2.9 28.3 + - + +
250L TYR* 3.8 34.3 - - + -
259L ASN* 3.9 8.1 - - + +
262L ALA* 4.0 5.8 - - + -
263L ALA* 3.6 27.3 - - - +
266L VAL* 3.9 12.8 - - + -
295L ALA* 4.0 5.6 - - + +
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Residues in contact with THR 216 (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* 3.9 12.7 - - - -
215L LEU* 1.3 72.6 - - - +
217L VAL* 1.3 60.5 + - + +
220L HIS* 2.9 34.5 + - + +
240L ILE* 4.6 13.5 - - + -
243L LEU* 3.4 45.9 + - + +
244L MET* 3.5 29.7 + - + -
247L GLU* 2.6 29.9 + - - -
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Residues in contact with VAL 217 (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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189L LEU* 4.6 11.0 - - + -
193L LEU* 3.4 37.7 - - + -
206L ILE* 4.5 7.9 - - + -
210L SER* 3.6 21.1 - - - -
213L ARG* 3.0 28.3 + - + +
214L PRO* 3.9 4.9 - - + +
216L THR* 1.3 78.3 - - + +
218L ILE* 1.3 51.7 + - - +
220L HIS* 3.6 4.7 + - - +
221L THR* 2.6 37.2 + - + +
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Residues in contact with ILE 218 (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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193L LEU* 4.2 17.0 - - + -
196L VAL* 4.7 4.7 - - + -
201L LEU* 4.1 16.4 - - + -
203L VAL* 4.0 18.4 - - + -
206L ILE* 4.3 9.9 - - + -
214L PRO* 2.8 29.6 + - + +
215L LEU 4.2 0.9 - - - +
217L VAL* 1.3 69.0 - - - +
219L MET* 1.3 66.3 + - + +
221L THR* 3.0 7.4 + - - -
222L ILE* 2.9 44.1 + - + +
263L ALA* 3.9 26.9 - - + +
266L VAL* 4.7 2.9 - - + -
267L GLN* 4.1 17.5 - - + +
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Residues in contact with MET 219 (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* 2.8 42.7 + - + +
218L ILE* 1.3 72.4 - - - +
220L HIS* 1.3 58.1 + - - +
222L ILE* 3.1 4.4 + - - +
223L PHE* 2.9 63.7 + - + -
239L LEU* 5.5 0.4 - - + -
242L TYR* 6.2 0.7 - - + -
243L LEU* 3.5 33.9 - - + -
246L LEU* 5.8 0.4 - - + -
266L VAL* 3.6 24.7 - - + -
291L ILE* 3.8 17.5 - - + +
292L PHE* 4.6 11.4 - - + -
295L ALA* 3.6 23.8 - - + -
345L ILE* 6.1 1.3 - - + -
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Residues in contact with HIS 220 (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* 2.9 20.2 + - + +
217L VAL* 3.6 5.1 + - - +
219L MET* 1.3 77.9 - - - +
221L THR* 1.3 64.2 + - - +
223L PHE* 3.2 8.0 + - - +
224L GLN* 3.0 68.0 + - + +
236L VAL* 4.0 14.2 - - + +
239L LEU* 4.1 13.5 - - + -
240L ILE* 3.4 28.9 - - + +
243L LEU* 3.9 9.1 - - + +
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Residues in contact with THR 221 (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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193L LEU* 3.7 38.7 - - + +
196L VAL* 4.8 11.8 - - - +
217L VAL* 2.6 24.0 + - + +
218L ILE* 3.0 16.5 + - - +
220L HIS* 1.3 82.3 - - - +
222L ILE* 1.3 57.0 + - - +
224L GLN* 3.4 8.9 + - + +
225L GLU* 2.9 29.5 + - - +
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Residues in contact with ILE 222 (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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196L VAL* 3.6 19.5 - - + -
218L ILE* 2.9 37.8 + - + +
219L MET* 3.7 4.7 - - - +
221L THR* 1.3 75.1 - - - +
223L PHE* 1.3 63.2 + - + +
225L GLU* 3.4 5.9 + - - +
226L ARG* 2.8 29.5 + - - +
266L VAL* 3.7 17.9 - - + -
267L GLN* 3.9 5.6 - - - -
270L HIS* 3.3 47.6 - - + +
291L ILE* 4.0 25.1 - - + -
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Residues in contact with PHE 223 (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* 2.9 56.0 + - + +
220L HIS 3.6 8.1 - - - +
222L ILE* 1.3 75.3 - - + +
224L GLN* 1.3 59.5 + - - +
227L ASP* 2.8 24.4 + - - -
228L LEU* 3.0 35.2 + - + -
229L LEU* 4.0 10.8 + - + -
234L ILE* 3.7 26.2 - - + -
239L LEU* 3.9 35.4 - - + -
288L LEU* 3.7 26.9 - - + -
291L ILE* 4.1 14.1 - - + -
292L PHE* 5.7 3.1 - - + -
345L ILE* 5.1 10.1 - - + -
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Residues in contact with GLN 224 (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* 3.0 54.8 + - + +
221L THR* 3.5 10.5 - - + +
223L PHE* 1.3 75.2 - - - +
225L GLU* 1.3 56.9 + - - +
227L ASP* 2.8 26.1 + - - +
229L LEU* 3.1 24.4 - - - +
236L VAL* 4.9 5.3 - - - +
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Residues in contact with GLU 225 (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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196L VAL* 4.4 10.2 - - + +
197L ASN* 3.4 36.6 + - - +
221L THR 2.9 18.7 + - - +
222L ILE* 3.4 8.3 - - - +
224L GLN* 1.3 78.2 - - - +
226L ARG* 1.3 59.2 + - + +
227L ASP* 3.6 1.4 + - - +
270L HIS* 4.1 14.6 - - + +
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Residues in contact with ARG 226 (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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222L ILE* 2.8 20.2 + - - +
225L GLU* 1.3 74.3 - - + +
227L ASP* 1.3 71.3 + - - +
228L LEU* 3.1 22.1 + - + +
231L THR* 4.7 1.9 + - - -
270L HIS* 2.9 43.6 + - + -
273L LEU* 3.5 15.5 - - - +
274L SER* 2.9 29.2 + - - +
284L ASP* 5.5 2.1 - - - +
287L ILE* 3.9 33.0 - - - +
291L ILE* 3.5 26.5 - - - +
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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