Contacts of the helix formed by residues 213 - 226 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D SER* 2.9 27.3 + - - +
211D GLY 4.0 5.5 + - - +
212D ASN* 1.3 83.9 + - - +
214D PRO* 1.4 64.6 - - - +
215D LEU 3.3 2.5 - - - -
216D THR* 3.4 4.7 + - + -
217D VAL* 3.0 30.4 + - + +
244D MET* 3.0 64.5 + - + +
247D GLU* 3.4 26.5 - - - +
248D ASP* 2.8 27.1 + - - -
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Residues in contact with PRO 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D VAL* 4.5 6.1 - - + +
206D ILE* 4.5 3.6 - - + -
207D ALA* 3.9 29.4 - - + +
210D SER* 3.4 6.6 - - - +
212D ASN* 3.3 5.4 - - - -
213D ARG* 1.4 90.3 - - - +
215D LEU* 1.3 57.1 + - - +
217D VAL* 4.5 3.6 - - + -
218D ILE* 2.8 44.7 + - + +
247D GLU* 3.1 7.0 - - - +
259D ASN* 3.2 28.7 - - - +
260D ILE* 4.1 10.3 - - + -
263D ALA* 3.7 10.8 - - + -
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Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D PRO* 1.3 80.5 - - - +
216D THR* 1.3 59.3 + - - +
218D ILE* 4.9 0.4 - - + -
219D MET* 2.8 54.9 + - + +
243D LEU* 5.1 3.1 - - + +
246D LEU* 4.0 18.6 - - + -
247D GLU* 2.9 29.0 + - + +
250D TYR* 3.8 33.0 - - + -
259D ASN* 3.9 8.3 - - + +
262D ALA* 4.0 6.5 - - + -
263D ALA* 3.7 26.7 - - - +
266D VAL* 3.9 12.8 - - + -
295D ALA* 4.0 5.2 - - + +
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Residues in contact with THR 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ARG* 3.4 13.2 + - + -
215D LEU* 1.3 73.0 - - - +
217D VAL* 1.3 66.1 + - + +
220D HIS* 3.0 28.0 + - + +
240D ILE* 4.6 13.5 - - + -
243D LEU* 3.4 43.8 + - + +
244D MET* 3.6 29.1 + - + -
247D GLU* 2.6 28.9 + - - -
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Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 4.6 10.8 - - + -
193D LEU* 3.4 38.1 - - + -
206D ILE* 4.5 7.0 - - + -
210D SER* 3.6 20.2 - - - -
213D ARG* 3.0 32.1 + - + +
214D PRO* 4.0 4.3 - - + +
216D THR* 1.3 78.9 - - + +
218D ILE* 1.3 52.7 + - + +
220D HIS* 3.6 4.7 + - - +
221D THR* 2.7 36.3 + - + +
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Residues in contact with ILE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 4.2 17.3 - - + -
196D VAL* 4.7 4.3 - - + -
201D LEU* 4.2 16.6 - - + -
203D VAL* 4.0 18.2 - - + -
206D ILE* 4.3 9.6 - - + -
214D PRO* 2.8 29.0 + - + +
215D LEU 4.2 0.9 - - - +
217D VAL* 1.3 70.2 - - - +
219D MET* 1.3 65.7 + - + +
221D THR* 3.0 8.6 + - - +
222D ILE* 2.9 44.6 + - + +
263D ALA* 3.8 26.7 - - + +
266D VAL* 4.7 2.2 - - + -
267D GLN* 4.1 17.0 - - + +
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Residues in contact with MET 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 2.8 42.4 + - + +
218D ILE* 1.3 74.5 - - - +
220D HIS* 1.3 58.2 + - - +
222D ILE* 3.1 4.7 + - - +
223D PHE* 2.8 65.1 + - + -
239D LEU* 5.4 0.4 - - + -
242D TYR* 6.2 1.3 - - + -
243D LEU* 3.5 36.6 - - + -
246D LEU* 5.8 0.2 - - + -
266D VAL* 3.6 24.7 - - + -
291D ILE* 3.9 15.9 - - + +
292D PHE* 4.6 11.0 - - + -
295D ALA* 3.6 23.8 - - + -
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Residues in contact with HIS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D THR* 3.0 20.1 + - + +
217D VAL* 3.6 4.5 - - - +
219D MET* 1.3 76.7 - - - +
221D THR* 1.3 64.1 + - - +
223D PHE* 3.2 7.0 + - - +
224D GLN* 2.9 69.0 + - + +
229D LEU* 4.7 0.7 - - + -
236D VAL* 4.0 14.4 - - + +
239D LEU* 4.2 12.1 - - + -
240D ILE* 3.5 29.3 - - + +
243D LEU* 3.9 9.5 - - + +
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Residues in contact with THR 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 3.7 38.1 - - + +
196D VAL* 4.8 13.0 - - - +
217D VAL* 2.7 19.1 + - + +
218D ILE* 3.0 16.5 + - - +
220D HIS* 1.3 81.5 - - - +
222D ILE* 1.3 55.9 + - - +
224D GLN* 3.5 9.0 + - + +
225D GLU* 2.9 29.1 + - - +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D VAL* 3.6 19.7 - - + -
218D ILE* 2.9 38.9 + - + +
219D MET* 3.1 4.7 + - - +
221D THR* 1.3 74.3 - - - +
223D PHE* 1.3 62.7 + - + +
225D GLU* 3.4 5.9 - - - +
226D ARG* 2.8 29.9 + - - +
266D VAL* 3.8 18.4 - - + -
267D GLN* 4.0 5.4 - - - -
270D HIS* 3.3 47.6 - - + +
291D ILE* 4.0 24.2 - - + -
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Residues in contact with PHE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D MET* 2.8 56.2 + - + +
220D HIS 3.5 7.4 - - - +
222D ILE* 1.3 76.3 - - + +
224D GLN* 1.3 61.4 + - - +
226D ARG 3.4 0.3 + - - -
227D ASP* 2.9 24.1 + - - -
228D LEU* 3.0 36.6 + - + -
229D LEU* 4.0 9.8 + - + -
234D ILE* 3.7 25.8 - - + -
239D LEU* 3.9 34.5 - - + -
288D LEU* 3.8 26.5 - - + -
291D ILE* 4.1 14.6 - - + -
292D PHE* 5.7 3.1 - + + -
345D ILE* 5.1 10.3 - - + -
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Residues in contact with GLN 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D HIS* 2.9 55.2 + - + +
221D THR* 3.5 10.5 - - + +
223D PHE* 1.3 76.1 - - - +
225D GLU* 1.3 59.8 + - - +
227D ASP* 2.8 23.3 + - - +
229D LEU* 3.1 23.2 - - - +
236D VAL* 4.9 4.9 - - - +
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D VAL* 4.4 9.9 - - + +
197D ASN* 3.4 39.0 + - - +
221D THR 2.9 19.3 + - - +
222D ILE* 3.4 8.3 - - - +
224D GLN* 1.3 77.7 - - - +
226D ARG* 1.3 59.5 + - + +
227D ASP* 3.6 1.2 + - - +
270D HIS* 4.1 13.5 - - + +
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Residues in contact with ARG 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ILE* 2.8 21.4 + - - +
225D GLU* 1.3 73.7 - - + +
227D ASP* 1.3 70.9 + - - +
228D LEU* 3.1 21.4 + - + +
231D THR* 4.7 1.9 + - - -
270D HIS* 2.8 44.6 + - + -
273D LEU* 3.5 16.1 - - - +
274D SER* 2.9 29.2 + - - +
284D ASP* 5.6 1.9 - - - +
287D ILE* 3.9 32.4 - - + +
291D ILE* 3.6 25.9 - - - +
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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