Contacts of the helix formed by residues 213 - 226 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210K SER* 2.9 27.6 + - - +
211K GLY 4.0 5.3 + - - +
212K ASN* 1.3 83.4 + - - +
214K PRO* 1.3 67.9 - - - +
215K LEU 3.3 2.6 + - - -
216K THR* 3.4 4.7 + - - -
217K VAL* 2.9 28.8 + - + +
244K MET* 3.0 62.2 + - + +
247K GLU* 3.4 26.9 - - - +
248K ASP* 2.8 26.9 + - - -
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Residues in contact with PRO 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K VAL* 4.5 5.8 - - + +
206K ILE* 4.5 5.4 - - + -
207K ALA* 3.9 27.8 - - + +
210K SER* 3.4 7.1 - - - +
212K ASN* 3.3 5.4 - - - +
213K ARG* 1.3 90.5 - - - +
215K LEU* 1.3 57.0 + - - +
217K VAL* 4.5 3.8 - - + -
218K ILE* 2.8 42.9 + - + +
247K GLU* 3.1 7.0 - - - +
259K ASN* 3.2 30.3 - - - +
260K ILE* 4.1 9.2 - - + -
263K ALA* 3.7 11.4 - - + -
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Residues in contact with LEU 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K PRO* 1.3 80.7 - - - +
216K THR* 1.3 58.7 + - - +
218K ILE* 4.9 0.4 - - + -
219K MET* 2.8 55.2 + - + +
243K LEU* 5.0 3.1 - - + +
246K LEU* 3.9 19.7 - - + -
247K GLU* 2.9 28.4 + - + +
250K TYR* 3.8 32.8 - - + -
259K ASN* 4.0 7.9 - - + +
262K ALA* 3.9 5.8 - - + -
263K ALA* 3.6 28.2 - - - +
266K VAL* 3.9 12.6 - - + -
295K ALA* 4.0 5.4 - - + +
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Residues in contact with THR 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K ARG* 3.4 12.7 + - - -
215K LEU* 1.3 73.0 - - - +
217K VAL* 1.3 66.3 + - + +
220K HIS* 3.0 27.6 + - + +
240K ILE* 4.5 13.5 - - + -
243K LEU* 3.4 44.0 + - + +
244K MET* 3.6 30.1 + - + -
247K GLU* 2.5 28.9 + - - -
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Residues in contact with VAL 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LEU* 4.6 11.4 - - + -
193K LEU* 3.4 37.9 - - + -
206K ILE* 4.5 7.0 - - + -
210K SER* 3.7 20.0 - - - -
213K ARG* 2.9 28.7 + - + +
214K PRO* 3.9 4.3 - - + +
216K THR* 1.3 79.3 - - + +
218K ILE* 1.3 53.2 + - - +
220K HIS* 3.6 4.7 + - - +
221K THR* 2.7 36.6 + - + +
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Residues in contact with ILE 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K LEU* 4.2 17.0 - - + -
196K VAL* 4.7 4.5 - - + -
201K LEU* 4.1 16.6 - - + -
203K VAL* 4.0 18.2 - - + -
206K ILE* 4.3 11.9 - - + -
214K PRO 2.8 26.8 + - - +
215K LEU* 4.2 0.9 - - + +
217K VAL* 1.3 69.0 - - - +
219K MET* 1.3 65.7 + - - +
221K THR* 3.0 8.0 + - - +
222K ILE* 2.9 43.6 + - + +
263K ALA* 3.9 26.9 - - + +
266K VAL* 4.7 2.7 - - + -
267K GLN* 4.1 17.3 - - + +
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Residues in contact with MET 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K LEU* 2.8 41.9 + - + +
218K ILE* 1.3 73.0 - - + +
220K HIS* 1.3 59.1 + - - +
222K ILE* 3.1 4.9 + - - +
223K PHE* 2.9 62.3 + - + -
239K LEU* 5.5 0.7 - - + -
242K TYR* 6.2 0.4 - - + -
243K LEU* 3.5 32.5 - - + -
246K LEU* 5.8 0.2 - - + -
266K VAL* 3.6 24.0 - - + -
291K ILE* 3.8 16.8 - - + +
292K PHE* 4.6 12.1 - - + -
295K ALA* 3.6 23.8 - - + -
345K ILE* 6.1 1.6 - - + -
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Residues in contact with HIS 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K THR* 3.0 20.6 + - + +
217K VAL* 3.6 5.1 + - - +
219K MET* 1.3 77.5 - - - +
221K THR* 1.3 64.4 + - - +
223K PHE* 3.2 7.0 + - - +
224K GLN* 3.0 67.6 + - + +
229K LEU* 4.7 0.7 - - + -
236K VAL* 4.0 14.2 - - + +
239K LEU* 4.2 12.3 - - + -
240K ILE* 3.4 28.8 - - + +
243K LEU* 3.9 8.7 - - + +
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Residues in contact with THR 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K LEU* 3.8 38.3 - - + +
196K VAL* 4.8 12.6 - - - +
217K VAL* 2.7 20.1 + - + +
218K ILE* 3.0 15.8 + - - +
220K HIS* 1.3 82.4 - - - +
222K ILE* 1.3 55.7 + - - +
224K GLN* 3.5 8.7 - - + +
225K GLU* 2.9 29.5 + - - +
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Residues in contact with ILE 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K VAL* 3.6 20.4 - - + -
218K ILE* 2.9 37.6 + - + +
219K MET* 3.7 4.3 - - - +
221K THR* 1.3 75.1 - - - +
223K PHE* 1.3 63.0 + - + +
225K GLU* 3.4 6.0 + - - +
226K ARG* 2.8 29.6 + - - +
266K VAL* 3.8 18.2 - - + -
267K GLN* 4.0 6.1 - - - -
270K HIS* 3.4 45.3 - - + +
291K ILE* 4.0 25.8 - - + -
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Residues in contact with PHE 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K MET* 2.9 57.2 + - + +
220K HIS 3.6 7.9 - - - +
222K ILE* 1.3 76.4 - - + +
224K GLN* 1.3 59.5 + - - +
226K ARG 3.4 0.2 + - - -
227K ASP* 2.9 23.9 + - - -
228K LEU* 3.0 36.3 + - + -
229K LEU* 4.0 10.6 + - + +
234K ILE* 3.7 25.4 - - + -
239K LEU* 3.9 35.4 - - + -
288K LEU* 3.7 26.2 - - + -
291K ILE* 4.1 14.4 - - + -
292K PHE* 5.8 2.9 - - + -
345K ILE* 5.2 10.1 - - + -
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Residues in contact with GLN 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K HIS* 3.0 55.0 + - + +
221K THR* 3.5 11.2 - - + +
223K PHE* 1.3 75.1 - - - +
225K GLU* 1.3 57.2 + - - +
227K ASP* 2.8 26.1 + - - +
229K LEU* 3.1 24.0 - - - +
236K VAL* 4.9 5.5 - - - +
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Residues in contact with GLU 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K VAL* 4.4 10.1 - - + +
197K ASN* 3.4 37.2 + - - +
221K THR 2.9 18.9 + - - +
222K ILE* 3.4 8.7 - - - +
224K GLN* 1.3 77.9 - - - +
226K ARG* 1.3 58.7 + - + +
227K ASP* 3.6 1.4 + - - +
270K HIS* 4.1 13.9 - - + +
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Residues in contact with ARG 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222K ILE* 2.8 19.8 + - - +
225K GLU* 1.3 74.3 - - + +
227K ASP* 1.3 72.1 + - - +
228K LEU* 3.0 21.4 + - + +
231K THR* 4.7 2.1 + - - -
270K HIS* 2.9 43.9 + - + -
273K LEU* 3.5 17.1 + - - +
274K SER* 2.9 28.6 + - - +
284K ASP* 5.5 2.1 - - - +
287K ILE* 3.9 32.4 - - + +
291K ILE* 3.5 27.1 - - - +
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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