Contacts of the helix formed by residues 213 - 226 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210E SER* 2.9 30.3 + - - +
211E GLY 3.9 5.2 + - - +
212E ASN* 1.3 81.0 + - - +
214E PRO* 1.3 66.0 - - - +
215E LEU 3.3 2.6 + - - -
216E THR* 3.4 4.4 + - - -
217E VAL* 3.0 28.5 + - + +
244E MET* 3.0 63.9 + - + +
247E GLU* 3.4 25.3 - - - +
248E ASP* 2.7 28.1 + - - -
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Residues in contact with PRO 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E VAL* 4.5 6.5 - - + +
206E ILE* 4.5 4.9 - - + -
207E ALA* 3.9 28.0 - - + +
210E SER* 3.3 6.9 - - - +
212E ASN* 3.3 5.2 - - - +
213E ARG* 1.3 90.5 - - - +
215E LEU* 1.3 58.2 + - - +
217E VAL* 4.5 3.6 - - + -
218E ILE* 2.8 41.6 + - + +
247E GLU* 3.1 7.2 - - - +
259E ASN* 3.2 28.9 - - - +
260E ILE* 4.1 9.9 - - + -
263E ALA* 3.7 11.7 - - + -
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E PRO* 1.3 80.1 - - - +
216E THR* 1.3 57.3 + - - +
219E MET* 2.8 54.1 + - + +
243E LEU* 5.0 3.6 - - + +
246E LEU* 4.0 19.3 - - + -
247E GLU* 3.0 32.6 + - + +
250E TYR* 3.8 29.8 - - + -
259E ASN* 4.0 8.3 - - + +
262E ALA* 4.0 6.3 - - + -
263E ALA* 3.6 27.1 - - - +
266E VAL* 3.9 12.6 - - + -
295E ALA* 4.0 4.9 - - + +
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Residues in contact with THR 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ARG* 3.9 9.7 - - - -
215E LEU* 1.3 75.1 - - - +
217E VAL* 1.3 64.5 + - + +
220E HIS* 3.0 26.3 + - + +
240E ILE* 4.5 12.6 - - + -
243E LEU* 3.4 45.4 + - + +
244E MET* 3.6 32.0 + - + -
247E GLU* 2.6 24.6 + - - -
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Residues in contact with VAL 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E LEU* 4.6 11.2 - - + -
193E LEU* 3.4 37.2 - - + -
206E ILE* 4.5 7.2 - - + -
210E SER* 3.7 20.2 - - - -
213E ARG* 3.0 23.9 + - + +
214E PRO* 3.9 3.8 - - + +
216E THR* 1.3 79.2 - - + +
218E ILE* 1.3 52.4 + - + +
220E HIS* 3.6 4.9 + - - +
221E THR* 2.7 36.7 + - + +
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Residues in contact with ILE 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E LEU* 4.2 16.8 - - + -
196E VAL* 4.8 4.5 - - + -
201E LEU* 4.1 17.7 - - + -
203E VAL* 4.0 18.2 - - + -
206E ILE* 4.3 11.4 - - + -
214E PRO 2.8 25.8 + - - +
215E LEU 4.2 0.7 - - - +
217E VAL* 1.3 70.0 - - - +
219E MET* 1.3 66.4 + - - +
221E THR* 3.0 7.7 + - - -
222E ILE* 2.9 44.0 + - + +
263E ALA* 3.9 27.8 - - + +
266E VAL* 4.7 2.9 - - + -
267E GLN* 4.1 15.5 - - + +
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Residues in contact with MET 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 2.8 41.9 + - + +
218E ILE* 1.3 72.2 - - + +
220E HIS* 1.3 58.6 + - - +
222E ILE* 3.2 4.2 + - - +
223E PHE* 2.9 61.9 + - + -
239E LEU* 5.5 0.4 - - + -
242E TYR* 6.2 0.9 - - + -
243E LEU* 3.5 33.2 - - + -
246E LEU* 5.7 0.2 - - + -
266E VAL* 3.6 24.2 - - + -
291E ILE* 3.8 16.4 - - + +
292E PHE* 4.6 11.4 - - + -
295E ALA* 3.6 23.8 - - + -
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Residues in contact with HIS 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E THR* 3.0 20.0 + - + +
217E VAL* 3.6 5.1 + - - +
219E MET* 1.3 76.9 - - - +
221E THR* 1.3 62.9 + - - +
223E PHE* 3.2 7.0 + - - +
224E GLN* 3.0 68.5 + - + +
229E LEU* 4.7 0.4 - - + -
236E VAL* 4.0 14.2 - - + +
239E LEU* 4.2 13.2 - - + -
240E ILE* 3.5 28.2 - - + +
243E LEU* 3.9 8.6 - - + +
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Residues in contact with THR 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E LEU* 3.8 38.6 - - + +
196E VAL* 4.8 12.4 - - - +
217E VAL* 2.7 19.2 + - + +
218E ILE* 3.0 15.9 + - - +
220E HIS* 1.3 82.2 - - - +
222E ILE* 1.3 56.3 + - - +
224E GLN* 3.5 9.7 + - + +
225E GLU* 2.9 28.4 + - - +
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Residues in contact with ILE 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E VAL* 3.6 20.4 - - + -
218E ILE* 2.9 38.2 + - + +
219E MET* 3.7 4.3 - - - +
221E THR* 1.3 72.8 - - - +
223E PHE* 1.3 63.5 + - + +
225E GLU* 3.5 6.4 - - - +
226E ARG* 2.9 29.5 + - - +
228E LEU* 5.6 0.2 - - + -
266E VAL* 3.8 17.7 - - + -
267E GLN* 4.0 5.6 - - - -
270E HIS* 3.4 47.1 - - + +
291E ILE* 4.0 25.1 - - + -
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Residues in contact with PHE 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E MET* 2.9 54.4 + - + +
220E HIS 3.6 7.2 - - - +
222E ILE* 1.3 76.6 - - + +
224E GLN* 1.3 60.8 + - - +
226E ARG 3.4 0.2 + - - -
227E ASP* 2.9 23.6 + - - -
228E LEU* 3.0 36.0 + - + -
229E LEU* 4.0 10.9 + - + -
234E ILE* 3.7 25.6 - - + -
239E LEU* 3.8 34.5 - - + -
288E LEU* 3.8 25.6 - - + -
291E ILE* 4.1 17.3 - - + -
292E PHE* 5.7 3.4 - + + -
345E ILE* 5.2 9.4 - - + -
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Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E HIS* 3.0 53.9 + - + +
221E THR* 3.6 11.4 - - + +
223E PHE* 1.3 76.1 - - - +
225E GLU* 1.3 56.6 + - - +
227E ASP* 2.8 26.1 + - - +
229E LEU* 3.1 23.8 - - - +
236E VAL* 4.9 5.3 - - - +
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Residues in contact with GLU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E VAL* 4.5 10.2 - - + +
197E ASN* 3.4 37.7 + - - +
221E THR 2.9 18.9 + - - +
222E ILE* 3.5 8.7 - - - +
224E GLN* 1.3 78.7 - - - +
226E ARG* 1.3 58.9 + - + +
227E ASP* 3.3 1.6 - - - +
270E HIS* 4.1 14.1 - - + +
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Residues in contact with ARG 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E ILE* 2.9 18.3 + - - +
225E GLU* 1.3 76.3 - - + +
227E ASP* 1.3 72.4 + - - +
228E LEU* 3.0 22.0 + - + +
231E THR* 4.7 1.7 + - - -
270E HIS* 2.9 44.7 + - + -
273E LEU* 3.5 16.3 - - - +
274E SER* 2.9 28.0 + - - +
284E ASP* 5.6 1.7 - - - +
287E ILE* 3.9 32.2 - - - +
291E ILE* 3.6 25.8 - - - +
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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