Contacts of the helix formed by residues 213 - 226 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210J SER* 2.9 27.8 + - - +
211J GLY 4.0 5.4 + - - +
212J ASN* 1.3 84.0 + - - +
214J PRO* 1.3 66.9 - - - +
215J LEU 3.3 2.7 - - - -
216J THR* 3.4 4.8 + - - -
217J VAL* 3.0 27.2 + - + +
244J MET* 3.0 63.4 + - + +
247J GLU* 3.3 26.8 - - - +
248J ASP* 2.8 27.1 + - - -
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Residues in contact with PRO 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J VAL* 4.5 5.8 - - + +
206J ILE* 4.5 5.6 - - + -
207J ALA* 3.9 29.4 - - + +
210J SER* 3.4 6.0 - - - +
212J ASN* 3.3 5.4 - - - +
213J ARG* 1.3 90.5 - - - +
215J LEU* 1.3 57.0 + - - +
217J VAL* 4.5 3.4 - - + -
218J ILE* 2.8 42.0 + - + +
247J GLU* 3.1 8.1 - - - +
259J ASN* 3.2 28.5 - - - +
260J ILE* 4.1 9.9 - - + -
263J ALA* 3.7 12.3 - - + -
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Residues in contact with LEU 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J PRO* 1.3 81.2 - - - +
216J THR* 1.3 58.2 + - - +
218J ILE* 4.9 0.4 - - - -
219J MET* 2.8 46.7 + - + +
243J LEU* 5.0 3.6 - - + +
246J LEU* 4.0 20.0 - - + -
247J GLU* 2.9 31.0 + - + +
250J TYR* 3.8 29.6 - - + -
259J ASN* 3.9 7.6 - - + +
262J ALA* 3.9 6.5 - - + -
263J ALA* 3.7 27.1 - - - +
266J VAL* 3.9 20.0 - - + -
295J ALA* 4.0 5.6 - - + +
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Residues in contact with THR 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J ARG* 3.4 9.5 + - - -
215J LEU* 1.3 72.4 - - - +
217J VAL* 1.3 65.0 + - + +
220J HIS* 3.0 25.2 + - + +
240J ILE* 4.6 13.0 - - + -
243J LEU* 3.4 45.7 + - + +
244J MET* 3.6 32.2 + - + -
247J GLU* 2.6 25.7 + - - -
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Residues in contact with VAL 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J LEU* 4.6 11.0 - - + -
193J LEU* 3.4 37.5 - - + -
206J ILE* 4.5 7.6 - - + -
210J SER* 3.6 21.3 - - - +
213J ARG* 3.0 27.4 + - + +
214J PRO* 3.9 4.3 - - + +
216J THR* 1.3 79.3 - - + +
218J ILE* 1.3 52.9 + - + +
220J HIS* 3.4 4.3 + - - +
221J THR* 2.7 36.6 + - + +
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Residues in contact with ILE 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J LEU* 4.2 17.0 - - + -
196J VAL* 4.8 3.8 - - + -
201J LEU* 4.1 17.5 - - + -
203J VAL* 4.0 17.9 - - + -
206J ILE* 4.3 12.6 - - + -
214J PRO 2.8 26.7 + - - +
215J LEU* 4.2 0.9 - - + +
217J VAL* 1.3 69.0 - - - +
219J MET* 1.3 66.4 + - - +
221J THR* 3.0 7.3 + - - +
222J ILE* 3.0 44.0 + - + +
263J ALA* 3.9 26.5 - - + +
266J VAL* 4.7 3.6 - - + -
267J GLN* 4.1 16.4 - - + -
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Residues in contact with MET 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J LEU* 2.8 41.0 + - + +
218J ILE* 1.3 71.5 - - - +
220J HIS* 1.3 58.6 + - - +
222J ILE* 3.1 4.6 + - - +
223J PHE* 2.9 64.2 + - + -
239J LEU* 5.5 0.4 - - + -
242J TYR* 6.2 0.9 - - + -
243J LEU* 3.6 33.7 - - + -
246J LEU* 5.8 0.2 - - + -
266J VAL* 3.6 23.6 - - + -
291J ILE* 3.8 17.3 - - + +
292J PHE* 4.6 11.7 - - + -
295J ALA* 3.6 22.0 - - + -
345J ILE* 6.1 1.6 - - + -
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Residues in contact with HIS 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J THR* 3.0 18.0 + - + +
217J VAL* 3.7 5.5 + - - +
219J MET* 1.3 78.0 - - - +
221J THR* 1.3 69.0 + - + +
223J PHE* 3.2 7.3 + - - +
224J GLN* 3.0 61.8 + - + +
229J LEU* 4.7 0.7 - - + -
236J VAL* 4.0 14.4 - - + +
239J LEU* 4.1 13.2 - - + -
240J ILE* 3.5 28.6 - - + +
243J LEU* 3.9 8.7 - - + +
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Residues in contact with THR 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J LEU* 3.7 39.5 - - + +
196J VAL* 4.8 11.9 - - - +
217J VAL* 2.7 19.2 + - + +
218J ILE* 3.0 15.9 + - - +
220J HIS* 1.3 81.9 - - - +
222J ILE* 1.3 55.9 + - - +
224J GLN* 3.5 9.3 + - + +
225J GLU* 2.9 28.6 + - - +
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Residues in contact with ILE 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196J VAL* 3.6 20.6 - - + -
218J ILE* 3.0 38.0 + - + +
219J MET* 3.6 4.3 - - - +
221J THR* 1.3 74.7 - - - +
223J PHE* 1.3 63.2 + - + +
225J GLU* 3.4 5.5 - - - +
226J ARG* 2.8 29.8 + - - +
266J VAL* 3.8 17.9 - - + -
267J GLN* 4.0 6.1 - - - -
270J HIS* 3.3 47.1 - - + +
291J ILE* 4.0 24.2 - - + -
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Residues in contact with PHE 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J MET* 2.9 57.0 + - + +
220J HIS 3.2 7.6 + - - +
222J ILE* 1.3 76.7 - - + +
224J GLN* 1.3 60.9 + - - +
226J ARG 3.4 0.3 + - - -
227J ASP* 2.9 22.7 + - - -
228J LEU* 3.0 36.2 + - + -
229J LEU* 4.0 11.2 + - + -
234J ILE* 3.7 26.0 - - + -
239J LEU* 3.9 33.4 - - + -
288J LEU* 3.7 26.2 - - + -
291J ILE* 4.1 14.4 - - + -
292J PHE* 5.7 3.1 - - + -
345J ILE* 5.1 10.1 - - + -
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Residues in contact with GLN 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220J HIS* 3.0 53.0 + - + +
221J THR* 3.6 11.4 - - + +
223J PHE* 1.3 75.9 - - - +
225J GLU* 1.3 57.4 + - - +
227J ASP* 2.8 26.3 + - - +
229J LEU* 3.1 23.4 - - - +
236J VAL* 4.9 5.3 - - - +
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Residues in contact with GLU 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196J VAL* 4.5 9.8 - - + +
197J ASN* 3.3 38.0 + - - +
221J THR 2.9 19.6 + - - +
222J ILE* 3.4 8.7 - - - +
224J GLN* 1.3 77.8 - - - +
226J ARG* 1.3 60.3 + - + +
227J ASP* 3.6 1.4 + - - +
270J HIS* 4.1 13.0 - - + +
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Residues in contact with ARG 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J ILE* 2.8 20.6 + - - +
225J GLU* 1.3 75.2 - - + +
227J ASP* 1.3 71.0 + - - +
228J LEU* 3.0 22.1 + - + +
231J THR* 4.7 1.9 + - - -
270J HIS* 2.8 44.3 + - + -
273J LEU* 3.5 16.5 - - - +
274J SER* 2.9 28.4 + - - +
284J ASP* 5.6 1.9 - - - +
287J ILE* 3.9 32.0 - - + +
291J ILE* 3.6 26.1 - - - +
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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