Contacts of the helix formed by residues 258 - 274 (chain C) 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 ASN 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C TYR* 3.4 18.6 - - - -
251C HIS 3.6 21.8 - - - +
252C ALA* 5.6 0.9 - - - -
254C VAL 2.8 21.6 + - - +
255C ALA 3.0 22.2 + - - -
256C TYR 2.7 11.4 + - - +
257C HIS* 1.3 74.4 - - - +
259C ASN* 1.3 71.4 + - - +
260C ILE* 2.7 41.4 + - - +
261C HIS* 3.0 6.6 + - - +
262C ALA* 3.0 17.7 + - - +
429C TRP* 5.3 0.9 - - - -
432C ARG* 4.0 8.5 - - - +
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Residues in contact with ASN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ASN* 3.4 32.4 + - - +
214C PRO* 3.2 21.5 - - - +
215C LEU* 3.9 4.9 - - + +
247C GLU* 2.7 43.0 + - + +
250C TYR* 3.4 28.7 - - + +
251C HIS 5.2 0.7 - - - +
252C ALA* 5.7 2.9 - - - -
258C ASN* 1.3 79.2 - - - +
260C ILE* 1.3 59.9 + - - +
262C ALA* 3.6 5.7 - - - +
263C ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL* 3.8 21.6 - - + +
204C PHE* 4.0 15.3 - - + -
207C ALA* 4.2 25.8 - - + -
212C ASN* 4.7 6.5 - - - +
214C PRO* 4.1 10.8 - - + -
258C ASN* 2.7 19.3 + - - +
259C ASN* 1.3 76.9 - - - +
261C HIS* 1.3 61.6 + - - +
263C ALA* 3.1 2.4 + - - +
264C ASP* 2.8 29.8 + - - +
429C TRP* 3.8 17.0 - - + -
432C ARG* 3.7 31.2 - - - +
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Residues in contact with HIS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C TYR* 3.1 58.8 + + - +
257C HIS* 4.3 7.4 - + - -
258C ASN* 3.0 8.4 + - - +
260C ILE* 1.3 78.6 - - - +
262C ALA* 1.3 63.3 + - - +
264C ASP* 2.9 7.6 + - - +
265C VAL* 2.9 36.3 + - + +
297C HIS* 3.1 11.9 + + - -
298C ASP* 3.2 20.4 - - + -
415C ASP* 2.9 19.6 + - - -
418C ASN* 5.2 2.2 + - - -
429C TRP* 3.7 17.6 - - + -
2005C ZN 2.4 24.6 - - - -
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LEU* 3.9 8.5 - - + -
250C TYR* 3.4 44.9 - - + +
258C ASN 3.0 5.8 + - - +
259C ASN* 3.6 9.0 - - - +
261C HIS* 1.3 78.9 - - - +
263C ALA* 1.3 62.9 + - - +
265C VAL* 3.3 2.1 + - - +
266C VAL* 3.0 27.2 + - - +
294C SER 4.3 1.1 - - - +
295C ALA 3.9 8.1 - - - +
297C HIS* 4.5 12.3 - - - -
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.2 2.0 - - + -
214C PRO* 3.7 14.6 - - + +
215C LEU* 3.6 33.6 - - - +
218C ILE* 3.9 17.0 - - + +
259C ASN 2.9 19.0 + - - +
260C ILE 3.4 4.5 - - - +
262C ALA* 1.3 76.5 - - - +
264C ASP* 1.3 57.8 + - - +
266C VAL* 3.4 4.7 + - - +
267C GLN* 3.0 28.9 + - - +
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Residues in contact with ASP 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU 5.7 0.5 - - - +
203C VAL* 4.4 16.4 - - + +
260C ILE 2.8 12.8 + - - +
261C HIS* 2.9 11.7 + - - +
263C ALA* 1.3 74.8 - - - +
265C VAL* 1.3 62.6 + - + +
267C GLN* 3.3 10.2 + - - +
268C SER* 2.9 34.4 + - - -
414C ALA 5.4 0.2 - - - +
417C SER* 4.4 2.5 + - - -
418C ASN* 3.3 25.6 + - - -
421C LYS* 3.0 25.6 + - - -
429C TRP* 3.5 24.3 + - + -
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C HIS* 2.9 37.0 + - + +
262C ALA 3.9 2.5 - - - +
264C ASP* 1.3 74.1 - - + +
266C VAL* 1.3 63.0 + - - +
268C SER* 4.5 4.7 - - - -
269C THR* 2.9 29.5 + - - -
294C SER* 4.0 15.7 - - - +
297C HIS* 3.3 36.8 - - + +
411C VAL* 4.3 8.7 - - + +
414C ALA* 3.8 20.4 - - + +
415C ASP* 3.7 18.4 - - + +
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LEU* 3.9 9.4 - - + -
218C ILE* 4.7 4.0 - - + -
219C MET* 3.6 24.5 - - + -
222C ILE* 3.8 18.4 - - + -
262C ALA 3.0 19.5 + - - +
263C ALA* 3.5 8.7 - - - +
265C VAL* 1.3 76.2 - - - +
267C GLN* 1.3 57.8 + - - +
269C THR* 3.2 3.8 + - - +
270C HIS* 2.9 26.9 + - - +
291C ILE* 4.1 12.0 - - + +
294C SER* 3.8 7.9 - - - -
295C ALA* 3.4 39.9 - - + +
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Residues in contact with GLN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 2.8 32.1 + - + +
198C LYS 2.9 22.8 + - - -
199C TRP* 3.7 10.2 + - - +
201C LEU* 3.5 38.9 - - + +
203C VAL* 6.5 0.2 - - + -
218C ILE* 4.2 13.2 - - + -
222C ILE* 4.0 9.2 - - + -
263C ALA 3.0 17.4 + - - +
264C ASP* 3.3 10.7 + - - +
266C VAL* 1.3 76.8 - - - +
268C SER* 1.3 63.7 + - - +
270C HIS* 3.1 4.3 - - - +
271C VAL* 3.0 44.6 + - - +
421C LYS* 5.0 0.2 + - - -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TRP* 3.6 22.3 - - - -
264C ASP* 2.9 18.9 + - - -
265C VAL* 3.9 0.9 - - - -
267C GLN* 1.3 78.6 + - - +
269C THR* 1.3 58.8 + - - +
271C VAL* 3.1 3.4 + - - +
272C LEU* 2.8 34.8 + - - +
414C ALA* 3.8 17.9 - - - -
417C SER* 3.7 6.3 + - - -
421C LYS* 3.1 27.7 + - - -
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Residues in contact with THR 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL 2.9 19.7 + - - -
266C VAL 3.6 4.3 - - - -
268C SER* 1.3 75.9 - - - +
270C HIS* 1.3 58.1 + - - +
272C LEU* 3.3 6.4 + - - +
273C LEU* 2.8 48.7 + - + +
290C ALA* 4.1 19.5 - - + +
291C ILE* 4.5 3.6 - - + +
294C SER* 2.8 26.6 + - - +
410C MET* 4.4 6.5 - - - -
411C VAL* 3.9 11.7 - - + +
414C ALA* 3.5 16.1 - - - +
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Residues in contact with HIS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C VAL* 3.4 24.4 - - + +
197C ASN* 2.8 27.5 + - - -
222C ILE* 3.4 38.8 - - + +
225C GLU* 4.1 11.6 - - + +
226C ARG* 2.9 70.1 + - + +
266C VAL 2.9 13.3 + - - +
267C GLN 3.1 8.7 - - - +
269C THR* 1.3 79.2 - - - +
271C VAL* 1.3 63.1 + - + +
273C LEU* 3.5 8.1 + - - -
274C SER* 3.3 8.7 + - - -
291C ILE* 4.9 3.1 - - + +
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C VAL 4.0 4.7 - - - +
197C ASN* 3.8 24.0 - - - +
198C LYS 4.0 4.9 - - - +
199C TRP* 3.7 29.4 - - + +
267C GLN* 3.0 38.0 + - - +
268C SER 3.1 6.0 + - - +
270C HIS* 1.3 76.0 - - + +
272C LEU* 1.3 67.0 + - + +
274C SER* 3.0 20.2 + - - -
275C THR* 3.6 5.4 + - - -
492C ILE* 6.2 0.4 - - + -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C TRP* 4.0 16.8 - - + -
268C SER 2.8 19.1 + - - +
269C THR 3.7 3.8 - - - +
271C VAL* 1.3 77.4 - - + +
273C LEU* 1.3 62.6 + - - +
275C THR* 3.0 30.7 + - - +
410C MET* 3.7 46.5 - - + +
413C CYS* 4.2 4.0 - - + -
414C ALA* 4.2 12.3 - - + +
478C TRP* 4.0 28.5 - - + -
481C TRP* 4.1 19.7 - - + +
492C ILE* 4.6 8.1 - - + -
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ARG* 3.5 16.9 + - - +
269C THR* 2.8 24.9 + - + +
271C VAL 3.2 0.2 - - - -
272C LEU* 1.3 77.1 - - - +
274C SER* 1.3 58.6 + - - +
275C THR 3.2 4.6 + - - +
278C LEU* 4.4 14.0 - - - +
282C PHE* 4.3 14.4 - - + -
287C ILE* 3.8 39.7 - - + +
290C ALA* 4.4 3.6 - - + -
291C ILE* 3.8 24.0 - - + -
407C LEU* 4.1 16.2 - - + -
410C MET* 3.4 28.5 - - + -
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Residues in contact with SER 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ARG* 2.9 22.6 + - - +
270C HIS* 3.3 8.4 + - - -
271C VAL* 3.0 14.3 + - - -
273C LEU* 1.3 76.4 - - - +
275C THR* 1.3 65.8 + - - +
276C PRO* 3.4 6.1 - - - +
279C GLU* 5.7 0.3 - - - +
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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
------------------------------------------------------------
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