Contacts of the helix formed by residues 275 - 285 (chain D) in PDB entry 1MK9
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 GLY 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D PHE* 4.0 24.9 - - - -
236D CYS* 4.9 1.8 - - - -
262D LEU* 4.8 2.2 - - - +
266D LEU* 5.3 3.8 - - - +
270D TYR 4.9 1.4 + - - -
273D GLN* 3.7 0.6 - - - +
274D LYS* 1.3 74.9 - - - +
276D GLU* 1.3 53.8 + - - +
277D ARG* 2.9 7.2 - - - -
278D LYS* 2.5 40.0 + - - +
279D ILE* 3.1 12.1 + - - +
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Residues in contact with GLU 276 (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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257D PRO* 3.5 10.8 - - + +
258D GLY* 2.8 36.0 + - - -
259D PHE 3.4 0.7 + - - -
260D LEU* 3.1 35.1 + - + +
262D LEU* 4.0 33.9 - - + +
274D LYS* 3.3 10.4 + - + -
275D GLY* 1.3 77.7 - - - +
277D ARG* 1.3 59.9 + - + +
279D ILE* 3.7 7.0 + - - +
280D PHE* 3.1 40.7 + - + -
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Residues in contact with ARG 277 (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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250D HIS* 5.9 1.2 - - - -
255D HIS 4.9 2.8 + - - -
257D PRO* 3.0 37.7 - - + +
274D LYS 5.9 1.6 - - - +
275D GLY* 2.9 2.6 - - - -
276D GLU* 1.3 76.0 - - + +
278D LYS* 1.3 65.8 + - + +
279D ILE 3.4 0.2 - - - -
280D PHE* 3.3 35.2 - - - +
281D MET* 3.3 30.6 + - + +
349F GLN* 5.7 15.3 - - + +
374F GLN* 5.0 9.3 + - - -
375F ASP* 5.2 14.0 + - - -
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Residues in contact with LYS 278 (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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232D PHE* 3.8 23.3 - - + -
233D ASP* 2.6 37.9 + - - +
236D CYS* 3.8 22.0 - - + +
275D GLY* 2.5 27.1 + - - +
277D ARG* 1.3 74.1 - - + +
279D ILE* 1.3 56.4 + - - +
281D MET* 3.3 17.5 + - + +
282D ALA* 3.0 28.1 + - - +
306H LYS* 5.9 1.6 - - - +
346H GLU* 4.8 7.9 + - - -
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Residues in contact with ILE 279 (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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236D CYS* 3.9 19.3 - - + -
239D ALA* 3.3 40.6 - - + -
240D GLY* 3.7 1.0 - - - -
243D CYS* 3.6 26.9 - - - -
260D LEU* 4.4 9.0 - - + -
262D LEU* 4.1 18.6 - - + -
265D PHE* 4.8 4.0 - - + -
266D LEU* 3.7 29.8 - - + -
275D GLY 3.1 10.0 + - - +
276D GLU* 4.0 7.0 - - - +
277D ARG 3.4 0.2 - - - -
278D LYS* 1.3 74.5 - - - +
280D PHE* 1.3 55.4 + - + +
282D ALA* 3.3 2.9 + - - +
283D HIS* 2.6 32.1 + - - +
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Residues in contact with PHE 280 (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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243D CYS* 5.0 1.3 - - - -
247D PHE* 5.3 0.2 - + - -
250D HIS* 3.6 15.2 + + + +
255D HIS* 3.1 50.7 - + + -
256D LYS 3.6 22.0 - - - -
257D PRO 4.1 3.4 - - - -
259D PHE* 4.0 12.6 - + + -
260D LEU* 3.8 27.6 - - + -
276D GLU* 3.1 41.5 + - + -
277D ARG* 3.3 25.1 - - - +
278D LYS 3.4 0.2 - - - -
279D ILE* 1.3 77.9 - - + +
281D MET* 1.3 57.3 + - - +
283D HIS* 3.2 13.0 - + - +
284D LYS* 2.7 35.2 + - - +
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Residues in contact with MET 281 (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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277D ARG* 3.3 30.2 + - + +
278D LYS* 3.5 20.4 - - + +
279D ILE 3.2 0.6 - - - -
280D PHE* 1.3 80.0 - - - +
282D ALA* 1.3 59.3 + - - +
284D LYS* 3.5 14.3 - - + +
285D ASN* 3.1 28.0 + - - -
234H LYS* 4.0 27.8 - - - +
301H LEU* 6.4 0.4 - - - -
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Residues in contact with ALA 282 (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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236D CYS 3.6 24.7 - - - +
237D GLU* 4.3 13.9 - - + +
240D GLY* 3.9 8.2 - - - -
241D TYR* 5.6 0.9 - - + -
278D LYS 3.0 12.6 + - - +
279D ILE 3.7 1.6 - - - +
281D MET* 1.3 74.5 - - - +
283D HIS* 1.3 65.9 + - - +
285D ASN* 3.1 25.0 + - - +
286D CYS* 3.7 11.6 - - - -
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Residues in contact with HIS 283 (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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240D GLY 3.9 8.1 - - - -
243D CYS* 3.3 23.9 - - + +
244D GLN* 3.1 38.5 + - - -
247D PHE* 3.6 17.0 - + + -
248D GLY 3.2 23.4 + - - -
250D HIS* 3.4 30.4 + + + +
255D HIS* 4.1 7.2 - + - -
279D ILE 2.6 22.2 + - - +
280D PHE* 3.2 18.6 - - - +
282D ALA* 1.3 74.5 - - - +
284D LYS* 1.3 62.6 + - - +
286D CYS* 3.0 18.2 + - - +
287D GLY 4.4 0.2 + - - -
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Residues in contact with LYS 284 (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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250D HIS* 3.9 29.1 - - + +
252D GLU* 4.2 23.4 + - - +
280D PHE 2.7 19.6 + - - +
281D MET* 3.5 15.5 - - + +
283D HIS* 1.3 73.9 - - - +
285D ASN* 1.3 58.8 + - - +
286D CYS 2.9 6.6 + - - -
287D GLY* 3.2 13.3 + - - -
237H GLU* 4.4 17.7 - - - -
285H ASN* 6.0 1.8 - - - +
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Residues in contact with ASN 285 (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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281D MET* 3.1 23.6 + - - +
282D ALA* 3.1 16.7 + - - +
283D HIS 3.1 1.2 - - - -
284D LYS* 1.3 77.1 - - - +
286D CYS* 1.3 60.5 + - - +
287D GLY 3.4 1.1 - - - -
289D MET* 4.8 3.8 - - - +
233H ASP* 3.4 37.6 - - - +
234H LYS* 4.0 25.9 + - - +
237H GLU* 5.1 3.6 - - - +
278H LYS* 5.4 1.7 + - - -
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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