Contacts of the helix formed by residues 275 - 286 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B PHE* 3.8 23.0 - - - -
236B CYS* 4.3 3.6 - - - -
262B LEU* 4.7 0.2 - - - +
266B LEU* 4.6 6.2 - - - +
270B TYR 4.6 2.2 + - - -
273B GLN 3.0 4.2 + - - -
274B LYS* 1.3 70.8 - - - +
276B GLU* 1.3 51.7 + - - +
277B ARG* 3.0 5.6 - - - -
278B LYS* 2.3 44.8 + - - +
279B ILE* 2.9 16.5 + - - +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B PRO* 3.4 18.7 - - + +
258B GLY* 2.9 33.3 + - - -
259B PHE 3.5 0.9 + - - -
260B LEU* 3.0 42.9 + - + +
262B LEU* 4.2 23.1 - - + +
274B LYS* 3.2 10.3 - - + +
275B GLY* 1.3 75.5 - - - +
277B ARG* 1.3 57.2 + - - +
278B LYS 3.1 0.9 - - - -
279B ILE* 3.6 12.4 - - - +
280B PHE* 3.3 32.3 + - + -
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B PRO* 4.6 16.7 - - + +
274B LYS 4.6 3.6 + - - +
275B GLY 2.8 3.2 + - - -
276B GLU* 1.3 75.6 - - - +
278B LYS* 1.3 72.7 + - - +
280B PHE* 4.4 5.6 - - - +
281B MET* 3.2 36.0 + - - +
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 3.2 38.8 - - + -
233B ASP* 3.6 29.0 + - - +
236B CYS* 3.8 19.4 - - + +
275B GLY* 2.3 30.3 + - - +
277B ARG* 1.3 81.6 - - - +
279B ILE* 1.3 65.8 + - - +
281B MET* 3.4 11.7 + - + +
282B ALA* 3.2 19.1 + - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B CYS* 3.9 16.8 - - - +
239B ALA* 3.3 28.9 - - + -
240B GLY* 4.1 4.0 - - - +
243B CYS* 3.5 33.0 - - + -
260B LEU* 3.8 15.5 - - + -
262B LEU* 4.1 16.4 - - + -
265B PHE* 5.3 0.2 - - + -
266B LEU* 4.2 12.6 - - + -
275B GLY* 2.9 39.8 + - - +
276B GLU* 3.6 9.2 - - - +
277B ARG 3.6 0.2 - - - -
278B LYS* 1.3 76.3 - - - +
280B PHE* 1.3 62.6 + - + +
282B ALA* 2.9 6.8 + - - +
283B HIS 2.8 26.3 + - - -
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B CYS* 4.9 2.7 - - - -
250B HIS* 2.9 46.0 + + + -
255B HIS* 3.2 40.4 - + + +
256B LYS* 3.1 34.1 - - - -
257B PRO* 3.4 9.4 - - + -
259B PHE* 3.7 22.0 - + + -
260B LEU* 4.0 15.5 - - + -
276B GLU* 3.3 29.9 + - + +
277B ARG* 4.7 3.8 - - - +
278B LYS 3.4 0.4 - - - -
279B ILE* 1.3 82.4 - - + +
281B MET* 1.3 62.1 + - + +
283B HIS* 3.9 13.5 - + + -
284B LYS* 3.0 5.9 + - - +
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Residues in contact with MET 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ARG* 3.2 41.2 + - - +
278B LYS* 3.4 15.0 + - + +
279B ILE 3.0 0.8 + - - -
280B PHE* 1.3 75.7 - - + +
282B ALA* 1.3 66.6 + - - +
284B LYS* 2.9 16.0 + - - +
285B ASN* 2.5 30.9 + - - +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B CYS 3.6 21.8 - - - +
237B GLU* 4.2 14.4 - - + +
240B GLY* 3.7 9.2 - - - -
278B LYS 3.2 6.3 + - - +
279B ILE 2.9 8.2 + - - +
281B MET* 1.3 79.3 - - - +
283B HIS* 1.3 67.2 + - - +
285B ASN* 2.9 24.2 + - - +
286B CYS* 3.3 9.4 + - - -
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Residues in contact with HIS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLY* 3.8 9.1 - - - +
243B CYS* 3.5 30.7 - - + +
244B GLN* 2.8 36.1 + - - +
247B PHE* 4.7 3.6 - + + -
248B GLY 2.9 25.7 + - - -
250B HIS* 3.3 31.2 + - + +
255B HIS* 3.8 18.2 - + - -
279B ILE 2.8 16.2 + - - +
280B PHE* 3.4 21.2 - - + +
282B ALA* 1.3 72.1 - - - +
284B LYS* 1.3 58.3 + - - +
286B CYS* 2.8 30.7 + - - +
287B GLY 4.2 0.2 + - - -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B HIS* 3.0 30.5 + - + +
252B GLU* 4.1 24.9 + - - +
280B PHE 3.0 7.9 + - - +
281B MET* 2.9 13.6 + - - +
283B HIS* 1.3 67.6 - - - +
285B ASN* 1.3 67.1 + - - +
286B CYS 2.8 12.4 + - - -
287B GLY* 2.8 17.3 + - - +
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B MET* 2.5 41.7 + - - +
282B ALA* 2.9 12.6 + - - +
284B LYS* 1.3 84.2 + - - +
286B CYS* 1.3 58.8 + - - +
287B GLY* 3.1 2.9 + - - -
289B MET* 5.1 1.0 - - - +
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Residues in contact with CYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 4.2 30.3 - - - -
244B GLN* 3.1 34.1 - - + +
282B ALA 3.3 11.6 + - - -
283B HIS* 2.8 20.7 + - - +
284B LYS 2.8 1.0 + - - -
285B ASN* 1.3 78.3 - - - +
287B GLY* 1.3 64.0 + - - +
288B ASN 3.4 0.2 + - - -
289B MET* 3.2 38.1 + - + +
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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