Contacts of the helix formed by residues 279 - 287 (chain A) in PDB entry 1MK2
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 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LEU* 3.9 17.4 - - - +
277A ASN 4.2 8.6 + - - +
278A ARG* 1.3 78.7 - - - +
280A ALA* 1.3 68.0 + - - +
281A ALA* 3.0 15.6 + - - +
282A VAL* 3.0 41.9 + - - +
283A GLU* 3.1 21.0 + - - +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASN* 1.3 74.2 - - - +
281A ALA* 1.3 58.2 + - - +
283A GLU* 3.3 10.9 - - + +
284A LEU* 2.8 45.1 + - + +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 6.5 0.2 - - + -
279A ASN* 3.0 11.1 + - - +
280A ALA* 1.3 77.4 - - - +
282A VAL* 1.3 64.8 + - + +
284A LEU* 3.7 7.2 - - - +
285A THR* 3.0 28.8 + - - +
385A ARG* 6.3 0.7 - - - +
392A PRO* 5.1 7.6 - - + -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 3.3 32.5 - - + +
239A LEU* 4.3 14.1 - - + -
275A ASN* 5.7 0.2 - - - +
278A ARG* 3.2 32.8 - - + -
279A ASN* 3.0 33.2 + - - +
281A ALA* 1.3 78.0 - - + +
283A GLU* 1.3 65.3 + - - +
285A THR* 3.1 2.3 + - - -
286A ARG* 2.7 28.4 + - + +
392A PRO* 3.9 24.7 - - + +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ARG* 3.8 13.0 - - + +
279A ASN 3.1 11.7 + - - +
280A ALA* 3.3 16.3 - - - +
282A VAL* 1.3 79.5 - - - +
284A LEU* 1.3 75.4 + - + +
286A ARG* 3.0 24.9 + - - +
287A ARG* 2.5 50.9 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ALA* 2.8 37.3 + - + +
281A ALA* 3.7 7.2 - - - +
283A GLU* 1.3 80.3 - - + +
285A THR* 1.3 61.7 + - - +
287A ARG* 3.2 30.9 - - - +
288A HIS* 3.0 26.7 + - + -
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA* 3.0 14.5 + - - +
282A VAL 3.5 7.0 - - - -
284A LEU* 1.3 71.7 - - - +
286A ARG* 1.3 54.4 + - - +
287A ARG 2.9 4.9 - - - -
288A HIS* 2.6 33.7 + - - +
289A ILE* 3.1 9.7 - - + +
375A PHE 4.2 6.3 - - - +
376A VAL* 3.8 30.7 - - + +
377A LYS* 4.8 7.1 - - + +
392A PRO* 3.5 31.8 - - + +
393A CYS* 4.0 9.9 - - - -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A TYR* 2.9 25.4 + - - +
238A GLU* 2.9 19.7 + - - -
258A GLY* 4.9 9.9 - - - +
270A LEU* 2.9 34.9 + - - +
271A GLY* 3.3 20.4 + - - -
273A LEU 3.4 9.3 + - - -
278A ARG* 3.2 38.1 - - - +
282A VAL* 2.7 21.0 + - - +
283A GLU* 3.0 13.0 + - - +
285A THR* 1.3 71.8 - - - +
287A ARG* 1.3 59.5 + - - +
288A HIS 3.2 0.2 - - - -
289A ILE* 3.1 23.8 + - + +
290A GLY 4.8 1.0 + - - -
393A CYS* 3.4 17.3 - - - -
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLU* 2.5 45.1 + - - +
284A LEU* 3.2 31.0 - - - +
285A THR 2.8 0.4 + - - -
286A ARG* 1.3 80.7 - - - +
288A HIS* 1.3 68.4 + - + +
289A ILE 3.4 0.7 + - - -
290A GLY* 4.2 7.3 + - - -
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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
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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