Contacts of the helix formed by residues 275 - 285 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H PHE* 3.5 28.7 - - - -
236H CYS* 4.6 2.5 - - - -
262H LEU* 5.1 1.6 - - - +
266H LEU* 5.3 3.6 - - - +
270H TYR 4.9 1.4 + - - -
271H ILE 4.8 1.8 + - - -
273H GLN 3.1 4.0 + - - -
274H LYS* 1.3 71.5 - - - +
276H GLU* 1.3 56.1 + - - +
277H ARG* 2.9 4.3 - - - -
278H LYS* 2.3 36.6 + - - +
279H ILE* 3.0 14.2 + - - +
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Residues in contact with GLU 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H PRO* 3.6 12.1 - - + -
258H GLY* 2.8 32.1 + - - -
259H PHE 3.6 0.2 + - - -
260H LEU* 3.4 34.7 + - - +
262H LEU* 3.8 23.5 - - + +
274H LYS* 3.4 11.8 + - + +
275H GLY* 1.3 74.6 - - - +
277H ARG* 1.3 66.0 + - - +
279H ILE* 2.8 29.0 + - + +
280H PHE* 2.9 43.2 + - + +
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Residues in contact with ARG 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR* 3.6 35.0 + - + +
257H PRO* 4.3 24.6 - - + +
274H LYS 4.8 2.3 + - - +
275H GLY* 2.7 5.1 + - - +
276H GLU* 1.3 78.0 - - - +
278H LYS* 1.3 54.5 + - + +
280H PHE* 3.5 7.1 + - - +
281H MET* 2.5 45.8 + - - +
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Residues in contact with LYS 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLN* 5.2 1.3 - - - +
285D ASN 5.4 2.0 + - - -
232H PHE* 3.1 41.1 - - + -
233H ASP* 3.0 34.6 + - - +
236H CYS* 4.0 20.0 - - + +
275H GLY* 2.3 25.4 + - - +
277H ARG* 1.3 69.9 - - + +
279H ILE* 1.3 62.2 + - - +
281H MET* 3.1 17.5 + - - +
282H ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H CYS* 4.0 20.4 - - + -
239H ALA* 3.5 32.1 - - + +
240H GLY* 3.8 1.4 - - - -
243H CYS* 3.7 27.8 - - - -
260H LEU* 4.6 8.3 - - + -
262H LEU* 3.8 16.8 - - + -
265H PHE* 4.7 2.9 - - + -
266H LEU* 3.5 33.7 - - + -
275H GLY 3.0 7.6 + - - +
276H GLU* 2.8 14.1 + - + +
278H LYS* 1.3 76.9 - - - +
280H PHE* 1.3 59.1 + - + +
282H ALA* 3.1 5.2 + - - +
283H HIS* 2.8 27.4 + - - +
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Residues in contact with PHE 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H CYS* 4.8 3.6 - - - -
250H HIS* 3.4 23.9 + + - +
255H HIS* 3.4 38.4 - + + +
256H LYS* 3.2 17.3 - - - -
257H PRO* 3.2 14.6 - - + -
259H PHE* 3.5 24.9 - + - -
260H LEU* 4.3 14.4 - - + -
276H GLU* 2.9 49.8 + - + +
277H ARG* 3.8 6.5 - - - +
279H ILE* 1.3 80.2 - - + +
281H MET* 1.3 58.3 + - + +
283H HIS* 3.8 9.6 - - + -
284H LYS* 3.2 22.2 + - - +
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Residues in contact with MET 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D GLY* 5.8 8.5 - - - -
288D ASN* 5.9 3.8 - - - +
277H ARG* 2.5 39.7 - - - +
278H LYS* 3.3 21.3 - - - +
279H ILE 3.0 0.4 - - - -
280H PHE* 1.3 79.2 - - + +
282H ALA* 1.3 63.4 + - - +
283H HIS 3.2 1.8 - - - -
284H LYS* 3.8 3.9 + - - +
285H ASN* 3.3 29.5 + - - +
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Residues in contact with ALA 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H CYS 3.9 10.1 - - - +
237H GLU* 4.0 17.3 - - + +
240H GLY* 3.7 16.3 - - - -
278H LYS 3.0 11.3 + - - +
279H ILE 3.6 6.5 - - - +
281H MET* 1.3 74.5 - - - +
283H HIS* 1.3 61.5 + - - +
285H ASN* 3.7 9.7 + - - +
286H CYS* 2.9 23.6 + - - -
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Residues in contact with HIS 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H GLY* 3.6 12.5 - - - +
243H CYS* 3.4 29.5 - - + +
244H GLN* 3.0 32.4 + - + +
247H PHE* 4.7 1.6 - - + -
248H GLY 3.2 18.3 + - - -
250H HIS* 3.0 51.0 + + + +
255H HIS* 4.1 14.4 + + - -
279H ILE 2.8 16.0 + - - +
280H PHE* 3.9 7.7 - - - +
282H ALA* 1.3 75.5 - - - +
284H LYS* 1.3 66.9 + - - +
286H CYS* 2.7 25.1 + - - +
287H GLY 5.5 0.2 - - - +
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Residues in contact with LYS 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H HIS* 3.6 27.1 - - + +
252H GLU* 3.7 35.8 + - + +
280H PHE 3.2 16.3 + - - +
281H MET* 4.0 6.3 - - - +
283H HIS* 1.3 79.3 - - - +
285H ASN* 1.3 66.8 + - - +
286H CYS 2.8 6.9 + - - -
287H GLY* 3.2 13.5 + - - +
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Residues in contact with ASN 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D LYS* 6.0 1.6 - - - +
287D GLY* 5.7 7.1 - - - -
288D ASN* 5.8 3.6 + - - +
281H MET 3.3 17.4 + - - +
282H ALA* 4.0 7.2 - - - +
283H HIS 3.0 1.8 + - - -
284H LYS* 1.3 83.8 - - - +
286H CYS* 1.3 60.5 + - - +
287H GLY 3.4 1.5 + - - -
289H MET* 5.4 0.9 - - - +
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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