Contacts of the helix formed by residues 270 - 277 (chain A) in PDB entry 3NYN
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 ASP 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLY* 1.3 73.4 - - - -
271A LEU* 1.3 62.5 + - - +
272A LYS* 3.0 15.0 + - - +
273A PHE* 2.8 44.6 + - - +
274A HIS* 3.3 14.5 + - - -
314A PRO 4.0 0.7 - - - +
315A GLU* 3.6 10.5 - - - +
317A ILE 3.3 7.0 - - - +
318A LEU* 3.3 22.2 - - + +
473A TYR 4.7 3.9 + - - +
474A CYS* 5.5 2.1 - - - +
577A SGV 2.7 34.7 + - - +
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Residues in contact with LEU 271 (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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270A ASP* 1.3 69.4 - - - +
272A LYS* 1.3 64.1 + - - +
273A PHE 3.3 0.2 - - - -
274A HIS* 3.7 4.6 - - + +
275A ILE* 3.0 34.5 + - + +
283A PHE* 4.4 12.3 - - + -
291A TYR* 3.6 40.2 - - + -
295A ILE* 4.6 7.9 - - + -
314A PRO* 3.5 13.7 + - + +
317A ILE* 3.0 44.6 + - + +
318A LEU 5.1 0.2 - - - +
319A LEU* 3.9 20.9 - - + -
325A ILE* 5.2 1.3 - - + -
374A LEU* 4.8 5.4 - - + -
378A MET* 4.3 15.5 - - + -
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Residues in contact with LYS 272 (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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270A ASP* 3.0 13.4 + - - +
271A LEU* 1.3 79.3 - - - +
273A PHE* 1.3 60.9 + - - +
275A ILE* 4.6 1.3 - - - -
276A TYR* 3.3 41.9 + - + +
277A HIS* 4.9 2.5 - - + +
314A PRO* 3.4 26.8 + - + +
315A GLU* 3.5 40.3 + - + +
584A SO4 3.1 38.5 + - - +
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Residues in contact with PHE 273 (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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270A ASP* 2.8 29.9 + - - +
272A LYS* 1.3 72.8 - - - +
274A HIS* 1.3 62.8 + + + +
277A HIS* 3.0 64.5 + + + -
278A MET* 3.4 30.1 - - + -
472A ILE 5.4 0.7 - - - -
473A TYR* 3.9 28.3 - - + +
474A CYS* 3.7 35.9 - - + -
475A LYS* 4.2 12.1 - - + -
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Residues in contact with HIS 274 (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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268A GLY* 2.7 29.3 + - - -
269A GLY 4.6 1.3 - - - -
270A ASP 3.3 16.2 + - - +
271A LEU* 3.3 9.7 + - + +
272A LYS 3.3 0.4 - - - -
273A PHE* 1.3 84.0 - + + +
275A ILE* 1.3 60.7 + - - +
278A MET* 3.4 32.9 - - + +
280A GLN 5.7 0.2 - - - +
282A GLY 4.8 1.7 - - - +
283A PHE* 3.2 30.5 - - + -
287A ARG* 3.5 17.3 + - - +
319A LEU* 4.3 11.9 - - + +
465A PHE* 3.8 24.6 - + - -
467A PRO* 5.6 0.9 - - + -
473A TYR* 3.6 30.5 - + + -
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Residues in contact with ILE 275 (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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271A LEU* 3.0 31.4 + - + +
272A LYS* 4.6 0.4 - - - -
274A HIS* 1.3 79.5 - - - +
276A TYR* 1.3 85.3 + - + +
278A MET 5.1 1.0 + - - +
280A GLN 4.5 0.9 - - - +
281A ALA* 3.3 10.3 - - + +
282A GLY* 3.1 28.9 + - - +
283A PHE* 3.6 23.1 - - + -
314A PRO* 4.1 22.2 - - + -
374A LEU* 5.2 1.8 - - + -
377A GLU* 4.3 21.3 - - + +
378A MET* 4.2 20.9 - - + -
381A GLY* 4.8 6.3 - - - +
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Residues in contact with TYR 276 (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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272A LYS* 3.3 30.3 + - + +
275A ILE* 1.3 102.9 - - + +
277A HIS* 1.3 76.2 + - + +
278A MET 3.0 10.3 + - - -
279A GLY 3.6 14.2 - - - +
281A ALA* 5.0 8.2 + - + +
314A PRO* 5.5 0.4 - - + -
377A GLU* 2.6 29.0 + - + +
381A GLY 4.8 11.0 - - - -
382A GLN* 4.3 2.7 - - + +
383A SER* 4.0 14.0 + - - -
386A GLN* 5.5 2.1 + - - -
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Residues in contact with HIS 277 (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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272A LYS* 4.9 2.9 - - + +
273A PHE* 3.0 53.8 + + + +
276A TYR* 1.3 83.4 - + + +
278A MET* 1.3 73.4 + - - +
279A GLY 4.0 0.7 - - - -
475A LYS* 4.9 7.5 - - + -
584A SO4 2.8 35.7 + - - -
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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