Contacts of the helix formed by residues 270 - 277 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B GLY* 1.3 73.6 - - - -
271B LEU* 1.3 62.7 + - - +
272B LYS* 2.9 17.8 + - - +
273B PHE* 2.9 34.8 + - - +
274B HIS* 3.3 26.6 + - - -
314B PRO 4.0 0.9 - - - +
315B GLU* 3.7 9.2 - - - +
317B ILE 3.3 16.2 - - - +
318B LEU* 3.5 14.8 - - + -
319B LEU* 5.7 0.7 - - - -
473B TYR 4.6 4.0 + - - +
474B CYS* 5.5 3.1 - - - +
577B SGV 2.5 30.1 + - - +
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Residues in contact with LEU 271 (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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270B ASP* 1.3 73.6 - - - +
272B LYS* 1.3 61.6 + - - +
274B HIS* 3.8 3.3 - - + +
275B ILE* 2.8 39.8 + - + +
283B PHE* 4.3 12.8 - - + -
291B TYR* 3.7 38.1 - - + -
295B ILE* 4.8 3.6 - - + -
314B PRO* 3.3 16.3 + - + +
317B ILE* 3.3 42.7 + - + +
319B LEU* 4.3 18.2 - - + -
325B ILE* 4.9 2.0 - - + -
374B LEU* 4.5 14.4 - - + -
378B MET* 4.7 9.2 - - + -
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Residues in contact with LYS 272 (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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270B ASP* 2.9 14.2 + - - +
271B LEU* 1.3 79.4 - - - +
273B PHE* 1.3 60.6 + - - +
275B ILE* 4.9 0.2 - - - -
276B TYR* 3.4 41.5 + - + +
277B HIS* 4.7 2.5 - - + +
314B PRO* 3.4 15.2 + - + +
315B GLU* 3.4 50.4 + - + +
584B SO4 3.3 40.4 + - - +
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Residues in contact with PHE 273 (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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270B ASP* 2.9 24.0 + - - +
272B LYS* 1.3 77.1 - - - +
274B HIS* 1.3 58.9 + + + +
277B HIS* 3.0 62.1 + + + -
278B MET* 3.4 28.9 - - + -
472B ILE 5.0 1.3 - - - -
473B TYR* 3.6 29.6 - + + +
474B CYS* 3.3 40.8 - - + -
475B LYS* 3.9 12.6 - - + -
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Residues in contact with HIS 274 (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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268B GLY* 3.3 23.4 + - - -
270B ASP 3.3 20.0 + - - +
271B LEU* 3.2 8.6 + - + +
273B PHE* 1.3 82.1 - + - +
275B ILE* 1.3 61.6 + - - +
278B MET* 3.2 34.3 - - + +
280B GLN 5.5 0.3 - - - +
282B GLY 5.5 0.5 - - - +
283B PHE* 3.3 26.2 - - + -
287B ARG* 3.3 17.1 + - - -
319B LEU* 4.2 11.6 - - + +
465B PHE* 3.5 35.3 - + - -
467B PRO* 5.4 0.8 - - - +
473B TYR* 3.5 30.2 - + + -
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Residues in contact with ILE 275 (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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271B LEU* 2.8 31.8 + - + +
274B HIS* 1.3 76.1 - - - +
276B TYR* 1.3 83.6 + - + +
278B MET 4.9 0.5 + - - -
280B GLN 3.9 2.9 - - - +
281B ALA* 3.3 7.5 - - + -
282B GLY* 3.0 35.9 + - - +
283B PHE* 3.5 24.9 - - + -
314B PRO* 4.3 16.8 - - + -
374B LEU* 6.2 0.7 - - + -
377B GLU* 4.1 29.8 - - + +
378B MET* 4.2 21.1 - - + -
381B GLY 4.5 8.5 - - - +
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Residues in contact with TYR 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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272B LYS* 3.4 32.6 + - + +
275B ILE* 1.3 99.1 - - + +
277B HIS* 1.3 77.1 + + + +
278B MET 3.2 7.2 + - - -
279B GLY 3.9 12.1 - - - +
281B ALA* 4.8 10.6 - - + +
314B PRO* 5.6 0.7 - - + -
377B GLU* 2.5 31.1 + - - +
381B GLY 4.3 14.8 + - - -
382B GLN* 4.5 1.4 - - + -
383B SER* 4.2 10.9 + - - -
386B GLN* 5.3 3.8 + - - -
584B SO4 5.7 2.7 - - - -
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Residues in contact with HIS 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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272B LYS* 4.7 1.8 - - + -
273B PHE* 3.0 49.1 + + + +
276B TYR* 1.3 87.6 - + + +
278B MET* 1.3 75.8 + - - +
279B GLY 4.1 0.7 - - - -
475B LYS* 4.9 9.9 - - - -
584B SO4 2.8 33.0 + - - -
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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