Contacts of the helix formed by residues 290 - 305 (chain N) in PDB entry 6AH0
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 290 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872A ASP* 2.9 30.6 - - - +
289N ASN* 1.3 73.5 - - - +
291N ILE* 1.3 64.9 + - - +
293N LYS* 3.0 12.9 + - - +
294N ALA* 3.4 7.8 + - - -
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Residues in contact with ILE 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871A TYR 4.4 2.0 + - - -
872A ASP 4.3 5.3 + - - -
289N ASN 3.3 2.2 - - - +
290N ASP* 1.3 75.7 - - - +
292N LYS* 1.3 56.0 + - - +
294N ALA* 2.9 18.9 + - - +
295N ARG* 3.1 10.4 + - - -
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Residues in contact with LYS 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289N ASN* 3.3 12.0 + - - +
290N ASP 3.2 0.8 - - - -
291N ILE* 1.3 75.6 - - - +
293N LYS* 1.3 60.1 + - - +
295N ARG* 3.3 3.4 + - - +
296N LEU* 3.2 18.2 + - - -
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Residues in contact with LYS 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289N ASN 3.3 8.1 + - - -
290N ASP* 3.0 11.5 + - - +
292N LYS* 1.3 74.9 - - - +
294N ALA* 1.3 62.7 + - - +
296N LEU* 3.2 10.4 + - - +
297N LEU* 3.3 10.0 + - - -
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Residues in contact with ALA 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290N ASP 3.4 6.6 + - - -
291N ILE* 2.9 8.8 + - - +
293N LYS* 1.3 75.6 - - - +
295N ARG* 1.3 63.1 + - - +
297N LEU* 3.2 4.0 + - - +
298N LEU* 3.0 19.9 + - - -
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Residues in contact with ARG 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291N ILE 3.1 11.1 + - - -
292N LYS* 3.3 4.7 + - - +
293N LYS 3.2 0.2 - - - -
294N ALA* 1.3 76.5 - - - +
296N LEU* 1.3 56.1 + - - +
298N LEU* 3.3 2.1 + - - +
299N LYS* 2.9 26.9 + - - -
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Residues in contact with LEU 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292N LYS 3.2 13.4 + - - -
293N LYS 3.2 3.1 + - - -
294N ALA 3.2 0.4 - - - -
295N ARG* 1.3 74.4 - - - +
297N LEU* 1.3 57.5 + - - +
299N LYS* 3.2 3.1 + - - +
300N SER* 2.9 25.6 + - - -
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Residues in contact with LEU 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N LYS 3.3 9.0 + - - -
294N ALA 3.2 6.7 + - - -
296N LEU* 1.3 76.5 - - - +
298N LEU* 1.3 62.0 + - - +
300N SER* 3.2 3.2 + - - +
301N VAL* 3.0 19.2 + - - -
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Residues in contact with LEU 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N ALA 3.0 14.4 + - - -
295N ARG* 3.8 2.5 - - - +
297N LEU* 1.3 77.4 - - - +
299N LYS* 1.3 55.6 + - - +
301N VAL* 3.2 3.2 + - - +
302N ARG* 2.9 25.6 + - - -
311N ALA 5.2 4.0 - - - +
315N SER* 5.8 9.0 - - - +
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Residues in contact with LYS 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295N ARG 2.9 14.5 + - - -
296N LEU* 3.2 4.2 + - - +
298N LEU* 1.3 77.2 - - - +
300N SER* 1.3 56.2 + - - +
302N ARG* 3.2 2.1 + - - +
303N GLU* 2.9 26.5 + - - -
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Residues in contact with SER 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296N LEU 2.9 14.2 + - - -
297N LEU* 3.2 4.6 + - - +
299N LYS* 1.3 73.5 - - - +
301N VAL* 1.3 56.9 - - - +
303N GLU* 3.2 1.9 + - - +
304N THR* 2.9 27.0 + - - -
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Residues in contact with VAL 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297N LEU 3.0 12.7 + - - -
298N LEU* 3.2 4.9 + - - +
300N SER* 1.3 75.8 - - - +
302N ARG* 1.3 62.0 + - - +
304N THR* 3.2 10.6 + - - +
305N ASN* 3.2 11.1 + - - +
311N ALA* 5.7 5.9 - - - -
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Residues in contact with ARG 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298N LEU 2.9 14.4 + - - -
299N LYS* 3.6 3.8 - - - +
301N VAL* 1.3 76.5 - - - +
303N GLU* 1.3 57.9 + - - +
305N ASN 2.3 31.6 - - - +
306N PRO* 4.1 2.6 - - - +
311N ALA* 5.1 12.4 + - - +
312N TRP* 6.3 0.4 - - - +
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Residues in contact with GLU 303 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299N LYS 2.9 14.7 + - - -
300N SER* 3.2 3.8 + - - +
302N ARG* 1.3 75.9 - - - +
304N THR* 1.3 62.7 + - - +
305N ASN 3.3 4.0 + - - -
306N PRO* 4.3 2.4 - - - +
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Residues in contact with THR 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300N SER 2.9 13.9 + - - -
301N VAL* 3.2 6.0 + - - +
303N GLU* 1.3 76.0 - - - +
305N ASN* 1.3 57.1 + - - +
306N PRO 4.2 0.5 - - - -
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Residues in contact with ASN 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301N VAL 3.2 8.7 + - - -
302N ARG* 2.3 27.5 - - - +
303N GLU 4.0 0.2 - - - -
304N THR* 1.3 77.3 - - - +
306N PRO* 1.3 62.4 - - - +
307N HIS 3.2 14.2 - - - +
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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
------------------------------------------------------------
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