Contacts of the helix formed by residues 286 - 297 (chain N) in PDB entry 3O3U
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 THR 286 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88N LYS* 6.3 0.2 - - - +
281N GLU 4.1 3.8 - - - +
282N ASN* 3.5 33.0 - - - +
283N TYR* 2.9 15.9 + - - +
284N LEU 2.8 4.9 + - - +
285N LEU* 1.3 79.6 - - - +
287N ASP* 1.3 64.7 + - - +
288N GLU* 3.3 22.0 - - - +
289N GLY 3.0 11.3 + - - -
290N LEU* 3.0 24.3 + - - +
304N LEU* 3.6 9.6 - - - -
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Residues in contact with ASP 287 (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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286N THR* 1.3 73.6 - - - +
288N GLU* 1.3 63.6 + - - +
290N LEU* 4.1 0.2 - - - -
291N GLU* 3.0 30.2 + - - +
304N LEU* 3.6 1.9 - - - +
306N SER* 2.7 33.1 + - - +
307N TYR* 3.3 38.4 + - + +
310N GLU* 4.8 6.7 - - - +
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Residues in contact with GLU 288 (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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26N LYS* 4.2 25.8 + - + +
282N ASN 5.1 1.7 - - - +
283N TYR* 5.0 1.3 - - - +
286N THR* 3.3 22.1 + - - +
287N ASP* 1.3 81.7 + - - +
289N GLY* 1.3 67.4 + - - +
291N GLU* 3.6 13.6 + - - +
292N ALA* 3.2 21.3 + - - +
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Residues in contact with GLY 289 (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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23N VAL* 3.6 20.3 - - - +
283N TYR 3.3 21.3 - - - -
284N LEU* 3.5 8.1 - - - -
286N THR* 3.0 9.7 + - - -
288N GLU* 1.3 76.8 - - - +
290N LEU* 1.3 64.2 + - - +
292N ALA* 3.2 13.5 + - - +
293N VAL* 3.3 12.3 + - - +
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Residues in contact with LEU 290 (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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108N ILE* 4.0 28.7 - - + +
284N LEU* 3.3 20.8 + - + +
285N LEU* 4.3 13.5 - - + -
286N THR 3.0 13.2 + - - +
289N GLY* 1.3 73.0 - - - +
291N GLU* 1.3 60.8 + - - +
293N VAL* 3.3 3.0 + - - +
294N ASN* 2.8 32.9 + - - +
299N LEU* 4.0 15.6 - - + +
302N VAL* 4.0 19.7 - - + -
304N LEU* 3.6 40.6 - - + +
307N TYR* 3.7 17.7 - - + -
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Residues in contact with GLU 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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287N ASP 3.0 19.2 + - - +
288N GLU* 3.7 13.4 - - - +
289N GLY 3.2 0.2 - - - -
290N LEU* 1.3 77.8 - - - +
292N ALA* 1.3 57.8 + - - +
294N ASN* 3.8 1.1 - - - -
295N LYS* 2.9 64.4 + - + +
307N TYR* 3.3 27.6 + - + +
310N GLU* 5.1 6.1 - - - +
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Residues in contact with ALA 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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19N GLY* 3.4 21.5 - - - +
22N GLU* 4.2 17.4 - - + +
23N VAL* 3.8 17.7 - - + +
288N GLU 3.2 10.1 + - - +
289N GLY 3.2 10.6 + - - +
291N GLU* 1.3 82.5 - - - +
293N VAL* 1.3 62.4 + - - +
295N LYS* 3.8 4.6 + - - +
296N ASP* 3.6 9.5 + - - +
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Residues in contact with VAL 293 (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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11N ILE* 5.8 4.9 - - + -
15N LYS* 6.1 0.2 - - + -
16N GLY* 3.9 20.4 - - - +
19N GLY* 4.1 6.5 - - - +
20N LEU* 3.8 28.9 - - + +
23N VAL* 4.4 0.9 - - + -
108N ILE* 6.3 0.4 - - + -
284N LEU* 3.9 19.7 - - + -
289N GLY 3.3 12.9 + - - +
290N LEU 3.9 4.9 - - - +
291N GLU 3.3 0.2 - - - -
292N ALA* 1.3 75.8 - - - +
294N ASN* 1.3 60.6 + - - +
296N ASP* 3.0 19.4 + - - +
297N LYS 3.1 12.7 + - - +
299N LEU* 3.8 30.5 - - + -
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Residues in contact with ASN 294 (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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290N LEU 2.8 23.3 + - - +
291N GLU* 3.8 5.2 - - - +
293N VAL* 1.3 72.9 - - - +
295N LYS* 1.3 66.4 + - - +
296N ASP 3.4 0.3 + - - -
297N LYS 3.6 5.6 - - - -
298N PRO* 3.3 29.2 - - - +
299N LEU* 2.8 37.8 + - + +
300N GLY 4.3 4.2 + - - +
302N VAL* 5.1 0.8 - - - +
307N TYR* 4.6 8.0 + - + +
311N LEU* 3.7 29.6 - - - +
317N ILE* 5.9 1.1 - - - +
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Residues in contact with LYS 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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233N SER* 5.3 2.9 - - - -
291N GLU* 2.9 50.0 + - + +
292N ALA* 4.1 6.1 - - - +
293N VAL 3.2 0.2 - - - -
294N ASN* 1.3 82.4 - - + +
296N ASP* 1.3 61.8 + - - +
298N PRO* 5.7 0.2 - - - +
307N TYR* 5.4 3.1 - - - +
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Residues in contact with ASP 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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15N LYS 4.7 0.2 - - - +
16N GLY* 3.1 14.3 - - - -
17N TYR 3.5 0.3 + - - -
18N ASN* 3.0 25.5 + - - +
19N GLY* 2.9 35.3 + - - +
233N SER* 3.3 19.6 + - - -
292N ALA 3.6 2.4 + - - +
293N VAL 3.0 9.9 + - - +
294N ASN 4.1 0.2 - - - -
295N LYS* 1.3 81.3 - - - +
297N LYS* 1.3 70.5 + - - +
298N PRO* 4.6 0.4 - - - -
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Residues in contact with LYS 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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13N GLY 5.8 1.8 - - - -
14N ASP* 3.9 11.9 - - - +
15N LYS* 3.7 24.0 - - - +
16N GLY* 3.7 13.6 + - - +
17N TYR* 6.6 0.4 - - - -
230N TRP* 3.5 21.4 + - + +
233N SER* 2.9 24.2 + - - +
234N ASN* 2.8 39.4 + - - +
293N VAL* 3.1 15.2 + - - +
294N ASN* 3.4 4.2 - - - +
296N ASP* 1.3 89.0 - - - +
298N PRO* 1.3 72.1 - - - +
299N LEU* 3.4 5.9 + - - +
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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