Contacts of the helix formed by residues 273 - 284 (chain A) in PDB entry 5AX3
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ASN* 2.6 43.6 + - - +
212A LEU* 5.3 1.8 - - - +
272A ALA* 1.3 72.7 - - - +
274A SER* 1.3 68.1 + - - +
275A LYS* 2.7 46.2 + - - +
276A ALA* 3.9 12.6 - - + +
277A LEU* 3.2 26.0 + - - +
302A TYR* 3.7 8.5 - - - -
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Residues in contact with SER 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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272A ALA 3.5 3.9 + - - -
273A ASP* 1.3 76.4 + - - +
275A LYS* 1.3 63.6 + - - +
277A LEU* 3.7 9.2 + - - +
278A ASP* 3.5 17.8 + - - +
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Residues in contact with LYS 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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273A ASP* 2.7 21.1 + - - +
274A SER* 1.3 77.1 - - - +
276A ALA* 1.3 65.0 + - - +
278A ASP* 3.1 13.3 + - - +
279A LEU 3.2 0.7 + - - -
300A HIS* 3.1 25.3 - - + -
301A PRO* 3.9 25.7 + - + +
302A TYR* 3.8 29.8 - - + +
304A GLU* 5.2 4.6 + - - -
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Residues in contact with ALA 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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114A ASN* 4.9 0.2 - - - +
208A LEU* 4.1 9.7 - - + +
212A LEU* 4.6 16.4 - - + -
273A ASP* 3.4 14.3 + - + +
275A LYS* 1.3 78.3 - - - +
277A LEU* 1.3 52.7 + - - +
279A LEU* 3.2 5.1 + - - +
280A LEU* 2.7 36.8 + - - +
302A TYR* 3.6 44.2 - - + +
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Residues in contact with LEU 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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212A LEU* 3.7 17.7 - - + -
265A TRP* 3.9 23.3 - - + +
266A ASN* 4.1 15.3 - - + +
269A PHE* 3.4 53.8 - - + +
272A ALA* 4.2 9.4 - - + +
273A ASP 3.2 17.4 + - - +
274A SER* 4.0 8.5 - - - +
275A LYS 3.2 0.2 - - - -
276A ALA* 1.3 74.2 - - - +
278A ASP* 1.3 63.6 + - - +
280A LEU* 3.7 10.4 - - + +
281A ASP* 3.1 23.6 + - - +
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Residues in contact with ASP 278 (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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274A SER 3.5 9.8 + - - +
275A LYS* 3.1 11.8 + - - +
277A LEU* 1.3 79.4 - - - +
279A LEU* 1.3 62.7 + - - +
281A ASP* 3.3 7.4 + - - +
282A LYS* 3.1 46.0 + - - +
300A HIS* 3.8 8.8 + - + +
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Residues in contact with LEU 279 (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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121A LEU* 3.7 22.9 - - + -
125A LEU* 5.1 0.4 - - + -
208A LEU* 4.7 1.6 - - + -
275A LYS 3.2 2.2 + - - +
276A ALA* 3.2 8.8 + - - +
278A ASP* 1.3 76.9 - - - +
280A LEU* 1.3 59.0 + - - +
282A LYS* 2.9 5.2 + - - +
283A MET* 2.8 48.2 + - + +
292A ILE* 3.7 27.6 - - + -
297A ALA* 4.1 13.2 - - + +
300A HIS* 3.5 33.3 + - + +
302A TYR* 4.5 6.1 - - + -
303A LEU* 3.6 30.5 - - + -
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Residues in contact with LEU 280 (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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205A GLY* 3.2 28.5 - - - +
208A LEU* 3.8 15.7 - - + +
209A ALA* 3.7 19.1 - - + +
212A LEU* 4.3 6.1 - - + -
265A TRP* 3.7 30.7 - - + -
269A PHE* 3.8 17.9 - - + -
276A ALA 2.7 21.0 + - - +
277A LEU* 3.7 18.2 - - + +
279A LEU* 1.3 73.9 - - - +
281A ASP* 1.3 57.8 + - - +
283A MET* 3.4 2.7 + - - +
284A LEU* 2.9 40.3 + - + +
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Residues in contact with ASP 281 (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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262A LYS* 3.6 20.4 + - - +
265A TRP* 2.5 43.9 + - + +
277A LEU 3.1 16.1 + - - +
278A ASP* 3.7 7.0 - - - +
279A LEU 3.2 0.2 - - - -
280A LEU* 1.3 76.2 - - - +
282A LYS* 1.3 66.0 + - - +
283A MET 3.5 0.3 + - - -
284A LEU 3.6 6.6 + - - +
285A THR* 3.2 19.9 + - - +
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Residues in contact with LYS 282 (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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278A ASP* 3.1 36.8 + - - +
279A LEU* 2.9 8.6 + - - +
281A ASP* 1.3 80.1 - - - +
283A MET* 1.3 58.5 + - - +
285A THR* 3.3 19.1 - - - +
290A LYS 5.1 0.2 - - - +
291A ARG 3.8 5.5 - - - -
292A ILE* 3.6 40.8 + - + +
300A HIS* 4.3 18.4 - - + -
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Residues in contact with MET 283 (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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121A LEU* 4.6 6.7 - - + -
125A LEU* 4.9 6.1 - - + -
201A ILE* 3.4 48.2 - - + +
202A TRP* 4.1 7.1 - - - -
204A VAL* 3.6 20.6 - - + -
205A GLY* 3.5 23.3 - - - +
208A LEU* 4.4 12.1 - - - -
279A LEU* 2.8 47.7 + - + +
280A LEU 3.9 3.8 - - - +
282A LYS* 1.3 80.3 - - - +
284A LEU* 1.3 58.1 + - - +
285A THR 3.4 5.2 + - - -
291A ARG* 3.5 19.9 - - - +
292A ILE* 4.3 5.8 - - + -
297A ALA* 5.2 4.3 - - + -
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Residues in contact with LEU 284 (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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202A TRP* 3.3 53.1 - - + +
205A GLY* 3.6 14.1 - - - +
206A CYS* 3.5 14.1 - - - +
209A ALA* 4.2 9.2 - - + -
217A ILE* 4.8 0.9 - - + -
218A PHE* 4.4 12.1 - - + -
234A LEU* 3.4 25.0 - - + +
265A TRP* 3.9 25.9 - - + -
280A LEU* 2.9 36.8 + - + +
281A ASP* 3.6 8.1 - - - +
283A MET* 1.3 76.8 - - - +
285A THR* 1.3 58.6 + - - +
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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