Contacts of the helix formed by residues 270 - 287 (chain A) in PDB entry 2CW9
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 ASN 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A ALA* 1.3 67.2 + - - +
272A PHE* 3.2 17.9 + - - +
273A ILE* 3.0 50.2 - - + +
274A ARG* 2.9 39.4 + - - +
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Residues in contact with ALA 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 ASN* 1.3 73.1 + - - +
272A PHE* 1.3 66.5 + - - +
274A ARG* 3.1 37.6 + - - +
275A ALA* 3.2 12.1 + - - +
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Residues in contact with PHE 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 ASN* 3.2 12.4 + - - +
271A ALA* 1.3 77.3 - - - +
273A ILE* 1.3 75.8 + - + +
275A ALA* 3.1 20.9 + - + +
276A SER* 3.2 23.3 + - - -
418A ARG* 3.6 41.5 - - - -
451A ILE 5.5 7.2 - - - -
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Residues in contact with ILE 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 ASN* 3.0 37.6 - - + +
272A PHE* 1.3 86.6 - - + +
274A ARG* 1.3 63.1 + - + +
276A SER* 2.9 22.8 + - - +
277A ARG* 3.2 33.5 + - - +
374A ASN* 5.1 1.1 + - - +
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Residues in contact with ARG 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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270A ASN 2.9 39.3 + - - +
271A ALA* 3.1 31.7 + - - +
273A ILE* 1.3 76.7 - - + +
275A ALA* 1.3 59.3 + - - +
277A ARG* 3.2 12.5 + - - +
278A ALA* 2.9 29.4 + - - +
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Residues in contact with ALA 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 ALA 3.2 8.2 + - - +
272A PHE* 3.1 17.8 + - + +
274A ARG* 1.3 79.4 - - - +
276A SER* 1.3 61.0 + - - +
278A ALA* 3.2 9.0 + - - +
279A LEU* 3.1 20.8 + - - +
451A ILE 6.2 4.5 - - - -
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Residues in contact with SER 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 PHE* 3.2 21.4 + - - -
273A ILE* 2.9 26.0 + - - +
275A ALA* 1.3 78.9 - - - +
277A ARG* 1.3 61.3 + - - +
279A LEU* 3.3 6.0 + - - +
280A THR* 3.3 10.0 + - - -
373A ASP* 5.0 2.9 + - - -
374A ASN* 3.6 18.7 + - - -
394A GLN* 2.8 35.7 + - - +
418A ARG* 6.0 1.6 - - - -
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Residues in contact with ARG 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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273A ILE* 3.2 34.5 + - - +
274A ARG* 3.2 11.3 + - - +
276A SER* 1.3 80.4 + - - +
278A ALA* 1.3 61.9 + - - +
280A THR* 3.4 4.4 + - - +
281A ASP* 2.9 39.1 + - - +
374A ASN* 3.6 22.1 - - - +
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Residues in contact with ALA 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 ARG 2.9 13.7 + - - +
275A ALA* 3.4 13.7 - - - +
276A SER 3.2 0.2 - - - -
277A ARG* 1.3 75.9 - - - +
279A LEU* 1.3 64.1 + - - +
281A ASP* 3.4 9.8 + - - +
282A LYS* 3.2 36.3 + - - +
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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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275A ALA 3.1 11.5 + - - +
276A SER* 3.5 11.2 - - - +
277A ARG 3.3 0.4 - - - -
278A ALA* 1.3 75.6 - - - +
280A THR* 1.3 64.5 + - - +
282A LYS* 3.3 15.6 + - + +
283A VAL* 3.2 29.9 + - + +
394A GLN* 4.5 13.7 - - - +
420A LEU* 4.6 11.0 - - + -
448A THR* 3.8 31.0 - - + -
451A ILE* 3.9 36.8 - - + -
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Residues in contact with THR 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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276A SER 3.3 3.6 + - - -
277A ARG* 3.7 9.6 - - - -
278A ALA 3.3 0.2 - - - -
279A LEU* 1.3 81.5 - - - +
281A ASP* 1.3 66.6 + - - +
283A VAL* 3.2 10.3 + - - +
284A THR* 3.1 20.6 + - - -
374A ASN* 3.5 30.3 + - + +
376A ASP* 4.0 19.5 - - + +
392A THR* 4.0 16.1 + - - +
393A PHE 5.6 0.3 - - - -
394A GLN* 3.0 27.2 + - - +
420A LEU* 4.4 5.1 - - - +
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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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277A ARG* 2.9 30.5 + - - +
278A ALA* 3.8 9.9 - - - +
279A LEU 3.3 0.4 - - - -
280A THR* 1.3 80.9 - - - +
282A LYS* 1.3 61.4 + - + +
284A THR* 3.4 9.5 + - - +
285A ASP* 3.1 29.0 + - - +
376A ASP* 4.9 6.6 - - - +
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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 ALA* 3.2 25.0 + - - +
279A LEU* 3.6 17.5 - - + +
280A THR 3.2 0.8 - - - -
281A ASP* 1.3 75.4 - - + +
283A VAL* 1.3 65.0 + - + +
285A ASP* 3.2 13.6 + - - +
286A LEU* 3.1 31.5 + - + +
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Residues in contact with VAL 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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279A LEU* 3.2 23.7 + - + +
280A THR* 3.2 7.4 + - - +
282A LYS* 1.3 77.8 - - + +
284A THR* 1.3 62.5 + - - +
286A LEU* 3.3 13.7 + - + +
287A LEU* 3.2 39.2 + - + +
392A THR* 4.2 16.6 - - + +
420A LEU* 4.2 31.4 - - + -
422A VAL* 4.6 5.8 - - + -
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Residues in contact with THR 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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280A THR 3.1 12.9 + - - -
281A ASP* 3.6 11.4 - - - +
283A VAL* 1.3 78.7 - - - +
285A ASP* 1.3 63.3 + - - +
287A LEU* 3.4 4.0 + - - +
288A GLY* 3.4 16.3 + - - -
376A ASP* 3.2 21.5 + - - +
377A LEU 4.3 5.6 - - - +
378A ALA* 4.2 35.9 - - - +
392A THR* 4.6 5.9 + - - -
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Residues in contact with ASP 285 (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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281A ASP* 3.1 22.1 + - - +
282A LYS* 3.4 15.8 - - - +
283A VAL 3.2 0.6 - - - -
284A THR* 1.3 80.8 - - - +
286A LEU* 1.3 61.3 + - + +
288A GLY* 3.1 24.4 + - - +
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Residues in contact with LEU 286 (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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282A LYS* 3.1 17.3 + - + +
283A VAL* 3.3 14.3 + - + +
285A ASP* 1.3 78.0 - - + +
287A LEU* 1.3 63.9 + - + +
288A GLY 3.3 2.3 + - - -
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Residues in contact with LEU 287 (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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283A VAL* 3.2 32.1 + - + +
284A THR 3.8 5.4 - - - +
285A ASP 3.1 1.0 - - - -
286A LEU* 1.3 81.8 - - + +
288A GLY* 1.3 57.2 + - - +
289A GLY 3.7 4.2 + - - -
292A SER* 4.8 1.4 - - - -
378A ALA* 3.6 31.0 - - + +
379A MSE 3.5 38.7 - - + +
390A ILE* 4.7 4.3 - - + -
392A THR* 4.2 1.3 - - + -
422A VAL* 4.2 25.8 - - + -
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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