Contacts of the helix formed by residues 276 - 296 (chain A) in PDB entry 1IZC
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 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.6 2.7 - - - +
47A ALA 3.0 13.4 + - - +
48A HIS* 2.8 29.0 + - - -
49A GLY 2.8 22.6 + - - -
50A ILE* 3.1 30.7 + - + +
55A VAL* 3.8 3.8 - - + +
59A LEU* 4.4 19.7 - - + -
275A PHE* 1.3 71.1 - - - +
277A VAL* 1.3 78.2 + - - +
279A GLY* 5.1 0.2 - - - -
280A LEU* 3.0 27.9 + - - +
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Residues in contact with VAL 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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49A GLY* 4.2 8.5 - - - +
50A ILE* 3.5 34.1 - - + +
275A PHE* 3.4 1.0 - - - +
276A ASP* 1.3 88.8 + - - +
278A TRP* 1.3 79.7 + - + +
280A LEU* 4.1 2.1 - - - +
281A SER* 3.0 27.2 + - - -
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Residues in contact with TRP 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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255A LEU* 5.7 9.2 - - + -
275A PHE* 3.7 28.1 + + + +
276A ASP 3.6 0.2 - - - -
277A VAL* 1.3 93.1 - - + +
279A GLY* 1.3 57.1 + - - +
281A SER* 3.7 5.3 - - - -
282A ARG* 2.9 74.8 + - - +
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Residues in contact with GLY 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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274A GLN* 3.6 20.8 + - - -
275A PHE 2.7 24.4 + - - -
278A TRP* 1.3 74.7 - - - +
280A LEU* 1.3 62.0 + - - +
282A ARG* 3.5 5.0 + - - +
283A LEU* 3.0 25.3 + - - +
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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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50A ILE* 4.6 17.3 - - + -
276A ASP* 3.0 19.1 + - - +
277A VAL* 4.1 2.0 - - - +
279A GLY* 1.3 75.6 - - - +
281A SER* 1.3 64.5 + - - +
283A LEU* 3.3 14.2 + - + +
284A VAL* 3.0 45.1 + - + +
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Residues in contact with SER 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 VAL* 3.0 21.8 + - - -
278A TRP* 3.7 8.1 - - - -
280A LEU* 1.3 78.9 - - - +
282A ARG* 1.3 58.7 + - - +
284A VAL* 3.8 3.2 - - - +
285A HIS* 2.9 34.8 + - - +
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Residues in contact with ARG 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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255A LEU* 4.7 12.9 + - - +
275A PHE* 6.1 2.8 - - - -
278A TRP* 2.9 66.1 + - - +
279A GLY* 4.0 4.5 - - - +
281A SER* 1.3 75.3 - - - +
283A LEU* 1.3 60.6 + - - +
285A HIS* 4.5 4.5 - - - -
286A GLY* 2.9 28.2 + - - -
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Residues in contact with LEU 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 GLY 3.0 19.0 + - - +
280A LEU* 3.3 17.7 + - + +
282A ARG* 1.3 77.5 - - - +
284A VAL* 1.3 60.2 + - + +
286A GLY* 4.0 0.5 - - - -
287A SER* 2.9 40.5 + - - +
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Residues in contact with VAL 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 LEU* 3.0 35.4 + - + +
281A SER* 4.0 2.9 - - - +
283A LEU* 1.3 78.2 - - + +
285A HIS* 1.3 66.5 + - - +
287A SER* 3.2 6.2 + - - -
288A LEU* 2.9 46.9 + - + +
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Residues in contact with HIS 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 SER* 2.9 24.2 + - - +
282A ARG* 4.1 4.5 - - - +
284A VAL* 1.3 73.9 - - - +
286A GLY* 1.3 65.9 + - - +
288A LEU* 3.4 14.5 + - - +
289A ALA* 3.0 28.1 + - + +
292A ARG* 6.4 0.4 - - - -
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Residues in contact with GLY 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 ARG 2.9 18.7 + - - -
283A LEU 4.0 0.4 - - - -
285A HIS* 1.3 79.9 - - - +
287A SER* 1.3 63.8 + - - +
289A ALA* 3.4 6.5 + - - +
290A GLN* 3.0 38.7 + - - +
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Residues in contact with SER 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 LEU* 2.9 30.9 + - - +
284A VAL* 3.2 6.0 + - - -
286A GLY* 1.3 75.5 - - - +
288A LEU* 1.3 59.7 + - - +
290A GLN* 3.4 9.3 + - - +
291A ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 288 (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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284A VAL* 2.9 39.3 + - + +
285A HIS* 3.6 12.6 - - - +
287A SER* 1.3 77.4 - - - +
289A ALA* 1.3 57.1 + - - +
291A ALA* 3.3 5.9 + - + +
292A ARG* 2.9 67.8 + - + +
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Residues in contact with ALA 289 (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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285A HIS* 3.0 25.9 + - + +
286A GLY* 3.7 7.2 - - - +
287A SER 3.3 0.2 - - - -
288A LEU* 1.3 77.3 - - - +
290A GLN* 1.3 58.2 + - + +
292A ARG* 3.9 8.7 - - - +
293A ALA* 3.0 31.3 + - - +
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Residues in contact with GLN 290 (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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286A GLY* 3.0 27.1 + - - +
287A SER* 3.8 6.6 - - - +
289A ALA* 1.3 76.9 - - + +
291A ALA* 1.3 63.5 + - - +
293A ALA* 3.4 6.3 + - - +
294A SER* 3.0 24.8 + - - -
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Residues in contact with ALA 291 (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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287A SER 2.9 19.0 + - - +
288A LEU* 3.6 7.2 - - + +
290A GLN* 1.3 77.7 - - - +
292A ARG* 1.3 64.2 + - + +
294A SER* 2.8 22.9 + - - -
295A ALA* 3.1 11.1 + - - +
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Residues in contact with ARG 292 (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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285A HIS* 6.4 0.2 - - - -
288A LEU* 2.9 59.3 + - + +
289A ALA* 4.0 6.4 - - - +
291A ALA* 1.3 76.5 - - + +
293A ALA* 1.3 63.7 + - - +
295A ALA* 3.1 17.2 + - - +
296A LYS* 3.3 20.1 + - - +
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Residues in contact with ALA 293 (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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289A ALA 3.0 18.3 + - - +
290A GLN* 3.6 8.1 - - - +
292A ARG* 1.3 78.4 - - - +
294A SER* 1.3 60.7 + - - +
295A ALA 3.3 0.5 + - - -
296A LYS* 3.3 24.1 + - - +
297A GLN 4.7 0.3 + - - -
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Residues in contact with SER 294 (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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290A GLN 3.0 14.9 + - - -
291A ALA* 2.8 21.3 + - - -
293A ALA* 1.3 76.0 - - - +
295A ALA* 1.3 58.5 + - - +
296A LYS 3.4 0.2 - - - -
297A GLN* 2.9 34.4 + - - +
298A PHE* 4.0 3.1 - - - -
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Residues in contact with ALA 295 (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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291A ALA 3.1 10.7 + - - +
292A ARG* 3.1 13.7 + - - +
294A SER* 1.3 77.1 - - - +
296A LYS* 1.3 65.1 + - - +
297A GLN 3.1 2.9 - - - -
298A PHE* 3.0 32.6 + - + +
299A ALA 4.2 1.2 + - - -
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Residues in contact with LYS 296 (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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292A ARG* 3.3 16.4 + - - +
293A ALA* 3.3 16.8 + - - +
295A ALA* 1.3 78.6 - - - +
297A GLN* 1.3 61.5 + - - +
298A PHE 3.0 2.1 + - - -
299A ALA* 3.1 27.6 + - + +
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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