Contacts of the helix formed by residues 278 - 299 (chain A) in PDB entry 1T9A
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 SER 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A THR* 1.3 73.5 - - - +
279A ARG* 1.3 66.9 + - - +
280A ALA* 3.3 18.0 + - - +
281A GLN* 3.1 21.7 + - - +
282A ASP* 2.9 26.2 + - - +
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Residues in contact with ARG 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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277A THR 3.5 2.6 + - - -
278A SER* 1.3 74.3 + - - +
280A ALA* 1.3 61.3 + - - +
282A ASP* 3.8 9.5 + - + +
283A GLU* 3.1 52.8 + - - +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 3.1 10.6 + - - +
279A ARG* 1.3 78.0 - - - +
281A GLN* 1.3 59.8 + - - +
283A GLU* 3.1 12.3 + - - +
284A PHE* 2.8 28.8 + - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR* 5.6 0.7 - - - -
278A SER* 3.1 26.6 + - - +
280A ALA* 1.3 78.2 - - - +
282A ASP* 1.3 54.0 + - - +
284A PHE* 2.8 46.5 + - - +
285A VAL* 2.8 40.1 + - - +
424A GLU* 4.0 16.0 + - - +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR* 3.5 25.5 - - - +
278A SER 2.9 21.7 + - - +
279A ARG* 4.0 8.3 - - + +
281A GLN* 1.3 76.4 - - - +
283A GLU* 1.3 56.9 + - - +
285A VAL* 3.3 8.7 + - - +
286A MET* 2.9 30.3 + - - +
433A LYS* 5.1 10.4 + - - +
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Residues in contact with GLU 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 ARG* 3.1 50.1 + - - +
280A ALA* 3.3 11.0 - - - +
281A GLN 3.1 0.4 - - - -
282A ASP* 1.3 76.7 - - - +
284A PHE* 1.3 57.9 + - - +
286A MET* 3.5 7.6 + - + +
287A GLN* 3.0 26.3 + - - +
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Residues in contact with PHE 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 ALA 2.8 11.2 + - - +
281A GLN* 2.8 31.4 + - - +
283A GLU* 1.3 76.1 - - - +
285A VAL* 1.3 67.6 + - + +
287A GLN* 3.2 24.3 + - - +
288A SER* 3.0 38.5 + - - -
422A ALA 5.5 2.9 - - - -
424A GLU* 3.5 27.1 - - - -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN* 2.8 34.5 + - - +
282A ASP* 3.7 11.2 - - - +
284A PHE* 1.3 79.9 - - + +
286A MET* 1.3 59.9 + - - +
288A SER* 3.0 8.9 + - - -
289A ILE* 2.8 36.1 + - + +
423A VAL* 4.5 3.6 - - + -
424A GLU* 3.9 27.6 - - + +
430A ASN* 3.6 25.4 - - - +
433A LYS* 5.4 6.7 - - + +
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Residues in contact with MET 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 ASP 2.9 18.4 + - - +
283A GLU* 3.7 9.0 - - + +
284A PHE 3.2 0.2 - - - -
285A VAL* 1.3 79.0 - - - +
287A GLN* 1.3 56.4 + - - +
289A ILE* 3.3 13.4 + - + +
290A ASN* 3.0 39.7 + - - +
433A LYS* 4.1 33.0 - - + +
437A LYS* 2.8 32.8 - - - +
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Residues in contact with GLN 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 GLU 3.0 14.7 + - - +
284A PHE* 3.5 30.6 - - - +
285A VAL 3.2 0.2 - - - -
286A MET* 1.3 75.9 - - - +
288A SER* 1.3 63.0 + - - +
290A ASN* 3.4 11.7 + - + +
291A LYS* 3.1 51.6 + - + +
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.0 30.6 + - - -
285A VAL* 3.0 13.6 + - - -
287A GLN* 1.3 74.5 - - - +
289A ILE* 1.3 60.5 + - - +
291A LYS* 3.2 7.2 + - - +
292A ALA* 2.8 29.3 + - - +
421A ILE* 3.7 10.2 - - - +
422A ALA 3.6 23.3 + - - -
423A VAL* 4.3 13.2 - - - -
424A GLU 5.4 0.4 + - - -
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Residues in contact with ILE 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 VAL* 2.8 25.8 + - + +
286A MET* 3.6 12.8 - - - +
287A GLN 3.3 0.2 - - - -
288A SER* 1.3 77.0 - - - +
290A ASN* 1.3 57.1 + - - +
292A ALA* 3.3 7.8 + - - +
293A ALA* 2.9 27.2 + - - +
406A PHE* 5.4 1.1 - - + -
423A VAL* 3.8 17.5 - - + -
430A ASN* 3.8 27.4 - - - +
433A LYS* 3.8 26.7 - - + -
434A MET* 3.3 36.4 - - + +
437A LYS* 4.3 15.0 - - + +
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Residues in contact with ASN 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 MET* 3.0 29.1 + - - +
287A GLN* 3.7 10.9 - - + +
288A SER 3.2 0.2 - - - -
289A ILE* 1.3 76.8 - - - +
291A LYS* 1.3 57.3 + - + +
293A ALA* 3.3 6.5 + - - +
294A ASP* 2.9 37.2 + - - +
437A LYS* 2.7 39.6 + - - +
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Residues in contact with LYS 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 GLN* 3.1 44.6 + - + +
288A SER* 3.6 10.1 - - - +
290A ASN* 1.3 72.8 - - + +
292A ALA* 1.3 66.2 + - - +
294A ASP* 3.3 10.4 + - - +
295A LEU* 3.0 19.1 + - - +
421A ILE* 3.4 29.5 - - + +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER 2.8 16.9 + - - +
289A ILE* 3.5 6.3 - - - +
291A LYS* 1.3 75.8 - - - +
293A ALA* 1.3 57.5 + - - +
295A LEU 3.3 0.9 + - - -
296A ILE* 2.9 34.8 + - - +
404A ILE* 3.5 30.3 - - + +
406A PHE* 4.6 0.2 - - + -
421A ILE* 3.7 11.2 - - + +
423A VAL* 4.1 11.2 - - + -
434A MET* 4.0 13.9 - - - -
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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 ILE 2.9 17.4 + - - +
290A ASN* 3.5 6.1 - - - +
291A LYS 3.2 0.2 - - - -
292A ALA* 1.3 77.2 - - - +
294A ASP* 1.3 58.1 + - - +
296A ILE* 3.2 1.9 + - - +
297A ASN* 2.9 36.0 + - - +
434A MET* 4.0 5.1 - - + -
437A LYS* 3.7 33.2 - - + +
438A ILE* 3.9 21.1 - - + -
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Residues in contact with ASP 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 ASN* 2.9 26.5 + - - +
291A LYS* 3.3 10.2 + - - +
293A ALA* 1.3 77.8 - - - +
295A LEU* 1.3 63.1 + - - +
297A ASN* 3.2 18.5 + - - +
298A LEU* 3.3 18.5 + - + +
439A PHE* 6.2 0.3 - - - -
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Residues in contact with LEU 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 LYS 3.0 15.9 + - - +
292A ALA 3.7 3.6 - - - +
294A ASP* 1.3 76.6 - - - +
296A ILE* 1.3 63.2 + - - +
298A LEU* 3.1 24.2 + - + +
299A ALA* 3.2 10.0 + - - -
369A LEU* 3.7 19.2 - - + +
399A GLY 5.1 2.9 - - - +
400A ARG* 4.1 6.1 - - - +
401A GLY* 3.7 38.5 - - - +
403A ILE 5.4 0.4 - - - +
404A ILE* 4.1 16.6 - - + -
420A GLN* 4.4 9.6 - - + -
421A ILE* 3.5 25.1 - - + -
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Residues in contact with ILE 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 ALA* 2.9 21.6 + - + +
293A ALA 3.6 4.3 - - - +
295A LEU* 1.3 71.6 - - - +
297A ASN* 1.3 61.9 + - - +
298A LEU 3.0 5.3 + - - -
299A ALA* 3.3 16.9 + - + +
302A PRO* 6.0 0.4 - - + -
323A LEU* 5.0 4.5 - - + -
327A ALA* 4.7 3.8 - - + -
329A ILE* 4.3 20.9 - - + -
369A LEU* 3.6 7.2 - - + -
371A ILE* 3.8 29.4 - - + -
404A ILE* 3.7 17.7 - - + -
406A PHE* 5.5 0.4 - - + -
434A MET* 3.5 33.4 - - + -
438A ILE* 4.1 23.1 - - + -
444A ARG* 4.6 6.9 + - - +
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Residues in contact with ASN 297 (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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293A ALA* 2.9 22.7 + - - +
294A ASP* 3.2 12.7 + - - +
296A ILE* 1.3 75.8 - - - +
298A LEU* 1.3 58.7 + - - +
299A ALA 4.8 2.1 - - - +
300A LYS* 5.4 1.6 + - - -
437A LYS 3.0 24.0 + - - -
438A ILE* 3.7 9.9 - - - +
439A PHE* 2.8 65.0 + - + +
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Residues in contact with LEU 298 (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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294A ASP* 3.3 11.7 + - + +
295A LEU* 3.1 19.2 + - + +
296A ILE 3.0 0.6 - - - -
297A ASN* 1.3 79.6 - - - +
299A ALA* 1.3 64.2 + - - +
300A LYS* 3.3 32.9 + - - +
368A ASP* 4.7 0.7 - - - +
399A GLY 4.5 6.5 - - - +
400A ARG* 4.5 33.2 - - + +
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Residues in contact with ALA 299 (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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295A LEU 3.2 5.4 + - - +
296A ILE* 3.3 9.5 + - - +
297A ASN 4.8 1.7 - - - +
298A LEU* 1.3 79.9 - - - +
300A LYS* 1.3 61.8 + - - +
302A PRO* 3.9 18.4 - - + -
368A ASP* 3.5 8.1 - - - +
369A LEU* 3.6 41.1 - - + -
400A ARG 5.0 3.1 + - - -
444A ARG* 3.1 19.0 + - - +
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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
------------------------------------------------------------
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