Contacts of the helix formed by residues 376 - 399 (chain A) in PDB entry 1T8U
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 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLU* 2.9 21.3 + - + +
374A GLU 4.0 0.4 + - - -
375A ILE* 1.3 73.2 - - - +
377A ARG* 1.3 66.9 + - - +
378A GLU* 3.1 18.4 + - - +
379A VAL* 2.9 51.1 + - + +
380A VAL* 3.0 10.7 + - - +
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Residues in contact with ARG 377 (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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374A GLU* 4.8 10.2 + - - +
375A ILE 3.2 8.5 + - - +
376A ASP* 1.3 75.1 + - - +
378A GLU* 1.3 58.2 + - - +
380A VAL* 3.2 32.1 + - - +
381A ARG* 2.8 29.8 + - - +
384A ARG* 6.0 0.8 - - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASP* 3.1 18.0 + - - +
377A ARG* 1.3 78.3 - - - +
379A VAL* 1.3 57.7 + - + +
381A ARG* 2.7 37.8 + - - -
382A ARG* 2.7 69.4 + - - +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.2 11.4 - - + -
267A GLU* 3.5 26.7 - - + -
270A THR* 4.2 16.4 - - + +
271A PHE* 3.8 33.9 - - + -
375A ILE* 4.1 16.4 - - + -
376A ASP* 2.9 22.2 + - + +
378A GLU* 1.3 76.5 - - + +
380A VAL* 1.3 65.9 + - - +
382A ARG* 3.4 1.6 + - - +
383A LEU* 3.0 24.8 + - + +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 4.6 10.3 - - + +
250A ILE* 5.0 9.2 - - + -
375A ILE* 3.8 28.7 - - + +
376A ASP 3.0 16.1 + - - +
377A ARG* 3.5 34.3 - - - +
379A VAL* 1.3 77.0 - - - +
381A ARG* 1.3 56.7 + - - +
383A LEU* 3.3 6.3 + - + +
384A ARG* 2.9 57.1 + - + +
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG 2.8 16.2 + - - +
378A GLU* 2.7 43.9 + - - +
380A VAL* 1.3 77.9 - - - +
382A ARG* 1.3 74.9 + - - +
384A ARG* 3.3 7.5 + - - +
385A GLU* 2.9 57.1 + - + +
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.6 41.8 - - + -
277A GLY* 4.4 17.4 - - - -
279A ILE* 3.7 8.3 - - + +
378A GLU* 2.7 51.4 + - - +
379A VAL 3.9 2.9 - - - +
381A ARG* 1.3 88.8 - - - +
383A LEU* 1.3 58.7 + - - +
385A GLU* 3.5 9.8 + - - +
386A PHE* 3.0 28.1 + - - +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 3.9 24.7 - - + -
249A ALA* 5.2 4.3 - - + -
266A PHE* 3.5 39.5 - - + -
270A THR* 3.7 25.1 - - + +
279A ILE* 4.0 21.1 - - + -
286A ILE* 4.6 8.5 - - + -
379A VAL* 3.0 20.7 + - + +
380A VAL* 3.8 4.9 - - + +
382A ARG* 1.3 74.4 - - + +
384A ARG* 1.3 65.8 + - - +
386A PHE* 3.2 4.1 + - + +
387A TYR* 3.0 43.6 + - + -
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Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASP* 2.7 39.0 + - - -
246A VAL* 3.6 22.0 - - + +
247A THR* 4.3 11.3 - - - +
377A ARG* 6.0 0.6 - - - +
380A VAL* 2.9 37.9 + - - +
381A ARG* 3.7 6.7 - - - +
383A LEU* 1.3 77.5 - - - +
385A GLU* 1.3 56.5 + - - +
387A TYR* 3.3 3.0 + - - +
388A ARG* 2.9 53.8 + - - +
391A ASN* 5.2 0.2 + - - -
404A TRP 3.6 16.8 + - - -
405A ASP* 4.5 2.6 + - - +
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Residues in contact with GLU 385 (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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381A ARG* 2.9 47.6 + - + +
382A ARG* 3.7 8.9 - - - +
384A ARG* 1.3 77.7 - - - +
386A PHE* 1.3 61.5 + - - +
388A ARG* 3.7 18.2 + - - +
389A PRO* 3.3 18.7 - - - +
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Residues in contact with PHE 386 (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 ILE* 3.3 36.1 - - + -
281A THR* 3.6 33.0 - - + -
286A ILE* 3.9 19.5 - - + -
290A ILE* 4.0 13.7 - - + -
382A ARG 3.0 7.6 + - - +
383A LEU* 3.2 4.7 + - + +
385A GLU* 1.3 76.8 - - - +
387A TYR* 1.3 90.9 + + - +
389A PRO* 3.3 12.1 - - - +
390A PHE* 3.5 33.7 - + - -
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Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO* 3.6 42.0 + - + -
246A VAL* 3.9 15.5 - - + -
249A ALA* 4.4 2.7 - - + +
285A ALA 3.7 5.0 + - - -
286A ILE* 2.7 47.7 + - + +
289A GLY* 3.6 18.6 - - - -
290A ILE* 4.0 6.3 - - + -
383A LEU* 3.0 37.7 + - + +
384A ARG* 3.9 3.6 - - - +
386A PHE* 1.3 95.8 - + - +
388A ARG* 1.3 66.5 + - - +
390A PHE* 2.9 13.1 + + + +
391A ASN* 2.9 36.0 + - - +
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 2.9 41.3 + - - +
385A GLU* 3.8 20.7 - - - +
387A TYR* 1.3 75.2 - - - +
389A PRO* 1.3 70.8 - - + +
391A ASN* 3.1 4.7 + - - +
392A LEU* 3.0 36.7 + - + +
404A TRP 5.2 1.0 + - - -
405A ASP* 2.8 49.0 + - + +
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Residues in contact with PRO 389 (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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385A GLU 3.3 11.2 - - - +
386A PHE 3.3 17.7 - - - +
387A TYR 3.4 0.4 - - - -
388A ARG* 1.3 93.0 - - + +
390A PHE* 1.3 68.7 + - + +
392A LEU* 3.5 7.7 + - + +
393A LYS* 3.2 21.5 + - - +
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Residues in contact with PHE 390 (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 GLY 5.8 0.2 - - - +
290A ILE* 3.7 42.4 - - + -
291A TYR 5.8 0.2 - - - +
292A ALA* 3.9 13.1 - - + +
293A LYS 5.9 0.2 - - - -
386A PHE* 3.5 50.5 - + - -
387A TYR* 2.9 12.0 + + + +
389A PRO* 1.3 78.2 - - + +
391A ASN* 1.3 63.3 + - - +
393A LYS* 3.3 13.9 + - + +
394A PHE* 2.9 29.0 + - - +
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Residues in contact with ASN 391 (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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244A ASP* 5.4 0.8 + - - -
245A PRO* 3.4 26.6 - - - +
289A GLY 4.8 1.6 - - - +
291A TYR* 5.4 1.2 - - - -
384A ARG 5.2 0.2 + - - -
387A TYR* 2.9 32.2 + - - +
388A ARG 3.4 4.2 - - - +
390A PHE* 1.3 77.3 - - - +
392A LEU* 1.3 56.8 + - - +
394A PHE* 3.0 10.2 + - - +
395A TYR* 2.9 40.1 + - + +
404A TRP* 3.9 21.6 + - + +
405A ASP* 3.1 34.4 + - - +
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Residues in contact with LEU 392 (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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388A ARG* 3.0 31.5 + - + +
389A PRO* 3.9 7.2 - - + +
391A ASN* 1.3 76.8 - - - +
393A LYS* 1.3 61.5 + - - +
395A TYR* 3.4 31.6 + - + +
396A GLN* 3.2 25.9 + - - +
401A ASP* 5.1 2.9 - - - +
405A ASP* 4.7 10.8 - - + +
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Residues in contact with LYS 393 (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* 3.9 16.4 - - + +
293A LYS* 5.5 0.8 - - - +
296A GLU* 3.0 35.2 + - - -
389A PRO 3.2 14.3 + - - +
390A PHE* 3.5 17.1 - - + +
391A ASN 3.2 0.2 - - - -
392A LEU* 1.3 77.3 - - - +
394A PHE* 1.3 57.9 + - - +
396A GLN* 3.2 9.7 + - + +
397A MET* 2.9 49.5 + - + +
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Residues in contact with PHE 394 (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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220A PHE* 5.5 1.3 - + - -
242A VAL* 3.8 14.6 - - + -
291A TYR* 3.6 27.1 - + + -
292A ALA* 3.9 16.6 - - + +
295A LEU* 4.1 15.0 - - + -
309A PHE* 3.7 28.9 - + - -
390A PHE 2.9 14.3 + - - +
391A ASN* 3.2 10.3 - - - +
393A LYS* 1.3 75.5 - - - +
395A TYR* 1.3 65.6 + + - +
397A MET* 3.3 3.4 + - - +
398A THR* 2.9 46.9 + - + +
402A PHE* 3.7 28.9 - + - -
404A TRP* 3.9 28.7 - + + -
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Residues in contact with TYR 395 (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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391A ASN* 2.9 20.9 + - + -
392A LEU* 3.5 37.9 - - + +
393A LYS 3.3 0.2 - - - -
394A PHE* 1.3 77.4 - + - +
396A GLN* 1.3 55.7 + - + +
398A THR* 3.8 0.2 - - - -
399A GLY* 2.6 33.1 + - - -
400A HIS 3.0 32.9 + - - +
401A ASP* 3.6 29.4 - - + -
402A PHE* 3.4 20.6 - + + -
404A TRP* 3.2 45.9 + + - +
405A ASP* 2.9 25.6 + - + -
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Residues in contact with GLN 396 (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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392A LEU 3.2 12.3 + - - +
393A LYS* 3.2 13.1 + - + +
395A TYR* 1.3 83.7 - - - +
397A MET* 1.3 63.1 + - + +
398A THR 3.4 0.2 + - - -
399A GLY* 3.5 8.5 + - - -
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Residues in contact with MET 397 (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* 3.8 31.2 - - - +
295A LEU* 3.6 33.7 - - + -
296A GLU* 3.6 26.5 - - + +
299A LEU* 4.0 17.8 - - + +
304A ILE* 4.1 16.5 - - - +
393A LYS* 2.9 35.1 + - + +
394A PHE* 3.3 4.9 + - - +
396A GLN* 1.3 76.9 - - + +
398A THR* 1.3 62.0 + - - +
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Residues in contact with THR 398 (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* 3.8 8.3 - - + -
304A ILE* 4.8 8.0 - - - +
309A PHE* 3.6 37.9 - - + -
394A PHE* 2.9 45.2 + - + +
395A TYR* 3.4 2.9 + - - -
397A MET* 1.3 76.4 - - - +
399A GLY* 1.3 61.9 + - - +
400A HIS* 3.6 17.7 + - - +
402A PHE* 4.0 10.1 - - - -
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Residues in contact with GLY 399 (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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395A TYR 2.6 16.1 + - - -
396A GLN* 3.5 7.0 + - - -
397A MET 3.5 2.2 - - - -
398A THR* 1.3 76.1 - - - +
400A HIS* 1.3 58.0 + - - +
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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
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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