Contacts of the helix formed by residues 374 - 394 (chain A) in PDB entry 1O8A
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 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR* 3.4 22.7 - - + +
305A MET* 3.4 14.7 - - - +
315A MET* 3.5 6.1 - - - +
372A THR* 3.0 34.8 + - - +
373A VAL* 1.3 75.0 - - - +
375A LEU* 1.3 63.1 + - - +
376A GLU* 3.2 13.1 + - - +
377A ASP* 2.8 36.6 + - - +
378A LEU* 3.2 15.6 + - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A THR* 3.8 30.9 - - + +
302A THR* 4.1 4.1 + - - +
305A MET* 3.6 5.6 - - - -
374A ASN* 1.3 73.8 - - - +
376A GLU* 1.3 65.8 + - - +
378A LEU* 3.0 35.5 + - + +
379A VAL* 3.1 24.4 + - + +
421A VAL* 5.7 1.8 - - + -
422A SER* 5.1 8.7 - - - +
427A LEU* 4.1 31.6 - - + -
449A LYS* 4.3 17.0 - - + +
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR* 5.4 7.6 - - - +
170A ALA* 5.5 1.0 - - - +
277A ASN* 5.0 5.4 + - - -
282A THR* 4.0 15.9 + - - -
284A SER* 4.4 10.9 + - - +
285A ASN* 3.3 34.1 + - - +
374A ASN* 3.2 13.6 + - - +
375A LEU* 1.3 79.9 - - - +
377A ASP* 1.3 61.6 + - - +
379A VAL* 3.4 9.1 + - - +
380A VAL* 3.2 32.1 + - + +
453A ASP* 5.0 3.4 - - - +
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Residues in contact with ASP 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A MET* 3.6 5.5 - - + +
369A GLN* 3.5 14.8 + - - +
370A CYS 4.1 2.4 - - - +
371A THR* 3.2 12.3 - - + -
372A THR* 2.7 53.0 + - - +
374A ASN* 2.8 15.7 + - - +
376A GLU* 1.3 76.6 - - - +
378A LEU* 1.3 60.8 + - - +
380A VAL* 3.6 12.9 - - - +
381A ALA* 2.8 27.9 + - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A MET* 4.7 6.5 - - + -
310A TRP* 4.2 17.3 - - + -
315A MET* 3.6 46.2 - - + +
318A GLU* 5.1 2.2 - - + -
374A ASN 3.2 13.1 + - - +
375A LEU* 3.0 31.0 + - + +
377A ASP* 1.3 76.7 - - - +
379A VAL* 1.3 63.5 + - + +
381A ALA* 3.2 4.6 + - + +
382A HIS* 2.8 43.8 + - + -
421A VAL* 4.4 17.7 - - + -
427A LEU* 5.1 0.7 - - + -
430A LEU* 4.9 4.9 - - + -
432A LEU* 4.8 10.8 - - + -
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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
----------------------------------------------------------
375A LEU* 3.1 24.3 + - + +
376A GLU* 3.5 9.6 - - - +
378A LEU* 1.3 78.5 - - + +
380A VAL* 1.3 65.0 + - + +
382A HIS* 3.1 5.2 + - - +
383A HIS* 2.9 20.1 + - + +
415A ASP* 5.5 6.3 - - - +
418A ALA* 3.8 25.1 - - + +
421A VAL* 6.4 2.2 - - + -
422A SER* 4.1 19.7 - - - +
454A LYS* 5.2 11.7 - - - +
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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
----------------------------------------------------------
354A ALA* 3.8 18.4 - - + -
369A GLN* 3.7 22.4 - - - +
376A GLU* 3.2 21.4 + - + +
377A ASP* 3.6 15.7 - - - +
378A LEU 3.3 0.2 - - - -
379A VAL* 1.3 78.9 - - + +
381A ALA* 1.3 62.7 + - - +
383A HIS* 3.1 11.3 + - + +
384A GLU* 3.0 25.5 + - + +
702A NXA 5.0 5.8 - - - +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A MET* 4.8 13.7 - - + +
316A PHE* 3.8 39.9 - - + -
319A ALA* 4.7 0.9 - - + -
369A GLN* 4.2 2.7 - - - +
371A THR* 5.6 0.2 - - + -
377A ASP 2.8 13.4 + - - +
378A LEU* 3.3 13.2 - - - +
379A VAL 3.2 0.2 - - - -
380A VAL* 1.3 78.0 - - - +
382A HIS* 1.3 59.0 + - - +
384A GLU* 3.4 2.8 + - - +
385A MET* 2.9 34.7 + - - +
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Residues in contact with HIS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 4.6 4.3 - - + +
319A ALA* 3.5 35.2 + - + +
322A PHE* 4.6 7.7 - - + +
323A PHE* 4.2 5.3 - + + -
378A LEU* 2.8 50.1 + - + -
379A VAL* 3.1 8.5 + - - +
381A ALA* 1.3 73.2 - - - +
383A HIS* 1.3 67.0 + - - +
385A MET* 3.2 7.9 + - - +
386A GLY 2.9 18.9 + - - -
414A GLY* 3.2 22.6 - - - +
417A LEU* 4.6 9.0 - - + -
418A ALA* 4.0 14.8 - - + -
421A VAL* 3.5 35.6 - - + +
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Residues in contact with HIS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 2.9 13.4 + - + +
380A VAL* 3.1 15.2 + - + +
382A HIS* 1.3 76.4 - - - +
384A GLU* 1.3 80.6 + - - +
386A GLY* 3.1 11.8 + - - -
387A HIS* 3.3 13.0 + - - -
410A HIS 5.3 1.0 - - - +
411A GLU* 3.0 29.7 + - + +
414A GLY* 3.8 11.8 + - - -
415A ASP* 2.8 28.1 + - - +
523A TYR* 4.6 7.6 - + - -
527A PHE* 6.5 0.7 - + - -
700A ACT 3.5 2.2 + - - -
701A ZN 2.0 36.3 - - - -
702A NXA 4.0 12.5 + - + -
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Residues in contact with GLU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ALA* 3.4 17.1 - - + +
355A SER* 3.0 12.7 - - - +
356A ALA* 3.0 31.0 + - - +
367A ILE* 3.6 21.8 - - + -
369A GLN* 3.5 19.3 - - - +
380A VAL* 3.0 21.7 + - + +
381A ALA* 3.8 2.9 - - - +
383A HIS* 1.3 82.4 - - - +
385A MET* 1.3 65.7 + - - +
386A GLY 3.0 1.6 - - - -
387A HIS* 3.0 18.0 + - - +
388A ILE* 3.1 15.2 + - - +
700A ACT 2.6 24.1 + - - -
702A NXA 3.7 2.9 + - - -
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Residues in contact with MET 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE* 3.7 17.9 - - + +
319A ALA* 3.8 13.2 - - + -
320A ASP* 3.6 37.2 - - + +
323A PHE* 3.6 22.3 - - + -
331A VAL* 3.5 30.7 - - + -
335A PHE* 3.8 17.3 - - + -
336A TRP* 4.9 0.4 - - + -
367A ILE* 3.7 16.6 - - - -
381A ALA 2.9 21.5 + - - +
382A HIS 3.2 2.2 + - - +
384A GLU* 1.3 76.9 - - - +
386A GLY* 1.3 58.1 + - - +
388A ILE* 3.3 5.1 + - - +
389A GLN* 2.9 28.1 + - - +
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Residues in contact with GLY 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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323A PHE* 3.5 19.3 - - - -
382A HIS 2.9 9.5 + - - -
383A HIS 3.1 6.0 + - - -
384A GLU 3.0 0.4 - - - -
385A MET* 1.3 75.5 - - - +
387A HIS* 1.3 63.7 + - - +
389A GLN* 3.3 3.5 + - - +
390A TYR* 3.1 21.1 + - - +
410A HIS 4.9 1.3 - - - -
413A ILE* 4.1 12.0 - - - +
414A GLY 3.6 16.2 - - - -
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Residues in contact with HIS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA* 3.3 16.6 - - + -
383A HIS* 3.3 15.6 + - - -
384A GLU* 3.0 19.4 + - - +
386A GLY* 1.3 78.0 - - - +
388A ILE* 1.3 61.7 + - - +
390A TYR* 3.1 5.2 + - - +
391A PHE* 3.0 31.8 + + + -
410A HIS* 2.9 50.7 + + + +
411A GLU* 3.2 19.3 + - - -
700A ACT 3.3 12.1 + - - -
701A ZN 2.1 36.2 - - - -
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Residues in contact with ILE 388 (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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331A VAL* 3.8 27.4 - - + -
332A PRO* 5.5 0.2 - - + -
335A PHE* 4.3 4.7 - - + -
356A ALA* 3.9 11.2 - - + -
365A PHE* 4.0 24.9 - - + -
366A ARG 3.6 26.7 - - - +
367A ILE* 3.7 19.7 - - + -
384A GLU 3.1 12.9 + - - +
385A MET* 3.5 9.2 - - - +
387A HIS* 1.3 78.4 - - - +
389A GLN* 1.3 63.3 + - - +
391A PHE* 3.2 17.4 + - + +
392A MET* 3.0 31.4 + - + +
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PHE* 3.7 28.7 - - + -
328A LEU* 3.4 7.6 - - + +
329A LEU* 2.8 52.2 + - - +
331A VAL* 6.1 0.2 - - - +
385A MET 2.9 13.8 + - - +
386A GLY 3.5 8.7 - - - +
387A HIS 3.2 0.4 - - - -
388A ILE* 1.3 76.2 - - - +
390A TYR* 1.3 58.1 + - - +
392A MET* 3.3 11.5 + - - +
393A GLN* 2.9 53.5 + - + +
413A ILE* 5.0 0.2 - - + -
566A MET* 3.7 24.0 - - + -
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Residues in contact with TYR 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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386A GLY 3.1 8.5 + - - +
387A HIS 3.1 2.8 + - - +
389A GLN* 1.3 77.2 - - - +
391A PHE* 1.3 62.8 + - - +
393A GLN* 3.2 1.6 + - - +
394A TYR* 3.1 53.9 + + - -
403A GLU 4.4 0.7 - - - -
404A GLY* 3.6 11.2 - - - -
405A ALA* 3.2 22.0 + - - +
409A PHE* 3.7 22.4 - - + +
410A HIS* 3.3 53.2 - + + -
413A ILE* 3.6 24.2 - - + -
565A ALA* 4.5 4.5 + - - +
566A MET* 3.5 44.8 - - + +
569A GLY* 4.7 2.1 + - - -
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Residues in contact with PHE 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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356A ALA* 3.8 26.0 - - + -
357A TRP 3.4 35.4 - - - -
358A ASP* 3.7 28.5 - - + +
365A PHE* 3.5 19.3 - + + -
387A HIS* 3.0 18.0 + + + -
388A ILE* 3.2 17.0 + - + +
390A TYR* 1.3 76.1 - - - +
392A MET* 1.3 62.5 + - - +
394A TYR* 3.3 27.4 + - - -
395A LYS* 3.1 24.9 + - - +
410A HIS* 3.4 23.3 - + - -
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Residues in contact with MET 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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329A LEU* 3.6 27.9 - - + +
330A PRO 3.5 30.5 - - - +
331A VAL* 4.0 7.4 - - + -
332A PRO* 3.7 22.9 - - - -
365A PHE* 3.8 28.3 - - + -
388A ILE* 3.0 25.9 + - + +
389A GLN* 3.6 29.6 - - - +
391A PHE* 1.3 75.6 - - - +
393A GLN* 1.3 62.6 + - - +
395A LYS* 3.2 27.9 - - + +
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 4.0 15.8 - - - +
329A LEU* 3.8 19.4 - - - +
389A GLN* 2.9 47.8 + - - +
390A TYR 3.2 4.9 + - - +
392A MET* 1.3 78.0 - - - +
394A TYR* 1.3 56.9 + - - +
395A LYS* 3.9 0.3 + - - +
396A ASP* 5.2 1.6 + - - +
563A ALA* 3.8 9.3 - - - +
566A MET* 3.7 34.3 - - + -
567A LYS* 2.6 59.5 + - - +
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Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ASP* 4.0 9.5 + - - -
390A TYR* 3.1 39.9 + + - -
391A PHE* 3.3 32.2 - + - -
393A GLN* 1.3 76.0 - - - +
395A LYS* 1.3 63.5 + - - +
396A ASP 3.0 6.9 + - - -
397A LEU* 3.1 39.8 + - + +
402A ARG* 3.2 44.4 + - + +
403A GLU* 3.4 30.3 - - - -
410A HIS* 3.0 21.7 + - - -
566A MET 3.8 8.3 - - - +
567A LYS 4.4 1.8 - - - +
569A GLY* 3.8 2.9 - - - -
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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