Contacts of the helix formed by residues 406 - 425 (chain A) in PDB entry 3U86
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 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ARG* 3.5 22.7 + - - +
402A SER 4.5 3.8 - - - +
403A ALA* 3.0 19.9 + - - +
404A LEU 3.5 1.0 - - - -
405A GLN* 1.3 77.8 - - - +
407A PRO* 1.3 70.3 - - - +
408A GLU* 2.9 33.5 + - - +
409A CYS* 3.1 33.0 + - - +
410A PHE 3.4 7.6 + - - -
447A PHE* 4.2 4.2 - - - -
451A VAL* 3.7 4.1 - - - +
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Residues in contact with PRO 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN 4.0 3.6 - - - +
406A ASP* 1.3 91.0 - - - +
408A GLU* 1.3 58.2 + - + +
410A PHE* 3.2 6.3 + - + -
411A ALA* 2.8 31.2 + - - +
451A VAL* 3.7 23.1 - - + +
454A LYS* 3.8 29.8 - - + -
455A VAL* 3.5 24.7 - - + +
548A GLY* 5.9 0.7 - - - -
549A PRO* 3.7 15.0 - - + -
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 2.9 22.5 + - - +
407A PRO* 1.3 79.1 - - + +
409A CYS* 1.3 57.1 + - - +
411A ALA* 3.6 5.8 - - - +
412A HIS* 2.8 53.9 + - + +
549A PRO* 3.9 24.7 - - + +
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Residues in contact with CYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 3.2 35.2 - - - -
338A LEU* 3.7 20.7 - - + +
403A ALA* 3.9 17.3 - - + +
406A ASP* 3.1 34.9 + - - +
408A GLU* 1.3 73.9 - - - +
410A PHE* 1.3 66.0 + - - +
412A HIS* 3.4 11.6 + - - +
413A LEU* 3.0 22.5 + - - +
447A PHE* 4.4 9.0 - - + -
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Residues in contact with PHE 410 (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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406A ASP 3.4 5.1 + - - +
407A PRO* 3.2 8.8 + - + +
409A CYS* 1.3 78.9 - - - +
411A ALA* 1.3 59.0 + - - +
413A LEU* 3.6 7.2 - - + +
414A LEU* 3.2 50.4 + - + +
444A LEU* 3.4 27.6 - - + -
447A PHE* 3.9 38.4 - + + -
451A VAL* 4.9 1.3 - - + +
452A ARG* 3.5 58.8 - - + -
455A VAL* 4.1 16.6 - - + -
457A ILE* 5.8 0.9 - - + -
565A LEU* 4.1 13.5 - - + -
566A VAL* 5.5 1.8 - - + -
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Residues in contact with ALA 411 (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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407A PRO 2.8 16.4 + - - +
408A GLU* 3.6 7.4 - - - +
410A PHE* 1.3 75.6 - - - +
412A HIS* 1.3 67.6 + - + +
413A LEU 3.0 1.3 + - - -
414A LEU* 3.1 4.7 + - - +
415A ARG* 3.1 24.5 + - - +
455A VAL* 4.1 14.4 - - + -
549A PRO* 4.9 7.6 - - + -
550A VAL 5.8 0.7 - - - +
551A LEU* 4.0 26.8 - - + +
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Residues in contact with HIS 412 (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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335A ARG* 3.7 14.4 + - + +
338A LEU* 3.7 19.4 - - + +
339A GLN* 3.4 50.2 + - + +
342A ALA* 3.3 15.8 - - - +
408A GLU* 2.8 43.1 + - + +
409A CYS* 3.4 11.7 - - - +
411A ALA* 1.3 75.8 - - - +
413A LEU* 1.3 60.2 + - - +
415A ARG* 3.5 17.9 + - - +
416A PHE* 3.2 18.0 + - - +
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Residues in contact with LEU 413 (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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338A LEU* 4.4 10.8 - - + -
372A ILE* 4.4 30.1 - - + -
376A LEU* 5.2 2.0 - - + -
409A CYS 3.0 17.1 + - - +
410A PHE* 3.6 9.9 - - + +
411A ALA 3.0 0.8 - - - -
412A HIS* 1.3 79.8 - - - +
414A LEU* 1.3 59.4 + - + +
416A PHE* 3.1 23.0 - - + +
417A TYR* 3.2 35.8 + - + -
440A LEU* 5.3 0.2 - - + -
443A SER* 4.1 22.9 - - - -
444A LEU* 4.4 19.5 - - + -
447A PHE* 4.3 20.0 - - + -
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Residues in contact with LEU 414 (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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410A PHE* 3.2 54.1 - - + +
411A ALA* 3.1 2.1 + - - +
413A LEU* 1.3 76.2 - - + +
415A ARG* 1.3 55.3 + - - +
416A PHE 3.0 1.8 - - - -
417A TYR* 3.1 6.4 + - + +
418A ASP* 2.7 36.8 + - - +
440A LEU* 5.5 4.3 - - + -
444A LEU* 4.1 12.8 - - + -
455A VAL* 4.7 4.0 - - + -
457A ILE* 4.8 5.2 - - + -
551A LEU* 3.5 29.4 - - + -
553A PHE* 4.0 13.7 - - + -
558A MET* 4.3 7.1 - - - +
565A LEU* 3.8 28.0 - - + -
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Residues in contact with ARG 415 (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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339A GLN* 4.3 5.1 + - - +
342A ALA* 3.7 22.3 - - + +
343A ASP* 2.5 35.8 + - - +
345A ALA* 4.1 3.6 - - - +
346A THR* 3.4 30.7 + - - +
411A ALA 3.1 16.5 + - - +
412A HIS* 3.5 26.2 + - - +
414A LEU* 1.3 75.7 - - - +
416A PHE* 1.3 56.1 - - - +
418A ASP* 3.4 12.4 - - + +
419A GLY* 3.1 23.2 + - - -
551A LEU* 4.6 16.6 - - + +
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Residues in contact with PHE 416 (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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338A LEU 5.5 0.7 - - - +
341A TRP* 3.3 35.2 - + + -
342A ALA* 4.4 6.0 - - - +
345A ALA* 3.4 13.6 - - + +
364A PHE* 3.9 24.5 - + - -
367A VAL* 3.7 26.5 - - + -
368A ALA* 3.7 26.0 - - + -
372A ILE* 4.4 11.0 - - + -
412A HIS 3.2 10.9 + - - +
413A LEU* 3.1 13.2 - - + +
414A LEU 3.0 0.4 - - - -
415A ARG* 1.3 79.3 - - - +
417A TYR* 1.3 84.0 + + - +
418A ASP 3.2 0.7 + - - -
419A GLY 3.3 0.5 + - - -
420A ILE* 3.2 43.8 + - + +
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Residues in contact with TYR 417 (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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368A ALA* 3.8 34.9 + - + +
369A ASN* 5.2 0.3 + - - -
372A ILE* 5.7 1.5 - - + +
413A LEU* 3.2 46.6 + - + +
414A LEU* 3.1 8.1 + - + +
416A PHE* 1.3 90.9 - + - +
418A ASP* 1.3 57.2 + - - +
420A ILE* 3.8 9.3 - - + +
421A CYS* 3.0 35.0 + - - -
432A LEU* 5.7 3.6 - - + -
436A TRP* 4.6 19.5 + + + -
439A PHE* 4.1 3.5 + - - +
440A LEU* 3.6 60.5 + - + -
443A SER* 4.5 3.0 + - - -
558A MET* 3.9 19.3 - - + -
579A LEU* 5.2 6.1 - - + -
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Residues in contact with ASP 418 (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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349A GLN* 4.7 2.0 - - - +
414A LEU 2.7 22.2 + - - +
415A ARG* 3.4 14.3 - - - +
417A TYR* 1.3 70.5 - - - +
419A GLY* 1.3 66.5 + - - +
421A CYS* 3.1 4.7 + - - +
422A LYS* 2.9 24.5 + - - +
551A LEU* 5.3 0.7 - - - +
552A THR 4.2 2.4 - - - +
553A PHE* 3.5 18.9 - - + +
554A GLN* 3.1 30.5 + - - +
555A SER* 2.8 39.9 + - - -
558A MET* 3.6 9.9 - - + +
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Residues in contact with GLY 419 (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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345A ALA* 3.6 27.4 - - - -
346A THR* 4.7 0.9 - - - -
348A ILE* 3.8 3.2 - - - +
349A GLN* 3.5 21.5 - - - -
415A ARG 3.1 9.0 + - - -
416A PHE 3.3 2.7 + - - -
418A ASP* 1.3 79.1 + - - +
420A ILE* 1.3 56.1 + - - +
422A LYS 3.4 0.3 + - - -
423A TRP* 2.9 27.2 + - - +
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Residues in contact with ILE 420 (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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345A ALA* 4.7 3.8 - - + -
348A ILE* 4.8 1.3 - - + -
364A PHE* 4.3 20.6 - - + -
416A PHE* 3.2 54.5 + - + +
417A TYR* 4.0 9.9 - - + +
418A ASP 3.2 1.0 - - - -
419A GLY* 1.3 73.6 - - - +
421A CYS* 1.3 66.7 + - - +
423A TRP* 3.2 25.3 - - + +
424A GLU* 3.2 9.0 + - - +
431A VAL* 3.8 24.2 - - + +
432A LEU* 3.9 18.2 - - + -
436A TRP* 4.0 20.0 - - + -
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Residues in contact with CYS 421 (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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417A TYR* 3.0 26.5 + - - +
418A ASP 3.1 0.2 + - - -
420A ILE* 1.3 76.7 - - - +
422A LYS* 1.3 62.2 + - - +
424A GLU* 3.3 14.3 + - - +
425A GLU* 3.2 17.3 + - - +
432A LEU* 4.5 11.7 - - - -
555A SER* 3.3 23.3 - - - +
557A LYS* 4.0 17.0 - - + +
558A MET* 3.2 25.8 - - - -
579A LEU* 3.7 21.3 - - - -
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Residues in contact with LYS 422 (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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349A GLN* 3.1 49.3 + - + +
350A ASP* 4.1 16.5 + - - +
351A TYR 4.4 0.3 - - - +
418A ASP 2.9 13.2 + - - +
421A CYS* 1.3 72.7 - - - +
423A TRP* 1.3 68.0 + - - +
425A GLU* 3.4 30.2 + - + +
554A GLN* 3.8 40.2 - - - +
555A SER* 3.6 5.1 - - - +
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Residues in contact with TRP 423 (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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348A ILE* 3.5 35.4 - - + +
349A GLN 3.9 3.3 + - - -
351A TYR* 3.0 43.3 - - - +
352A ASN 3.5 5.9 + - - -
353A TYR* 3.5 47.8 - + + +
357A ASP* 4.5 5.3 + - - -
360A ILE* 3.8 29.4 - - + -
361A TYR* 3.9 23.6 - + - -
364A PHE* 3.9 23.6 - + + -
419A GLY 2.9 14.8 + - - +
420A ILE* 3.2 19.1 - - + +
422A LYS* 1.3 78.4 - - - +
424A GLU* 1.3 58.7 + - - +
425A GLU 2.9 9.7 + - - +
427A SER* 3.0 14.1 + - - -
431A VAL* 4.1 21.8 - - + -
436A TRP* 5.9 0.9 - + - -
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Residues in contact with GLU 424 (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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420A ILE 3.2 5.2 + - - +
421A CYS* 3.3 10.2 + - - +
423A TRP* 1.3 79.0 - - - +
425A GLU* 1.3 61.7 + - + +
426A GLY 3.5 0.5 + - - -
427A SER* 3.3 20.8 + - - +
429A THR 4.9 0.2 - - - +
430A PRO* 3.9 14.9 - - + +
431A VAL* 3.5 36.6 + - + +
432A LEU* 3.1 34.4 + - + +
557A LYS* 3.0 36.4 + - - +
580A THR* 5.6 0.7 - - - -
581A ALA 5.8 0.3 + - - -
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Residues in contact with GLU 425 (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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351A TYR 4.7 0.2 - - - +
352A ASN* 3.0 18.5 - - - +
421A CYS* 3.2 15.7 - - - +
422A LYS* 3.5 31.7 + - + +
423A TRP 2.9 8.3 + - - +
424A GLU* 1.3 76.1 - - + +
426A GLY* 1.3 58.4 + - - +
427A SER 3.2 0.7 - - - -
554A GLN 4.8 1.0 - - - +
555A SER* 3.5 9.6 - - - -
556A GLU* 3.1 51.9 + - - +
557A LYS* 4.6 4.4 + - + +
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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
------------------------------------------------------------
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