Contacts of the helix formed by residues 425 - 444 (chain A) in PDB entry 3U78
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 GLN 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLU* 3.4 42.2 + - - +
153A LYS* 5.1 2.0 - - - +
417A LEU* 5.2 0.6 - - - +
423A GLN 3.9 1.2 + - - +
424A PRO* 1.3 78.1 - - - +
426A THR* 1.3 67.2 + - - +
427A TYR* 3.7 29.8 + - + -
428A LEU* 3.3 17.7 + - + +
429A VAL* 3.4 10.2 + - - +
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Residues in contact with THR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PRO 3.7 1.7 + - - -
425A GLN* 1.3 73.4 - - - +
427A TYR* 1.3 64.8 + - - +
429A VAL* 3.0 8.6 + - + +
430A GLN* 3.0 49.4 + - + +
705A EDO 5.4 10.5 - - - -
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Residues in contact with TYR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLU* 3.4 36.0 + - + +
372A ASN* 3.4 39.0 + - + +
373A LEU* 4.0 32.9 - - + +
375A ILE* 5.1 0.3 + - - +
425A GLN* 3.3 36.8 + - + -
426A THR* 1.3 78.6 - - - +
428A LEU* 1.3 85.8 + - + +
430A GLN* 3.9 15.5 + - - +
431A GLY* 3.0 24.1 + - - -
705A EDO 5.1 14.5 - - - +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ASN* 5.3 1.6 - - + +
375A ILE* 5.7 0.9 - - + -
410A LEU* 3.9 31.9 - - + +
413A THR* 4.0 23.1 - - + -
414A LEU* 3.6 31.8 - - + +
417A LEU* 4.7 3.6 - - + -
424A PRO* 4.6 5.8 - - + -
425A GLN* 3.3 15.0 + - + +
426A THR 3.1 0.4 - - - -
427A TYR* 1.3 108.9 - - + +
429A VAL* 1.3 60.4 + - - +
431A GLY* 5.1 0.4 - - - -
432A VAL* 3.0 38.2 + - + +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 5.2 2.9 - - + -
423A GLN* 6.0 0.4 - - - +
424A PRO* 4.3 19.5 - - + +
425A GLN 3.4 12.5 + - - +
426A THR* 3.0 10.4 + - + +
428A LEU* 1.3 76.4 - - - +
430A GLN* 1.3 67.6 + - + +
432A VAL* 3.2 4.4 + - - +
433A LYS* 2.9 51.5 + - + +
472A ILE* 5.6 2.9 - - + +
475A ILE* 3.7 38.4 - - + -
476A GLU* 5.9 0.2 - - + -
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Residues in contact with GLN 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU 5.3 3.6 + - - -
376A GLY* 5.7 0.9 - - - -
426A THR* 3.0 38.7 + - + +
427A TYR* 3.9 17.0 + - - +
429A VAL* 1.3 79.9 - - + +
431A GLY* 1.3 62.9 + - - +
433A LYS* 3.4 8.8 + - - +
434A ALA* 3.0 23.5 + - - +
705A EDO 5.1 8.0 + - - -
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Residues in contact with GLY 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.5 41.0 - - - +
376A GLY 4.7 2.0 - - - -
427A TYR 3.0 15.8 + - - -
428A LEU 4.1 0.2 - - - -
430A GLN* 1.3 78.5 - - - +
432A VAL* 1.3 58.1 + - - +
434A ALA* 3.2 5.0 + - - +
435A LEU* 2.8 25.6 + - - +
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Residues in contact with VAL 432 (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 LEU* 4.0 30.3 - - + -
411A LEU 5.3 0.2 - - - +
414A LEU* 3.6 30.1 - - + -
428A LEU* 3.0 29.8 + - + +
429A VAL* 3.8 2.5 - - - +
431A GLY* 1.3 72.6 - - - +
433A LYS* 1.3 69.1 + - - +
435A LEU* 3.0 9.2 + - + +
436A HIS* 2.8 21.8 + - - +
468A LEU* 4.1 22.9 - - + -
471A VAL* 5.2 0.4 - - + -
472A ILE* 3.7 22.7 - - + -
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Residues in contact with LYS 433 (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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429A VAL* 2.9 41.7 + - + +
430A GLN* 3.6 7.9 - - - +
432A VAL* 1.3 76.2 - - - +
434A ALA* 1.3 57.8 + - - +
436A HIS* 3.4 4.0 + - - +
437A THR* 3.0 31.9 + - - -
472A ILE* 3.4 30.5 - - + -
476A GLU* 2.8 34.1 + - - +
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Residues in contact with ALA 434 (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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376A GLY* 3.8 29.6 - - - +
379A LEU* 3.4 16.3 - - + +
430A GLN 3.0 14.6 + - - +
431A GLY 3.4 8.5 - - - +
432A VAL 3.0 0.2 - - - -
433A LYS* 1.3 74.7 - - - +
435A LEU* 1.3 65.9 + - - +
437A THR* 3.3 8.9 + - - -
438A ALA* 3.2 16.3 + - - +
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Residues in contact with LEU 435 (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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250A TRP* 5.2 1.8 - - + -
375A ILE* 4.0 11.0 - - + -
379A LEU* 3.8 12.3 - - + +
403A CYS* 3.7 38.8 - - + +
406A VAL* 4.0 5.4 - - + -
407A ALA* 3.5 39.7 - - + +
410A LEU* 3.9 23.8 - - + -
431A GLY 2.8 16.0 + - - +
432A VAL* 3.5 10.8 - - + +
434A ALA* 1.3 73.1 - - - +
436A HIS* 1.3 52.3 + - - +
438A ALA* 3.2 1.4 + - - -
439A LEU* 2.8 51.0 + - + +
468A LEU* 4.9 3.4 - - + -
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Residues in contact with HIS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL 2.8 15.8 + - - +
433A LYS* 3.4 6.5 - - - +
435A LEU* 1.3 77.4 - - - +
437A THR* 1.3 69.1 + - - +
439A LEU* 3.9 2.1 - - - +
440A LYS* 3.0 43.7 + - + +
465A ILE* 3.5 41.9 + - + +
468A LEU* 4.0 19.7 - - + +
469A SER* 3.7 21.2 - - - -
472A ILE* 4.0 21.8 - - + -
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Residues in contact with THR 437 (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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383A GLU* 6.0 1.3 - - - +
433A LYS 3.0 15.7 + - - -
434A ALA* 3.3 10.2 + - - -
436A HIS* 1.3 82.2 - - - +
438A ALA* 1.3 58.8 + - - +
440A LYS* 3.7 6.6 + - - +
441A LEU* 3.1 27.0 + - + +
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Residues in contact with ALA 438 (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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379A LEU* 3.8 28.3 - - + -
383A GLU* 3.9 17.3 - - - +
434A ALA 3.2 12.4 + - - +
435A LEU 3.2 3.9 + - - +
436A HIS 3.1 0.4 - - - -
437A THR* 1.3 78.5 - - + +
439A LEU* 1.3 66.6 + - + +
440A LYS 3.2 0.2 - - - -
441A LEU* 3.4 5.6 + - - -
442A TRP* 3.0 42.3 + - + -
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Residues in contact with LEU 439 (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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403A CYS* 4.7 4.7 - - + +
404A TRP* 3.5 41.3 - - + -
407A ALA* 3.9 14.1 - - + -
435A LEU* 2.8 42.1 + - + +
436A HIS* 4.0 3.4 - - - +
438A ALA* 1.3 73.8 - - + +
440A LYS* 1.3 63.2 + - - +
442A TRP* 3.3 24.9 + - + +
443A MET* 3.1 27.5 + - - +
464A LEU* 3.8 15.7 - - + -
465A ILE* 3.7 17.7 - - + -
468A LEU* 4.1 12.3 - - + -
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Residues in contact with LYS 440 (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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436A HIS* 3.0 39.4 + - + +
437A THR* 3.7 6.5 - - - +
439A LEU* 1.3 78.1 - - - +
441A LEU* 1.3 63.0 + - - +
443A MET* 3.2 11.5 + - - +
444A LYS* 3.3 17.5 + - + +
465A ILE* 3.8 21.7 - - + +
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Residues in contact with LEU 441 (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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383A GLU* 4.2 24.9 - - + +
437A THR* 3.1 20.3 + - + +
438A ALA* 3.6 5.6 - - - +
439A LEU 3.2 0.2 - - - -
440A LYS* 1.3 75.7 - - - +
442A TRP* 1.3 71.1 + - + +
443A MET 2.9 6.2 + - - -
444A LYS* 3.2 29.8 + - + +
447A LEU* 3.5 35.6 - - + +
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Residues in contact with TRP 442 (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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379A LEU* 4.1 7.9 - - + -
382A TYR* 3.9 20.4 - + - -
383A GLU* 4.6 7.9 + - - +
399A PHE* 4.1 13.9 - + - -
400A GLU* 3.5 52.2 + - + -
403A CYS* 4.1 18.2 - - + -
404A TRP* 4.2 16.4 - + + -
438A ALA* 3.0 32.8 + - + +
439A LEU* 3.3 17.5 + - + +
441A LEU* 1.3 92.1 - - + +
443A MET* 1.3 62.4 + - + +
444A LYS 4.9 0.4 - - - -
447A LEU* 5.0 0.2 - - - -
448A VAL* 3.7 10.8 - - - +
451A HIS* 3.3 59.4 - + + +
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Residues in contact with MET 443 (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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404A TRP* 4.1 8.3 - - + -
439A LEU 3.1 17.3 - - - +
440A LYS* 3.2 5.4 + - - +
441A LEU 2.9 1.4 + - - -
442A TRP* 1.3 81.4 - - - +
444A LYS* 1.3 68.8 + - - +
445A LYS* 3.2 3.1 + - - -
448A VAL* 3.5 25.2 - - + +
451A HIS* 6.2 0.2 - - - -
455A ILE* 3.5 28.0 - - + -
461A PRO* 3.4 25.4 - - + -
462A GLY* 4.6 6.1 - - - +
465A ILE* 3.6 20.4 - - + -
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Residues in contact with LYS 444 (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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440A LYS* 3.3 14.3 + - + +
441A LEU* 3.2 34.9 + - + +
443A MET* 1.3 74.6 - - - +
445A LYS* 1.3 58.0 + - - +
446A GLU* 3.1 25.6 + - - +
447A LEU* 2.9 17.3 + - + +
448A VAL* 2.8 31.2 + - - +
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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