Contacts of the helix formed by residues 433 - 453 (chain N) in PDB entry 4UJ3
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 433 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431N GLN 3.9 3.4 + - - -
432N GLN* 1.3 71.5 - - - +
434N VAL* 1.3 63.6 + - - +
435N ASP* 3.9 14.0 - - - +
436N GLN* 3.0 35.9 + - - +
437N MET* 3.0 20.2 + - - +
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Residues in contact with VAL 434 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302N TYR* 4.6 9.6 - - + +
305N PHE* 3.8 21.3 - - + -
306N ARG* 4.0 31.0 - - + -
309N LYS* 3.4 38.1 - - + +
310N ASP* 5.6 0.9 - - - +
432N GLN 3.9 0.4 + - - -
433N ASP* 1.3 74.0 - - - +
435N ASP* 1.3 57.4 + - - +
437N MET* 3.6 6.7 - - - +
438N PHE* 2.8 29.1 + - - +
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Residues in contact with ASP 435 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302N TYR* 2.5 36.5 + - - -
433N ASP* 3.2 16.0 - - - +
434N VAL* 1.3 77.8 - - - +
436N GLN* 1.3 61.5 + - + +
438N PHE* 3.6 4.3 + - - +
439N TRP* 3.3 33.0 + - + -
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Residues in contact with GLN 436 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431N GLN 4.7 1.9 - - - +
432N GLN* 3.5 32.8 + - + +
433N ASP* 3.0 34.9 + - - +
435N ASP* 1.3 77.4 - - + +
437N MET* 1.3 58.1 + - - +
439N TRP* 3.3 6.2 + - - +
440N GLU* 2.9 28.1 + - - +
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Residues in contact with MET 437 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305N PHE* 3.9 9.9 - - + -
309N LYS* 3.9 31.2 - - + -
420N TYR* 3.5 19.4 + - - +
424N ILE* 3.2 46.0 - - + -
429N VAL* 4.3 16.8 - - + +
432N GLN* 3.5 29.6 - - + +
433N ASP 3.0 19.1 + - - +
434N VAL* 3.2 6.3 + - - +
436N GLN* 1.3 73.9 - - - +
438N PHE* 1.3 68.3 + - - +
440N GLU* 3.2 2.4 + - - +
441N VAL* 3.1 25.3 + - - +
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Residues in contact with PHE 438 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297N ALA* 3.9 23.8 - - + -
298N ASP 4.3 6.7 - - - -
301N LEU* 3.9 9.0 - - + -
302N TYR* 3.4 52.7 - + + -
305N PHE* 3.6 37.4 - + + -
434N VAL 2.8 20.7 + - - +
435N ASP 3.9 3.1 - - - +
437N MET* 1.3 71.5 - - - +
439N TRP* 1.3 75.6 + + - +
441N VAL* 3.0 9.8 + - + +
442N MET* 3.0 66.9 + - + +
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Residues in contact with TRP 439 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295N LYS* 3.8 59.5 - - + +
296N GLU* 3.6 20.0 - - - -
297N ALA* 3.3 32.5 - - + +
298N ASP 5.4 0.4 - - - -
302N TYR* 6.2 0.6 - + - -
435N ASP* 3.3 25.4 + - + +
436N GLN* 3.3 6.8 + - - +
437N MET 3.3 0.2 - - - -
438N PHE* 1.3 88.7 - + - +
440N GLU* 1.3 61.9 + - - +
442N MET* 3.7 31.6 - - + +
443N GLN* 3.1 24.9 + - - +
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Residues in contact with GLU 440 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420N TYR* 3.5 39.1 + - + +
432N GLN* 3.8 17.7 + - - +
436N GLN 2.9 16.5 + - - +
437N MET* 3.6 5.4 - - - +
438N PHE 3.2 0.4 - - - -
439N TRP* 1.3 73.8 - - - +
441N VAL* 1.3 61.8 + - - +
443N GLN* 3.2 13.7 + - - +
444N LEU* 2.9 33.4 + - + +
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Residues in contact with VAL 441 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305N PHE* 3.8 22.9 - - + -
320N PHE* 4.1 16.8 - - + -
324N ILE* 4.5 2.5 - - + -
417N PHE* 4.0 25.1 - - + -
420N TYR* 3.8 19.7 - - + -
421N ILE* 4.7 7.2 - - + -
424N ILE* 4.9 0.2 - - + -
437N MET 3.1 15.0 + - - +
438N PHE* 3.0 8.0 + - + +
440N GLU* 1.3 75.9 - - - +
442N MET* 1.3 65.3 + - - +
444N LEU* 3.2 9.6 + - - +
445N ARG* 3.0 31.1 + - + +
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Residues in contact with MET 442 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298N ASP* 5.2 5.8 - - + +
301N LEU* 3.6 30.5 - - + -
438N PHE* 3.0 56.0 + - + +
439N TRP* 3.7 31.2 - - + +
441N VAL* 1.3 82.1 - - - +
443N GLN* 1.3 56.8 + - - +
445N ARG* 3.3 21.2 + - + +
446N LYS* 2.9 29.7 + - - +
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Residues in contact with GLN 443 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439N TRP 3.1 15.1 + - - +
440N GLU* 3.3 17.0 - - - +
442N MET* 1.3 76.1 - - - +
444N LEU* 1.3 64.5 + - + +
446N LYS* 3.1 47.5 + - - +
447N GLU* 3.1 37.1 + - + +
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Residues in contact with LEU 444 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413N SER 4.4 2.7 - - - +
416N ASN* 3.4 21.1 - - + +
417N PHE* 3.4 45.1 - - + +
420N TYR* 3.7 41.3 - - + -
440N GLU* 2.9 24.2 + - + +
441N VAL* 3.2 12.1 + - - +
443N GLN* 1.3 77.5 - - + +
445N ARG* 1.3 61.1 + - - +
447N GLU* 3.5 11.8 - - + +
448N MET* 3.3 26.0 + - - +
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Residues in contact with ARG 445 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301N LEU* 3.8 36.7 - - - +
323N LYS* 4.6 4.0 - - - +
324N ILE* 3.7 32.7 - - + +
327N GLU* 3.1 30.5 + - - +
328N ASP* 2.5 34.8 + - - +
417N PHE* 5.0 1.6 - - + -
441N VAL* 3.0 25.2 + - + +
442N MET* 3.6 18.3 - - + +
443N GLN 3.2 0.2 - - - -
444N LEU* 1.3 72.4 - - - +
446N LYS* 1.3 57.5 + - - +
447N GLU 3.1 1.8 - - - -
448N MET* 3.1 16.7 + - + +
449N SER* 2.7 40.6 + - - +
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Residues in contact with LYS 446 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442N MET 2.9 13.8 + - - +
443N GLN* 3.1 44.3 + - - +
445N ARG* 1.3 75.0 - - - +
447N GLU* 1.3 60.2 + - - +
449N SER* 3.7 6.9 - - - -
450N LEU* 3.0 54.9 + - + +
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Residues in contact with GLU 447 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409N TYR* 2.2 41.0 + - - -
413N SER* 4.2 17.1 + - - +
416N ASN* 6.2 1.6 - - - +
443N GLN* 3.1 37.4 + - + +
444N LEU* 3.5 12.6 - - + +
446N LYS* 1.3 79.3 - - - +
448N MET* 1.3 57.6 + - - +
450N LEU* 3.2 13.2 + - - +
451N ALA* 2.9 30.3 + - - +
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Residues in contact with MET 448 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324N ILE* 4.0 13.7 - - + -
328N ASP* 3.6 33.7 - - + +
329N ILE* 4.3 11.7 - - - -
332N CYS* 3.1 15.6 - - - -
413N SER* 3.7 22.0 - - - +
414N VAL* 3.9 31.4 - - + -
417N PHE* 4.2 16.6 - - + -
444N LEU 3.3 9.1 + - - +
445N ARG* 3.1 25.9 + - + +
447N GLU* 1.3 78.6 - - - +
449N SER* 1.3 53.2 + - - +
451N ALA* 4.4 1.6 - - - -
452N LYS* 2.7 37.2 + - - +
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Residues in contact with SER 449 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328N ASP* 3.5 17.2 + - - -
445N ARG* 2.7 24.6 + - - +
446N LYS* 3.7 7.9 - - - -
448N MET* 1.3 73.7 - - - +
450N LEU* 1.3 59.3 + - - +
452N LYS* 3.3 18.2 + - - +
453N LEU* 3.0 33.1 - - - +
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Residues in contact with LEU 450 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409N TYR* 5.5 3.4 - - + +
446N LYS* 3.0 44.7 + - + +
447N GLU* 3.7 12.1 - - - +
449N SER* 1.3 77.3 - - - +
451N ALA* 1.3 65.1 + - - +
452N LYS 3.2 0.2 - - - -
453N LEU* 3.0 11.2 + - + +
454N GLY 3.2 0.2 + - - -
455N TYR* 2.9 56.1 + - + +
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Residues in contact with ALA 451 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332N CYS* 4.2 4.9 - - - -
406N PHE* 3.9 1.2 - - - -
409N TYR* 3.8 19.0 - - + -
410N ARG* 3.6 45.0 + - + +
413N SER* 4.4 3.6 - - - +
447N GLU 2.9 17.2 + - - +
448N MET 3.8 2.9 - - - +
450N LEU* 1.3 75.4 - - - +
452N LYS* 1.3 63.1 + - - +
454N GLY* 3.0 14.4 + - - -
455N TYR 3.5 10.0 + - - -
456N PHE* 5.2 1.1 - - - -
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Residues in contact with LYS 452 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327N GLU* 3.2 30.0 + - - +
328N ASP* 4.5 2.4 + - - +
331N PRO* 3.6 28.7 - - + -
332N CYS* 3.9 11.3 - - - -
406N PHE* 5.5 0.2 - - - -
410N ARG* 3.9 18.9 + - - +
448N MET 2.7 17.9 + - - +
449N SER* 3.3 23.3 + - - +
451N ALA* 1.3 76.8 - - - +
453N LEU* 1.3 78.7 + - + +
454N GLY 3.6 0.2 + - - -
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Residues in contact with LEU 453 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449N SER 3.0 19.7 - - - +
450N LEU* 3.0 7.5 + - + +
452N LYS* 1.3 107.3 - - + +
454N GLY* 1.3 60.4 + - - +
455N TYR* 3.4 31.3 - - + -
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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