Contacts of the helix formed by residues 433 - 453 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B GLN 3.9 2.4 + - - -
432B GLN* 1.3 76.5 - - - +
434B VAL* 1.3 65.0 + - - +
435B ASP* 4.0 12.7 - - - +
436B GLN* 2.8 46.4 + - - +
437B MET* 3.0 18.3 + - - +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR* 4.3 4.9 - - + -
305B PHE* 4.0 16.2 - - + -
306B ARG* 2.9 55.4 - - + +
309B LYS* 3.2 34.8 - - + -
433B ASP* 1.3 74.4 - - - +
435B ASP* 1.3 56.1 + - - +
437B MET* 3.7 7.6 - - - +
438B PHE* 2.9 27.7 + - - +
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR* 2.4 37.6 + - - -
306B ARG* 5.3 1.1 - - - -
433B ASP* 3.3 13.3 + - - +
434B VAL* 1.3 78.0 - - - +
436B GLN* 1.3 64.5 + - + +
438B PHE* 3.3 4.9 + - - +
439B TRP* 3.1 39.0 + - + -
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B GLN 4.5 2.6 - - - +
432B GLN* 3.4 32.3 + - + +
433B ASP* 2.8 43.5 + - - +
435B ASP* 1.3 78.3 - - + +
437B MET* 1.3 60.9 + - - +
439B TRP* 3.3 7.5 + - - +
440B GLU* 3.0 20.6 + - - +
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Residues in contact with MET 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 3.9 13.7 - - + -
309B LYS* 4.2 25.8 - - + +
420B TYR* 3.5 19.1 - - + +
424B ILE* 3.2 46.4 - - + -
429B VAL* 4.2 17.7 - - + +
432B GLN* 3.7 26.2 - - + +
433B ASP 3.0 14.5 + - - +
434B VAL* 3.7 8.3 - - - +
435B ASP 3.3 0.2 - - - -
436B GLN* 1.3 74.4 - - - +
438B PHE* 1.3 64.6 + - - +
440B GLU* 3.0 13.0 + - - +
441B VAL* 3.0 17.0 + - - +
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 3.2 31.6 - - + -
298B ASP 4.5 0.2 - - - -
301B LEU* 3.8 8.3 - - + -
302B TYR* 3.4 49.1 - + + -
305B PHE* 3.5 35.4 - + + -
434B VAL 2.9 17.5 + - - +
435B ASP* 3.5 3.8 - - - +
437B MET* 1.3 76.9 - - - +
439B TRP* 1.3 73.1 + + - +
441B VAL* 2.9 10.7 + - + +
442B MET* 2.9 67.1 + - + +
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Residues in contact with TRP 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LYS* 3.7 39.7 - - + +
296B GLU* 3.5 12.3 - - - -
297B ALA* 3.2 44.4 - - + +
435B ASP* 3.1 31.1 + - + +
436B GLN* 3.9 5.8 - - - +
437B MET 3.3 0.2 - - - -
438B PHE* 1.3 85.5 - + - +
440B GLU* 1.3 60.8 + - - +
442B MET* 3.7 18.3 - - + +
443B GLN* 3.1 25.5 + - - +
453H LEU 3.9 15.9 - - - -
454H GLY 4.3 0.9 - - - -
455H TYR* 3.8 29.9 + + - -
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TYR* 3.3 43.1 + - + +
432B GLN* 4.1 13.0 + - - +
436B GLN 3.0 11.5 + - - +
437B MET* 3.0 13.6 + - - +
439B TRP* 1.3 79.2 - - - +
441B VAL* 1.3 54.6 + - - +
443B GLN* 3.1 8.4 + - - +
444B LEU* 2.8 53.1 + - + +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B PHE* 3.9 26.0 - - + -
320B PHE* 3.9 23.8 - - + -
417B PHE* 4.2 18.4 - - + -
420B TYR* 4.2 17.0 - - + -
421B ILE* 4.5 8.7 - - + -
437B MET 3.0 12.9 + - - +
438B PHE* 2.9 9.1 + - + +
440B GLU* 1.3 76.4 - - - +
442B MET* 1.3 58.7 + - + +
444B LEU* 3.1 8.5 + - - +
445B ARG* 2.8 40.5 + - + +
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Residues in contact with MET 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ASP 4.5 5.6 - - - +
301B LEU* 3.4 30.3 - - + -
438B PHE* 2.9 53.6 + - + +
439B TRP* 3.7 32.3 - - + +
441B VAL* 1.3 79.7 - - - +
443B GLN* 1.3 57.2 + - - +
445B ARG* 3.3 12.2 + - - +
446B LYS* 2.8 30.0 + - - +
453H LEU* 2.9 37.2 - - + +
455H TYR* 3.6 9.8 - - + +
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B TRP 3.1 16.0 + - - +
440B GLU* 3.3 13.2 - - - +
442B MET* 1.3 76.9 - - - +
444B LEU* 1.3 67.2 + - + +
446B LYS* 3.1 39.2 + - - +
447B GLU* 3.1 40.6 + - + +
455H TYR* 3.3 9.2 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B SER 4.6 3.4 - - - +
416B ASN* 3.6 34.3 - - + +
417B PHE* 3.7 30.7 - - + +
420B TYR* 4.6 10.5 - - + -
440B GLU* 2.8 60.9 + - + +
441B VAL* 3.4 11.4 - - - +
443B GLN* 1.3 76.7 - - + +
445B ARG* 1.3 61.9 + - - +
447B GLU* 3.5 10.7 + - + +
448B MET* 3.3 26.2 + - - +
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B LEU* 3.7 32.5 - - - +
323B LYS* 4.4 7.7 - - - +
324B ILE* 3.7 31.6 - - + +
327B GLU* 3.0 30.5 + - - +
328B ASP* 2.5 35.1 + - - +
417B PHE* 5.0 1.6 - - + -
441B VAL* 2.8 30.4 + - + +
442B MET* 3.6 13.1 - - - +
444B LEU* 1.3 73.4 - - - +
446B LYS* 1.3 55.5 + - - +
448B MET* 2.9 17.0 + - + +
449B SER* 2.6 36.9 + - - -
452H LYS* 3.9 9.9 - - - +
453H LEU* 3.7 18.1 - - + +
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Residues in contact with LYS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B MET 2.8 17.1 + - - +
443B GLN* 3.1 26.6 + - - +
445B ARG* 1.3 75.9 - - - +
447B GLU* 1.3 69.8 - - - +
449B SER* 3.4 4.9 + - - -
450B LEU* 3.1 37.0 + - + +
450H LEU* 3.4 30.5 - - + -
453H LEU* 3.5 9.1 - - + +
455H TYR* 3.2 39.1 - - + -
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B TYR* 2.1 37.4 + - - -
413B SER* 4.1 16.3 + - - +
443B GLN* 3.1 34.7 + - + +
444B LEU* 3.6 13.5 - - + +
445B ARG 3.1 0.2 - - - -
446B LYS* 1.3 83.3 - - - +
448B MET* 1.3 56.9 + - - +
450B LEU* 3.2 11.4 + - - +
451B ALA* 2.9 28.9 + - - +
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Residues in contact with MET 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B ILE* 4.3 4.0 - - + -
328B ASP* 3.8 31.9 - - + +
329B ILE* 4.3 9.6 - - - -
332B CYS* 3.4 11.5 - - - -
413B SER* 3.7 26.7 - - - +
414B VAL* 3.8 33.2 - - + +
417B PHE* 3.9 28.5 - - + -
444B LEU 3.3 15.6 + - - +
445B ARG* 2.9 15.5 + - + +
447B GLU* 1.3 78.4 - - - +
449B SER* 1.3 59.0 + - - +
451B ALA* 4.5 0.2 - - - -
452B LYS* 2.8 32.4 + - - +
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Residues in contact with SER 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ASP* 3.7 15.5 + - - -
445B ARG 2.6 20.7 + - - -
446B LYS* 3.6 10.3 - - - -
448B MET* 1.3 73.4 - - - +
450B LEU* 1.3 60.2 + - - +
452B LYS* 3.2 31.3 + - - +
453B LEU* 3.6 12.6 + - - +
449H SER* 3.9 20.4 - - - -
450H LEU* 6.1 1.1 - - - -
452H LYS* 3.9 14.2 + - - -
453H LEU* 4.0 11.9 - - - +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B TYR* 5.5 2.7 - - - +
446B LYS* 3.1 39.0 + - + +
447B GLU* 3.7 12.1 - - - +
449B SER* 1.3 76.2 - - - +
451B ALA* 1.3 65.4 + - - +
452B LYS 3.1 1.1 - - - -
453B LEU* 3.0 10.6 + - + +
454B GLY 3.2 0.2 + - - -
455B TYR* 2.9 46.7 + - + +
446H LYS* 3.3 38.1 - - + +
449H SER* 6.0 1.1 - - - -
450H LEU* 4.9 9.6 - - + -
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B CYS* 4.1 4.9 - - - -
406B PHE* 3.7 2.1 - - - -
409B TYR* 3.5 27.8 - - + -
410B ARG* 3.7 38.6 + - + +
413B SER* 4.3 3.4 - - - +
447B GLU 2.9 14.7 + - - +
448B MET* 3.9 2.9 - - - +
450B LEU* 1.3 75.0 - - - +
452B LYS* 1.3 63.7 + - - +
454B GLY* 3.0 14.4 + - - -
455B TYR 3.4 11.1 + - - -
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Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B GLU 3.3 25.7 + - - +
328B ASP* 4.7 2.0 - - - -
331B PRO* 3.7 23.9 - - + +
332B CYS* 3.8 12.3 - - - +
410B ARG* 4.0 16.8 + - - +
448B MET 2.8 20.0 + - - +
449B SER* 3.2 21.0 + - - +
451B ALA* 1.3 77.2 - - - +
453B LEU* 1.3 65.3 + - + +
454B GLY 3.6 0.3 + - - -
298H ASP* 4.4 3.8 - - - +
301H LEU* 4.0 13.6 - - + +
327H GLU* 3.4 26.6 + - - +
328H ASP* 3.9 6.5 + - - -
445H ARG* 4.2 6.7 - - - +
449H SER* 3.6 14.3 + - - -
452H LYS* 3.6 21.2 - - - +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B SER 3.6 14.6 - - - +
450B LEU 3.0 8.9 + - - +
452B LYS* 1.3 83.4 - - + +
454B GLY* 1.3 61.5 + - - +
455B TYR* 3.5 11.4 - - + -
298H ASP* 5.4 1.1 - - - -
301H LEU* 4.2 2.9 - - + -
439H TRP* 3.9 11.3 - - - -
442H MET* 3.0 43.5 - - + +
445H ARG* 3.6 48.9 - - + +
446H LYS* 3.4 41.1 - - + +
449H SER* 4.2 7.6 - - - +
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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