Contacts of the helix formed by residues 421 - 444 (chain D) in PDB entry 1U3Q
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 421 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422D SER* 1.3 69.5 + - - +
423D SER* 3.1 8.4 + - - +
424D ARG* 2.9 66.3 + - - +
425D LYS* 3.7 20.3 + - - +
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Residues in contact with SER 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D GLU 5.9 1.3 - - - -
322D LEU* 3.9 9.4 - - - +
323D SER* 3.3 24.2 + - - -
326D ASP* 2.7 29.9 + - - +
421D ASP* 1.3 81.1 + - - +
423D SER* 1.3 60.4 + - - +
424D ARG 3.5 0.2 - - - -
425D LYS* 3.6 11.9 - - - +
426D LEU* 3.4 15.8 + - - +
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Residues in contact with SER 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ASP* 5.4 2.5 + - - -
411D TYR* 3.2 49.5 - - - +
421D ASP 3.1 5.6 - - - +
422D SER* 1.3 76.5 - - - +
424D ARG* 1.3 64.0 + - - +
425D LYS 3.1 1.8 - - - -
426D LEU* 3.2 9.2 + - - +
427D ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D ASP* 2.9 55.7 + - - +
423D SER* 1.3 78.0 - - - +
425D LYS* 1.3 57.6 + - + +
427D ALA* 3.5 4.7 + - - +
428D HIS* 2.9 31.4 + - - +
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Residues in contact with LYS 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D GLY* 5.6 1.1 - - - +
321D GLU* 3.8 39.2 + - - +
322D LEU* 3.8 12.8 - - + -
421D ASP* 3.8 22.3 + - - +
422D SER* 3.6 11.9 + - - +
423D SER 3.1 0.2 - - - -
424D ARG* 1.3 76.4 - - + +
426D LEU* 1.3 58.6 + - - +
428D HIS* 3.4 12.1 + - + +
429D LEU* 2.8 34.1 + - + +
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Residues in contact with LEU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D LEU* 3.9 22.6 - - + +
326D ASP* 6.0 4.9 - - + +
330D LEU* 3.9 11.9 - - + -
406D LEU* 3.6 43.5 - - + +
409D SER* 3.5 36.8 - - - +
410D MET 4.8 3.6 - - - +
411D TYR* 4.6 10.1 - - - -
422D SER 3.4 10.0 + - - +
423D SER* 3.2 12.5 + - - +
425D LYS* 1.3 79.4 - - - +
427D ALA* 1.3 52.9 + - - +
429D LEU* 3.1 4.5 - - + +
430D LEU* 2.7 35.1 + - + +
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Residues in contact with ALA 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 5.6 7.2 - - - +
423D SER 3.1 12.2 + - - +
424D ARG* 3.9 5.8 - - - +
426D LEU* 1.3 76.4 - - - +
428D HIS* 1.3 60.6 + - - +
429D LEU 2.9 1.6 - - - -
430D LEU* 3.8 8.7 - - - +
431D ASN* 2.8 35.2 + - - +
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Residues in contact with HIS 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D ARG 2.9 19.6 + - - +
425D LYS* 3.8 11.4 - - + +
427D ALA* 1.3 77.9 - - - +
429D LEU* 1.3 57.0 + - + +
431D ASN* 3.5 8.3 - - - +
432D ALA* 3.2 27.1 + - + +
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ILE* 4.2 8.1 - - + -
317D PRO* 2.8 24.0 - - + +
318D GLY* 3.0 36.1 - - - +
319D PHE* 3.7 5.6 - - - +
322D LEU* 4.1 18.2 - - + -
406D LEU* 3.6 24.5 - - + -
425D LYS* 2.8 19.8 + - + +
426D LEU 3.1 5.8 - - - +
428D HIS* 1.3 77.9 - - + +
430D LEU* 1.3 65.9 + - - +
431D ASN 2.9 1.6 - - - -
432D ALA* 2.9 20.6 + - + +
433D VAL* 3.3 12.7 + - + +
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Residues in contact with LEU 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG* 4.1 14.1 - - - +
457B ASN* 6.0 2.0 - - - +
460B MET* 3.8 28.9 - - + -
403D MET* 4.1 18.6 - - + +
406D LEU* 3.9 37.1 - - + +
407D ASN* 3.5 32.3 - - + +
426D LEU* 2.7 19.9 + - + +
427D ALA* 3.8 7.6 - - - +
429D LEU* 1.3 72.6 - - - +
431D ASN* 1.3 56.8 + - - +
433D VAL* 3.5 2.4 + - - +
434D THR* 2.9 33.7 + - - +
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Residues in contact with ASN 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B MET* 4.1 22.6 - - - +
457B ASN* 4.4 17.8 + - - +
427D ALA* 2.8 20.9 + - - +
428D HIS* 3.5 12.1 - - - +
430D LEU* 1.3 78.4 - - - +
432D ALA* 1.3 59.1 + - - +
434D THR* 3.3 6.7 + - - -
435D ASP* 3.0 29.1 + - - +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D PRO* 5.5 1.2 - - - +
268D LEU* 3.3 26.0 - - + +
428D HIS* 3.2 14.3 + - + +
429D LEU* 2.9 15.0 + - + +
431D ASN* 1.3 78.9 - - - +
433D VAL* 1.3 63.5 + - + +
435D ASP* 3.5 7.3 + - - +
436D ALA* 3.1 15.1 + - - +
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Residues in contact with VAL 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 4.0 15.3 - - + -
272D LEU* 4.5 7.0 - - + -
316D ILE* 5.0 5.2 - - + -
399D CYS* 3.3 35.4 - - + +
402D ALA* 3.9 16.8 - - + -
403D MET* 3.5 11.4 - - + -
406D LEU* 3.7 21.5 - - + -
429D LEU* 3.6 16.4 - - + +
430D LEU* 3.7 6.1 - - - +
431D ASN 3.2 0.4 - - - -
432D ALA* 1.3 76.5 - - + +
434D THR* 1.3 64.6 + - - +
436D ALA* 3.0 12.6 + - + +
437D LEU* 3.0 13.5 + - - +
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Residues in contact with THR 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B MET* 3.6 16.2 - - + -
456B ALA* 3.4 33.2 - - + -
457B ASN* 5.7 1.8 - - - +
460B MET* 3.2 22.6 - - + +
403D MET* 3.4 19.3 - - + +
430D LEU* 2.9 18.6 + - - +
431D ASN* 3.6 8.2 - - - -
432D ALA 3.3 0.2 - - - -
433D VAL* 1.3 77.8 - - - +
435D ASP* 1.3 61.2 + - - +
437D LEU* 3.3 4.2 + - - +
438D VAL* 3.2 25.7 + - + +
455D LEU* 5.5 1.8 - - + -
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Residues in contact with ASP 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B GLN* 3.2 26.4 - - - +
453B MET* 3.2 27.0 - - + +
265D PRO* 3.6 21.3 - - + +
431D ASN* 3.0 19.9 + - - +
432D ALA* 3.7 8.1 - - - +
434D THR* 1.3 77.1 - - - +
436D ALA* 1.3 61.5 + - - +
438D VAL* 3.6 3.1 + - - +
439D TRP* 3.2 20.1 + - - +
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Residues in contact with ALA 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D PRO* 3.9 29.1 - - + +
268D LEU* 4.2 11.0 - - + -
269D VAL* 4.0 12.6 - - + -
272D LEU* 5.8 0.4 - - + -
399D CYS* 4.0 8.3 - - - -
432D ALA 3.1 12.7 + - - +
433D VAL* 3.0 14.2 + - + +
435D ASP* 1.3 76.3 - - - +
437D LEU* 1.3 59.5 + - - +
439D TRP* 3.1 6.1 + - - +
440D VAL* 3.0 30.7 + - - +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D GLU* 4.1 28.0 - - + +
399D CYS* 3.7 20.1 - - + -
400D VAL* 4.3 12.1 - - + -
403D MET* 3.4 28.5 - - + -
433D VAL 3.0 8.1 + - - +
434D THR 3.5 8.1 - - - +
436D ALA* 1.3 74.2 - - - +
438D VAL* 1.3 59.8 + - - +
440D VAL* 3.3 3.4 + - + +
441D ILE* 3.0 40.4 + - + +
455D LEU* 3.7 27.8 - - + -
458D LEU* 4.2 12.1 - - + -
459D LEU* 4.5 4.5 - - + -
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Residues in contact with VAL 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B GLN* 4.2 13.2 - - - +
452B SER* 3.9 35.4 - - - +
453B MET* 4.5 9.6 - - + -
434D THR* 3.2 18.8 + - + +
435D ASP* 3.8 9.2 - - - +
436D ALA 3.3 0.2 - - - -
437D LEU* 1.3 74.6 - - - +
439D TRP* 1.3 66.6 + - - +
441D ILE* 3.3 9.7 + - + +
442D ALA* 2.9 24.3 + - + +
451D GLN* 5.0 3.2 - - - +
455D LEU* 4.2 20.4 - - + -
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Residues in contact with TRP 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D PRO* 3.7 21.1 - - + -
266D GLU* 3.5 56.0 - - + +
269D VAL* 4.3 14.1 - - + -
395D LYS* 5.5 10.1 - - + -
435D ASP* 3.2 11.7 + - - +
436D ALA 3.1 10.1 + - - +
438D VAL* 1.3 79.8 - - - +
440D VAL* 1.3 89.8 + - + +
442D ALA* 3.1 8.1 + - + +
443D LYS* 2.9 69.8 + - + +
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Residues in contact with VAL 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D VAL* 3.7 17.7 - - + -
393D GLN* 5.6 2.7 - - + -
395D LYS* 3.9 32.3 - - + +
396D GLU* 3.9 25.4 - - + -
399D CYS* 4.6 1.3 - - - -
436D ALA 3.0 18.1 + - - +
437D LEU* 3.3 8.9 + - - +
439D TRP* 1.3 98.6 - - + +
441D ILE* 1.3 62.3 + - - +
443D LYS* 3.2 15.3 + - + +
444D SER* 3.4 9.7 + - - -
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Residues in contact with ILE 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLU* 3.6 20.2 - - - +
437D LEU* 3.0 37.0 + - + +
438D VAL* 3.8 7.0 - - - +
440D VAL* 1.3 74.8 - - - +
442D ALA* 1.3 59.6 + - - +
444D SER* 2.7 30.2 + - - -
446D ILE* 4.1 12.4 - - + +
451D GLN* 3.6 35.2 - - + +
454D ARG* 4.2 7.6 - - + +
455D LEU* 3.7 41.5 - - + +
458D LEU* 4.2 7.4 - - + -
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Residues in contact with ALA 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D VAL* 2.9 16.1 + - + +
439D TRP* 3.1 12.5 + - + +
441D ILE* 1.3 73.5 - - - +
443D LYS* 1.3 59.9 + - + +
444D SER 2.9 4.9 - - - -
445D GLY* 2.8 24.6 + - - -
451D GLN* 3.6 26.3 + - - +
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Residues in contact with LYS 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D TRP* 2.9 71.6 + - + +
440D VAL* 3.2 9.4 + - + +
442D ALA* 1.3 77.3 - - + +
444D SER* 1.3 58.9 + - - +
445D GLY* 3.1 2.5 + - - -
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Residues in contact with SER 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D GLN* 6.5 1.1 - - - -
396D GLU* 6.0 1.1 - - - -
440D VAL 3.4 6.2 + - - -
441D ILE* 2.7 22.9 + - - -
442D ALA 2.9 1.0 + - - -
443D LYS* 1.3 77.0 - - - +
445D GLY* 1.3 55.8 + - - +
446D ILE* 3.1 37.1 + - - +
454D ARG* 6.1 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