Contacts of the helix formed by residues 419 - 439 (chain D) in PDB entry 1JIQ
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 GLY 419 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D THR* 5.9 0.4 - - - -
415D PRO* 3.4 17.1 + - - -
416D ILE 2.8 8.7 + - - -
418D LYS* 1.3 78.0 - - - +
420D LEU* 1.3 62.7 + - - +
421D HIS 3.3 2.9 - - - -
422D HIS* 3.2 10.4 + - - +
423D LYS* 2.9 24.0 + - - +
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Residues in contact with LEU 420 (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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220C THR* 4.0 15.3 - - + +
223C GLU* 5.5 1.3 - - - +
416D ILE 3.5 1.4 + - - -
417D ARG* 3.6 52.5 - - + +
418D LYS 3.4 3.8 + - - -
419D GLY* 1.3 75.6 - - - +
421D HIS* 1.3 64.5 + - - +
423D LYS* 3.2 24.9 + - + +
424D ILE* 3.1 40.2 + - + +
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Residues in contact with HIS 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ILE* 2.8 39.6 + - + +
189C GLY* 3.6 20.3 - - - +
192C ILE* 3.9 10.8 - - + -
220C THR* 3.8 19.4 - - + +
221C ASN* 3.1 28.0 + - - -
224C THR* 2.7 26.4 + - - -
414D HIS 5.6 1.1 - - - +
416D ILE* 3.6 15.7 + - + +
417D ARG* 3.6 20.9 - - + -
419D GLY 3.3 0.8 - - - -
420D LEU* 1.3 79.5 - - - +
422D HIS* 1.3 57.8 + - - +
424D ILE* 3.2 4.6 + - - +
425D LEU* 2.9 28.2 + - - +
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Residues in contact with HIS 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ASP* 5.0 2.0 + - - -
189C GLY 5.1 1.7 - - - +
408D ILE* 4.7 3.6 - - + -
409D PRO* 2.9 25.0 + - + -
410D VAL 2.7 30.1 + - - -
412D THR* 3.3 45.5 + - + -
414D HIS 5.8 0.6 + - - +
419D GLY* 3.2 11.5 + - - +
421D HIS* 1.3 76.6 - - - +
423D LYS* 1.3 61.5 + - - +
425D LEU* 3.8 25.9 - - + +
426D LEU* 2.8 54.3 + - + +
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Residues in contact with LYS 423 (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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526C GLU* 3.9 27.5 - - + +
527C PRO* 5.7 0.4 - - - +
529C LEU* 3.5 28.1 - - + +
530C ASP* 3.2 40.2 + - - +
419D GLY 2.9 17.4 + - - +
420D LEU* 3.6 24.3 - - + +
422D HIS* 1.3 77.7 - - - +
424D ILE* 1.3 58.4 + - + +
426D LEU* 3.4 4.0 + - - -
427D ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ILE* 3.7 23.8 - - + -
216C GLN* 3.9 29.2 - - - +
217C GLU* 4.8 2.9 - - + -
220C THR* 3.9 24.5 - - + +
526C GLU* 3.9 19.7 - - - +
420D LEU* 3.1 37.3 + - + +
421D HIS 3.2 5.6 + - - +
423D LYS* 1.3 75.7 - - + +
425D LEU* 1.3 65.9 + - - +
427D ALA* 3.2 3.1 + - - +
428D ASN* 2.8 45.1 + - - +
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ASN* 3.8 15.3 - - - +
187C ILE* 3.8 23.1 - - + +
188C ASP* 3.6 27.4 - - + -
341D TYR* 3.4 44.4 - - + +
384D GLY 4.0 6.1 - - - +
385D THR* 4.1 2.2 - - + -
408D ILE* 4.1 6.5 - - + -
421D HIS 2.9 17.3 + - - +
422D HIS* 3.6 27.4 - - + +
424D ILE* 1.3 77.3 - - - +
426D LEU* 1.3 62.4 + - - +
428D ASN* 3.2 5.0 + - - +
429D PHE* 2.9 23.2 + - - +
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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
----------------------------------------------------------
529C LEU* 3.9 13.0 - - + -
549C ILE* 3.9 42.0 - - + -
553C ARG* 6.0 4.3 - - - +
408D ILE* 3.7 31.0 - - + -
409D PRO 4.3 3.8 - - - +
410D VAL* 4.3 6.1 - - - +
422D HIS* 2.8 49.9 + - + +
423D LYS* 3.7 6.7 - - - +
425D LEU* 1.3 78.4 - - - +
427D ALA* 1.3 62.2 + - - +
429D PHE* 3.2 3.1 + - + +
430D LEU* 3.0 33.1 + - + +
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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
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522C ALA* 3.7 9.1 - - + +
525C ILE* 3.6 26.2 - - + +
526C GLU* 3.5 32.5 - - + +
529C LEU* 4.0 1.5 - - + +
423D LYS 2.9 17.6 + - - +
424D ILE 3.2 4.7 + - - +
426D LEU* 1.3 75.8 - - - +
428D ASN* 1.3 58.4 + - - +
430D LEU* 3.9 1.6 - - - +
431D ALA* 2.9 31.0 + - - +
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Residues in contact with ASN 428 (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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216C GLN* 4.7 3.8 + - - -
217C GLU* 4.4 7.7 + - - +
518C GLY 4.8 3.6 - - - +
519C LYS* 5.5 3.3 - - - +
522C ALA* 3.9 21.4 - - - +
526C GLU* 4.7 2.4 + - - -
341D TYR* 4.1 2.7 - - + -
385D THR* 4.2 13.1 - - + +
388D GLN* 3.0 34.6 - - - +
389D HIS* 5.6 0.2 - - - -
424D ILE* 2.8 45.5 + - - +
425D LEU 3.7 3.6 - - - +
427D ALA* 1.3 74.8 - - - +
429D PHE* 1.3 64.8 - - - +
431D ALA* 4.4 0.9 - - - +
432D GLN* 2.9 32.8 + - - +
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Residues in contact with PHE 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C LEU* 4.8 0.9 - - + -
549C ILE* 5.4 1.1 - - + -
341D TYR* 3.7 27.6 - + + -
406D PHE* 3.5 42.4 - + + -
407D LEU 3.5 15.5 - - - -
408D ILE* 3.5 39.5 - - + -
425D LEU 2.9 13.2 + - - +
426D LEU* 3.4 9.4 - - + +
428D ASN* 1.3 75.8 - - - +
430D LEU* 1.3 84.5 + - + +
432D GLN 3.9 0.2 + - - -
433D THR* 3.8 21.3 + - - +
476D SER* 4.0 19.5 - - - -
478D VAL* 3.8 22.0 - - + -
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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
----------------------------------------------------------
525C ILE* 3.9 18.8 - - + -
529C LEU* 4.1 13.7 - - + -
542C THR* 4.5 9.9 + - + +
545C LEU* 3.4 37.9 - - + +
546C ILE* 3.7 26.5 - - + +
549C ILE* 3.9 19.3 - - + -
57D LYS* 5.2 0.2 + - - -
426D LEU 3.0 23.1 + - - +
427D ALA 3.9 2.9 - - - +
429D PHE* 1.3 89.0 - - + +
431D ALA* 1.3 65.3 + - - +
433D THR* 3.2 9.5 + - - -
434D GLU* 3.1 21.0 + - - +
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Residues in contact with ALA 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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518C GLY 3.8 5.4 - - - +
521C LEU* 3.5 12.3 - - + +
522C ALA* 3.2 35.7 - - + +
525C ILE* 3.9 6.9 - - + +
427D ALA 2.9 19.7 + - - +
428D ASN* 4.0 1.6 - - - +
430D LEU* 1.3 76.8 - - - +
432D GLN* 1.3 53.2 + - + +
434D GLU* 3.3 5.8 + - - +
435D ALA* 2.8 37.6 + - - +
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Residues in contact with GLN 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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515C VAL 5.3 3.0 + - - -
518C GLY* 3.6 26.5 + - - -
519C LYS* 4.7 1.2 - - - +
341D TYR* 3.7 3.8 - - - +
388D GLN* 3.5 37.0 + - - +
392D TYR* 3.2 15.8 - - + +
396D HIS* 2.8 33.0 - - - -
406D PHE* 3.7 21.5 - - + -
428D ASN* 2.9 22.4 + - - +
429D PHE 4.3 0.2 - - - +
431D ALA* 1.3 75.8 - - - +
433D THR* 1.3 58.5 + - - +
435D ALA* 3.3 3.5 + - - +
436D LEU* 2.9 36.3 + - + +
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Residues in contact with THR 433 (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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545C LEU* 4.6 1.2 - - - +
57D LYS* 3.0 26.9 + - - +
406D PHE* 3.5 39.9 - - + -
429D PHE 3.8 6.6 + - - +
430D LEU* 3.2 11.4 + - - -
432D GLN* 1.3 73.9 - - - +
434D GLU* 1.3 65.8 + - - +
436D LEU* 3.7 5.8 - - - +
437D MET* 3.0 24.9 + - - +
472D ARG 5.0 0.2 - - - +
474D THR* 3.4 24.7 + - - +
476D SER* 3.6 15.7 + - - +
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Residues in contact with GLU 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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521C LEU* 3.7 28.2 - - + +
525C ILE* 3.6 21.5 - - - +
538C HIS* 2.9 33.5 + - - +
539C ASP* 3.7 8.3 + - - +
542C THR* 3.5 19.1 - - - +
57D LYS* 4.2 7.6 - - - +
430D LEU 3.1 13.5 + - - +
431D ALA 3.4 7.0 - - - +
433D THR* 1.3 77.9 + - - +
435D ALA* 1.3 56.9 + - - +
437D MET* 3.3 2.9 + - - +
438D ARG* 2.8 46.7 + - + +
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Residues in contact with ALA 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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517C LEU* 3.7 28.6 - - + +
518C GLY* 4.1 11.2 - - - +
521C LEU* 3.7 11.6 - - + +
396D HIS* 3.8 17.6 - - - +
431D ALA 2.8 20.5 + - - +
432D GLN* 3.7 4.3 - - - +
434D GLU* 1.3 72.4 - - - +
436D LEU* 1.3 60.2 + - - +
438D ARG* 4.7 0.2 - - - -
439D GLY* 2.9 31.5 + - - +
468D PHE* 5.4 0.2 - - - +
470D GLY* 4.6 0.9 - - - -
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Residues in contact with LEU 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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392D TYR* 6.0 1.6 - - + -
395D ILE* 3.7 31.0 - - + -
396D HIS* 3.6 30.9 + - + +
404D CYS* 4.9 2.5 - - - -
406D PHE* 3.9 19.7 - - + -
432D GLN* 2.9 24.0 + - + +
433D THR* 3.7 4.7 - - - +
435D ALA* 1.3 75.3 - - - +
437D MET* 1.3 60.8 + - - +
470D GLY* 3.3 7.3 - - - -
471D ASN 3.2 4.7 + - - -
472D ARG* 2.9 50.9 + - + +
474D THR* 3.4 26.0 - - + -
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Residues in contact with MET 437 (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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539C ASP* 3.6 37.7 - - + +
26D LEU* 3.3 42.5 - - + +
27D ARG* 4.1 14.9 + - - +
30D PHE* 3.8 19.3 - - + -
57D LYS* 4.0 17.5 - - + -
433D THR 3.0 17.3 + - - +
434D GLU 3.6 1.8 - - - +
436D LEU* 1.3 78.6 - - - +
438D ARG* 1.3 81.5 + - + +
471D ASN* 3.0 22.8 + - - +
472D ARG 3.8 6.5 + - - +
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Residues in contact with ARG 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 5.3 4.7 - - + -
539C ASP* 4.9 9.4 - - - +
27D ARG* 2.6 82.9 + - - +
31D ASP* 4.6 15.0 + - - -
434D GLU* 2.8 38.1 + - + +
435D ALA* 4.4 2.0 - - - +
437D MET* 1.3 98.2 - - + +
439D GLY* 1.3 64.8 + - - +
444D GLU* 4.7 3.6 + - - -
469D GLU 5.3 0.7 - - - +
470D GLY* 4.4 1.9 - - - -
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Residues in contact with GLY 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C LEU* 3.5 15.4 - - - +
27D ARG* 3.6 5.4 + - - -
435D ALA 2.9 23.1 + - - -
437D MET 3.6 1.4 + - - -
438D ARG* 1.3 82.8 - - - +
440D LYS* 1.3 62.9 + - - +
444D GLU* 4.1 0.9 - - - +
468D PHE* 3.5 21.1 - - - -
469D GLU 4.5 0.4 - - - -
470D GLY* 3.8 9.8 - - - -
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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