Contacts of the helix formed by residues 419 - 439 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B THR* 6.0 0.2 - - - -
415B PRO* 3.6 16.9 + - - -
416B ILE 2.9 9.4 + - - -
418B LYS* 1.3 76.8 - - - +
420B LEU* 1.3 57.4 + - - +
421B HIS 3.4 2.5 - - - -
422B HIS* 3.3 10.5 + - - +
423B LYS* 2.9 30.2 + - - +
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Residues in contact with LEU 420 (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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220A THR* 3.9 19.7 - - + +
416B ILE 3.5 1.4 + - - -
417B ARG* 3.1 50.8 + - + +
418B LYS 3.4 1.2 + - - -
419B GLY* 1.3 73.6 - - - +
421B HIS* 1.3 67.4 + - - +
423B LYS* 3.3 22.1 + - + +
424B ILE* 3.1 42.1 + - + +
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Residues in contact with HIS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE* 2.8 43.8 - - + +
189A GLY* 3.6 25.1 - - - +
192A ILE* 4.0 3.8 - - - +
220A THR* 3.8 18.6 - - + +
221A ASN* 3.2 25.6 + - - -
224A THR* 2.8 30.6 + - - -
414B HIS 5.6 1.1 - - - +
416B ILE* 3.6 25.3 + - + +
417B ARG* 3.8 8.4 - - + +
419B GLY 3.4 0.6 - - - -
420B LEU* 1.3 79.0 - - - +
422B HIS* 1.3 59.4 + - - +
424B ILE* 3.2 4.3 + - - +
425B LEU* 2.9 27.8 + - - +
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Residues in contact with HIS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASP* 4.9 2.6 + - - -
189A GLY 5.6 2.6 + - - +
408B ILE* 4.4 8.7 - - + -
409B PRO* 3.0 24.2 + - + -
410B VAL 2.9 30.5 + - - -
412B THR* 3.6 43.4 + - + -
414B HIS 5.7 0.7 - - - +
415B PRO* 5.9 0.2 - - + -
419B GLY* 3.3 12.0 + - - +
420B LEU 3.2 0.4 - - - -
421B HIS* 1.3 76.7 - - - +
423B LYS* 1.3 61.0 + - - +
425B LEU* 3.6 28.6 - - + +
426B LEU* 2.9 48.6 + - + +
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Residues in contact with LYS 423 (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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526A GLU* 3.6 34.6 + - + +
527A PRO* 4.5 1.8 - - - +
529A LEU* 3.4 24.9 - - + +
530A ASP* 2.8 40.3 + - - +
419B GLY 2.9 17.7 + - - +
420B LEU* 3.5 21.3 - - + +
421B HIS 3.2 0.2 - - - -
422B HIS* 1.3 77.6 - - - +
424B ILE* 1.3 58.7 + - + +
426B LEU* 3.4 3.8 + - - -
427B ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE* 3.8 23.1 - - + -
216A GLN* 3.9 36.8 - - - +
217A GLU* 4.8 3.8 - - + -
220A THR* 4.0 24.5 - - + +
526A GLU* 4.0 11.4 - - - +
420B LEU* 3.1 37.0 + - + +
421B HIS 3.7 4.7 - - - +
423B LYS* 1.3 75.7 - - + +
425B LEU* 1.3 66.7 + - - +
427B ALA* 3.2 5.3 + - - +
428B ASN* 2.9 42.7 + - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASN* 4.0 13.7 - - - +
187A ILE* 3.9 23.3 - - + +
188A ASP* 3.8 24.9 - - + +
341B TYR* 3.4 44.8 - - + +
384B GLY 4.0 6.3 - - - +
385B THR* 4.0 3.1 - - + -
408B ILE* 4.1 7.6 - - + -
421B HIS 2.9 16.8 + - - +
422B HIS* 3.6 30.1 - - + +
424B ILE* 1.3 77.8 - - - +
426B LEU* 1.3 63.0 + - - +
428B ASN* 3.2 5.1 + - - +
429B PHE* 2.9 22.3 + - - +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 4.0 11.2 - - + -
549A ILE* 3.8 46.2 - - + -
553A ARG* 6.1 2.2 - - - +
408B ILE* 3.6 31.4 - - + -
409B PRO 4.4 7.9 - - - +
410B VAL* 4.3 8.3 - - - +
422B HIS* 2.9 43.9 + - + +
423B LYS* 3.8 6.7 - - - +
425B LEU* 1.3 76.7 - - - +
427B ALA* 1.3 63.7 + - - +
429B PHE* 3.2 2.8 + - + +
430B LEU* 3.0 30.4 + - + +
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Residues in contact with ALA 427 (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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522A ALA* 3.8 14.6 - - + +
525A ILE* 4.0 21.1 - - + +
526A GLU* 3.6 31.0 - - + +
529A LEU* 4.0 1.7 - - + +
423B LYS 2.9 18.8 + - - +
424B ILE 3.2 4.7 + - - +
426B LEU* 1.3 75.4 - - - +
428B ASN* 1.3 58.5 + - - +
430B LEU* 3.5 1.6 + - - +
431B ALA* 2.9 30.7 + - - +
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Residues in contact with ASN 428 (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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216A GLN* 4.8 3.5 - - - +
217A GLU* 4.4 6.9 + - - +
518A GLY 5.0 3.6 + - - -
519A LYS* 5.5 3.8 - - - +
522A ALA* 3.9 22.8 - - - +
526A GLU* 4.8 0.5 - - - +
341B TYR* 4.1 6.7 - - + -
385B THR* 4.3 10.3 - - + +
388B GLN* 2.9 36.2 - - - +
424B ILE* 2.9 39.5 + - - +
425B LEU 3.7 3.4 - - - +
426B LEU 3.1 0.2 - - - -
427B ALA* 1.3 76.1 - - - +
429B PHE* 1.3 64.7 + - - +
431B ALA* 4.4 0.7 - - - -
432B GLN* 3.0 32.9 + - - +
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A LEU* 4.9 0.7 - - + -
549A ILE* 5.3 2.9 - - + -
341B TYR* 3.7 27.8 - + + -
406B PHE* 3.4 43.8 - - + -
407B LEU 3.5 14.8 - - - -
408B ILE* 3.5 39.3 - - + -
425B LEU 2.9 12.8 + - - +
426B LEU* 3.4 7.4 - - - +
428B ASN* 1.3 77.1 - - - +
430B LEU* 1.3 84.3 + - + +
433B THR* 3.8 21.0 + - - +
476B SER* 3.9 20.9 - - - -
477B ILE 4.4 0.7 - - - -
478B VAL* 3.8 22.7 - - + -
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 3.8 29.2 - - + -
529A LEU* 4.1 8.5 - - + -
542A THR* 4.5 8.9 + - + +
545A LEU* 3.4 37.4 - - + +
546A ILE* 3.6 26.7 - - + +
549A ILE* 4.0 23.3 - - + -
57B LYS* 5.2 0.2 + - - -
426B LEU 3.0 20.9 + - - +
427B ALA 3.9 0.7 - - - +
429B PHE* 1.3 87.8 - - + +
431B ALA* 1.3 64.1 + - - +
433B THR* 3.2 10.2 + - - -
434B GLU* 3.1 21.8 + - - +
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Residues in contact with ALA 431 (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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518A GLY* 3.7 7.2 - - - +
521A LEU* 3.6 9.0 - - + +
522A ALA* 3.3 35.0 - - + +
525A ILE* 3.8 8.9 - - + +
427B ALA 2.9 20.2 + - - +
428B ASN* 3.3 2.2 + - - +
430B LEU* 1.3 74.8 - - - +
432B GLN* 1.3 61.3 + - + +
434B GLU* 3.5 5.5 - - - +
435B ALA* 2.8 32.3 + - - +
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Residues in contact with GLN 432 (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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515A VAL 5.4 1.7 - - - +
518A GLY* 3.6 22.2 - - - -
519A LYS 4.7 0.2 + - - -
341B TYR* 3.7 4.0 - - - +
388B GLN* 3.5 34.4 + - - +
392B TYR* 3.1 20.8 - - + +
396B HIS* 2.7 34.6 + - - -
406B PHE* 3.8 20.9 - - + -
428B ASN* 3.0 22.3 + - - +
429B PHE 4.2 0.2 - - - +
430B LEU 3.3 0.2 - - - -
431B ALA* 1.3 78.3 - - + +
433B THR* 1.3 57.6 + - - +
435B ALA* 3.3 3.3 + - - +
436B LEU* 2.9 36.4 + - - +
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Residues in contact with THR 433 (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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545A LEU* 4.7 0.9 - - - +
57B LYS* 3.1 26.4 + - - +
406B PHE* 3.5 42.6 - - + -
429B PHE* 3.8 6.6 + - - +
430B LEU* 3.2 10.6 + - - -
432B GLN* 1.3 73.1 - - - +
434B GLU* 1.3 66.8 + - - +
436B LEU* 3.4 8.5 + - - +
437B MET* 3.0 25.1 + - - +
472B ARG 5.1 0.2 - - - +
474B THR* 3.5 20.4 + - - +
476B SER* 3.7 16.7 + - - +
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Residues in contact with GLU 434 (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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521A LEU* 3.7 27.9 - - + +
525A ILE* 3.6 22.3 - - - +
538A HIS* 2.7 34.7 + - - +
539A ASP* 3.8 8.3 + - - +
542A THR* 3.6 20.6 - - - +
57B LYS* 4.2 4.9 - - - +
430B LEU 3.1 13.5 + - - +
431B ALA 3.5 5.8 - - - +
432B GLN 3.3 0.2 - - - -
433B THR* 1.3 78.8 + - - +
435B ALA* 1.3 57.0 + - - +
437B MET* 3.3 3.3 + - - +
438B ARG* 2.9 44.6 + - + +
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Residues in contact with ALA 435 (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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517A LEU* 3.7 26.5 - - + +
518A GLY* 4.1 10.5 - - - +
521A LEU* 3.6 13.4 - - + +
396B HIS* 3.8 18.4 + - + -
431B ALA 2.8 20.8 + - - +
432B GLN 3.7 3.8 - - - +
434B GLU* 1.3 71.5 - - - +
436B LEU* 1.3 66.6 + - - +
438B ARG* 4.7 0.2 - - - -
439B GLY* 2.9 26.5 + - - +
468B PHE* 5.5 0.2 - - - +
470B GLY* 4.6 0.5 - - - -
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Residues in contact with LEU 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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392B TYR* 5.7 1.6 - - + -
395B ILE* 3.7 35.7 - - + +
396B HIS* 3.5 31.6 - - + +
404B CYS* 5.2 1.6 - - - -
406B PHE* 4.0 19.7 - - + -
432B GLN* 2.9 23.5 + - - +
433B THR* 3.7 4.7 - - - +
435B ALA* 1.3 76.6 - - - +
437B MET* 1.3 60.4 + - - +
470B GLY* 3.3 7.0 - - - -
471B ASN 3.2 5.0 + - - -
472B ARG* 3.0 50.2 + - + +
474B THR* 3.9 22.4 - - + -
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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
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539A ASP* 3.4 42.4 - - + +
26B LEU* 3.3 40.9 - - + +
27B ARG* 3.9 16.3 + - - +
30B PHE* 3.8 20.9 - - + -
57B LYS* 4.0 13.7 - - + -
433B THR 3.0 17.1 + - - +
434B GLU 3.7 1.8 - - - +
436B LEU* 1.3 78.3 - - - +
438B ARG* 1.3 83.8 + - + +
471B ASN* 3.1 22.1 + - - +
472B ARG 4.0 6.0 + - - +
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Residues in contact with ARG 438 (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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521A LEU* 5.3 4.7 - - + -
539A ASP* 5.1 6.5 - - - +
27B ARG* 2.8 69.1 + - - +
31B ASP* 4.4 17.4 + - - -
434B GLU* 2.9 37.8 + - + +
435B ALA* 4.4 2.0 - - - +
437B MET* 1.3 99.1 - - + +
439B GLY* 1.3 68.9 + - - +
444B GLU* 4.4 5.3 + - - -
469B GLU 5.1 1.6 - - - +
470B GLY* 4.4 2.1 - - - -
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LEU* 3.5 14.8 - - - +
27B ARG* 3.3 7.2 + - - -
435B ALA 2.9 22.3 + - - -
437B MET 3.6 1.4 + - - -
438B ARG* 1.3 82.9 - - - +
440B LYS* 1.3 61.9 - - - +
444B GLU* 4.3 0.2 - - - +
468B PHE* 3.3 22.0 - - - -
469B GLU 4.5 0.2 - - - -
470B GLY* 3.7 10.0 - - - -
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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