Contacts of the helix formed by residues 418 - 438 (chain C) in PDB entry 1JLH
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 418 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C THR* 6.0 0.2 - - - -
414C PRO* 3.5 19.6 + - - +
415C ILE 2.9 9.4 + - - -
417C LYS* 1.3 77.0 - - - +
419C LEU* 1.3 57.8 + - - +
420C HIS 3.3 3.1 - - - -
421C HIS* 3.2 11.1 + - - +
422C LYS* 2.9 30.0 + - - +
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Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ILE 3.5 0.8 + - - -
416C ARG* 2.9 55.1 + - + +
417C LYS 3.3 1.4 + - - -
418C GLY* 1.3 75.7 - - - +
420C HIS* 1.3 63.0 + - - +
422C LYS* 3.3 16.8 + - + +
423C ILE* 3.2 41.0 + - + +
219D THR* 4.2 14.8 - - + +
222D GLU* 5.7 2.0 - - - +
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Residues in contact with HIS 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C HIS 5.6 1.6 - - - +
415C ILE* 3.5 25.5 + - + +
416C ARG* 3.6 10.0 - - + +
418C GLY 3.3 0.8 - - - -
419C LEU* 1.3 79.7 - - - +
421C HIS* 1.3 57.2 + - - +
423C ILE* 3.4 6.0 + - - +
424C LEU* 3.0 27.0 + - - +
186D ILE* 2.9 42.3 - - + +
188D GLY* 3.6 25.4 - - - +
191D ILE* 4.1 4.0 - - - +
219D THR* 3.7 19.5 + - + +
220D ASN* 3.3 23.3 + - - -
223D THR* 2.8 30.6 + - - -
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Residues in contact with HIS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ILE* 4.6 2.7 - - + -
408C PRO* 3.0 26.2 + - + -
409C VAL 2.9 29.5 + - - -
411C THR* 3.5 43.5 + - + -
413C HIS 5.9 0.4 - - - +
414C PRO* 5.9 0.2 - - + -
418C GLY* 3.2 12.8 + - - +
420C HIS* 1.3 75.8 - - - +
422C LYS* 1.3 60.3 + - - +
424C LEU* 4.0 24.6 - - + +
425C LEU* 2.8 61.4 + - + +
187D ASP* 5.1 2.4 + - - -
188D GLY 5.2 1.8 - - - +
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Residues in contact with LYS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLY 2.9 16.8 + - - +
419C LEU* 3.4 20.0 - - + +
420C HIS 3.2 0.2 - - - -
421C HIS* 1.3 76.7 - - - +
423C ILE* 1.3 59.2 + - + +
425C LEU* 3.3 4.2 + - - -
426C ALA* 2.9 25.3 + - - +
525D GLU* 2.8 47.3 + - + +
526D PRO* 4.4 3.0 - - - +
528D LEU* 3.5 20.3 - - + +
529D ASP* 3.3 32.8 + - - +
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C LEU* 3.2 36.2 + - + +
420C HIS 3.8 5.4 - - - +
421C HIS 3.3 0.2 - - - -
422C LYS* 1.3 75.9 - - + +
424C LEU* 1.3 65.0 + - - +
426C ALA* 3.2 7.2 + - - +
427C ASN* 2.9 44.9 + - - +
186D ILE* 3.7 24.9 - - + -
215D GLN* 3.6 35.4 - - + +
216D GLU* 5.5 1.8 - - + -
219D THR* 4.0 20.9 - - + +
525D GLU* 4.1 11.9 - - + +
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Residues in contact with LEU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C TYR* 3.4 34.7 - - + +
341C ASP* 6.0 0.2 - - - +
383C GLY 3.8 13.9 - - - +
384C THR* 3.8 14.4 - - + -
407C ILE* 4.2 6.1 - - + -
420C HIS 3.0 18.4 + - - +
421C HIS* 3.3 27.1 + - + +
423C ILE* 1.3 76.3 - - - +
425C LEU* 1.3 63.4 + - - +
427C ASN* 3.3 3.5 + - - +
428C PHE* 3.0 22.3 + - - +
185D ASN* 3.9 3.8 - - - +
186D ILE* 3.5 26.0 - - + +
187D ASP* 3.7 26.0 - - + +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ILE* 3.5 30.7 - - + -
408C PRO 4.3 3.6 - - - +
409C VAL* 4.4 6.5 - - - +
421C HIS* 2.8 52.0 + - + +
422C LYS* 3.6 7.0 - - - +
424C LEU* 1.3 74.1 - - - +
426C ALA* 1.3 62.8 + - - +
428C PHE* 3.2 3.4 + - + +
429C LEU* 3.0 30.2 + - - +
528D LEU* 4.1 12.1 - - + -
548D ILE* 4.0 44.9 - - + -
552D ARG* 6.2 2.5 - - - +
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C LYS 2.9 16.8 + - - +
423C ILE* 3.2 5.4 + - - +
425C LEU* 1.3 76.4 - - - +
427C ASN* 1.3 57.1 + - - +
429C LEU* 3.8 1.4 - - - +
430C ALA* 2.8 31.9 + - - +
521D ALA* 3.7 15.9 - - + +
524D ILE* 4.1 14.4 - - + +
525D GLU* 3.6 34.1 - - + +
528D LEU* 3.9 5.6 - - + +
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Residues in contact with ASN 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C TYR* 4.0 6.3 - - + -
384C THR* 4.3 10.9 - - + +
387C GLN* 2.8 34.0 - - - +
423C ILE* 2.9 45.9 + - - +
424C LEU 3.7 3.6 - - - +
426C ALA* 1.3 74.3 - - - +
428C PHE* 1.3 65.8 + - - +
430C ALA* 4.4 0.9 - - - +
431C GLN* 2.9 33.4 + - - +
186D ILE* 5.1 0.4 - - - +
215D GLN* 4.7 4.0 - - - +
216D GLU* 4.5 10.3 + - - +
517D GLY 5.0 1.6 - - - +
518D LYS* 5.4 3.3 - - - -
521D ALA* 4.0 20.3 - - - +
525D GLU* 5.1 0.4 + - - -
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Residues in contact with PHE 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C TYR* 3.7 22.6 - + + -
405C PHE* 3.4 46.8 - - + -
406C LEU 3.6 7.0 - - - -
407C ILE* 3.6 42.0 - - + -
424C LEU 3.0 13.4 + - - +
425C LEU* 3.2 7.8 + - + +
427C ASN* 1.3 76.1 - - - +
429C LEU* 1.3 86.1 + - + +
432C THR* 3.8 21.9 + - - +
475C SER* 3.9 20.0 - - - -
476C ILE 4.3 0.4 - - - -
477C VAL* 3.8 26.9 - - + -
544D LEU* 4.7 0.9 - - + -
548D ILE* 5.3 2.7 - - + -
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 5.1 0.3 + - - -
425C LEU 3.0 20.9 + - - +
426C ALA 3.8 2.2 - - - +
428C PHE* 1.3 91.2 - - + +
430C ALA* 1.3 66.2 + - - +
431C GLN 3.2 0.2 - - - -
432C THR* 3.2 9.3 + - - -
433C GLU* 3.1 21.8 + - - +
524D ILE* 3.9 26.5 - - + -
528D LEU* 4.1 8.5 - - + -
541D THR* 4.7 8.4 + - + +
544D LEU* 3.5 36.3 - - + -
545D ILE* 3.7 26.2 - - + -
548D ILE* 4.0 19.7 - - + -
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Residues in contact with ALA 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C ALA 2.8 20.8 + - - +
427C ASN* 4.1 2.0 - - - +
429C LEU* 1.3 73.3 - - - +
431C GLN* 1.3 57.8 + - - +
433C GLU* 3.3 2.8 + - - +
434C ALA* 2.8 32.3 + - - +
517D GLY 3.6 10.5 - - - +
520D LEU* 3.5 11.9 - - + +
521D ALA* 3.1 36.6 - - + +
524D ILE* 3.8 8.2 - - + +
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Residues in contact with GLN 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C TYR* 3.5 6.3 - - - +
387C GLN* 3.5 35.1 + - - +
391C TYR* 3.1 17.7 - - + +
395C HIS* 2.9 32.4 + - - -
405C PHE* 3.7 20.6 - - + -
427C ASN* 2.9 22.8 + - - +
428C PHE 4.2 0.7 - - - +
429C LEU 3.2 0.2 - - - -
430C ALA* 1.3 77.1 - - - +
432C THR* 1.3 58.8 + - - +
434C ALA* 3.7 2.7 - - - +
435C LEU* 2.9 34.0 + - + +
514D VAL 5.5 1.4 + - - -
517D GLY* 3.5 28.8 + - - -
518D LYS 4.6 0.2 - - - +
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Residues in contact with THR 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 3.0 34.5 + - - +
405C PHE* 3.6 32.8 - - + -
428C PHE 3.8 10.0 + - - +
429C LEU* 3.2 11.0 + - - -
431C GLN* 1.3 76.0 - - - +
433C GLU* 1.3 62.6 + - - +
435C LEU* 3.7 8.9 - - - +
436C MET* 3.1 16.5 + - - +
471C ARG 5.1 0.3 - - - +
473C THR* 3.4 22.0 + - - +
475C SER* 3.6 19.4 + - - +
544D LEU* 4.7 1.0 - - - +
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Residues in contact with GLU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 4.1 7.9 - - - +
429C LEU 3.1 12.7 + - - +
430C ALA 3.6 3.1 - - - +
432C THR* 1.3 79.1 + - - +
434C ALA* 1.3 60.8 + - - +
436C MET* 3.3 3.1 + - - +
437C ARG* 2.9 44.8 + - + +
520D LEU* 3.6 26.2 - - + +
524D ILE* 3.5 22.0 - - - +
537D HIS* 2.7 34.0 + - - +
538D ASP* 3.6 9.7 + - - +
541D THR* 3.5 19.1 - - - +
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Residues in contact with ALA 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395C HIS* 3.9 14.3 - - - +
430C ALA 2.8 17.5 + - - +
431C GLN 3.7 3.6 - - - +
433C GLU* 1.3 75.1 - - - +
435C LEU* 1.3 66.0 + - - +
437C ARG* 4.9 0.4 - - - -
438C GLY* 2.8 26.3 + - - +
469C GLY* 4.6 0.5 - - - -
516D LEU* 3.6 23.7 - - + +
517D GLY* 4.0 14.6 - - - +
520D LEU* 3.5 15.8 - - + +
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Residues in contact with LEU 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C TYR* 5.7 1.3 - - + -
394C ILE* 4.2 19.5 - - + -
395C HIS* 3.1 41.3 - - + +
403C CYS* 5.2 1.1 - - - -
405C PHE* 4.0 20.2 - - + -
431C GLN* 2.9 21.2 + - - +
432C THR* 3.7 6.3 - - - +
434C ALA* 1.3 76.3 - - - +
436C MET* 1.3 61.4 + - - +
469C GLY* 3.3 7.9 - - - -
470C ASN 3.2 5.2 + - - -
471C ARG* 3.0 57.5 + - + +
473C THR* 3.8 21.3 - - + -
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Residues in contact with MET 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.4 40.9 - - + +
26C ARG* 4.7 7.1 + - - +
29C PHE* 3.4 35.2 - - + -
56C LYS* 4.1 19.3 - - + -
432C THR 3.1 15.5 + - - +
433C GLU* 3.7 2.7 - - - +
434C ALA 3.1 0.4 - - - -
435C LEU* 1.3 77.8 - - - +
437C ARG* 1.3 76.0 + - + +
470C ASN* 2.9 22.3 + - - -
471C ARG 3.9 2.0 + - - +
538D ASP* 3.2 45.3 - - + +
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Residues in contact with ARG 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 2.8 63.8 + - + +
433C GLU* 2.9 38.7 + - + +
434C ALA* 4.9 0.9 - - - -
436C MET* 1.3 90.6 - - + +
438C GLY* 1.3 73.6 + - - +
443C GLU* 3.2 16.6 + - - -
468C GLU 4.8 2.8 - - - +
469C GLY* 4.5 1.7 - - - -
516D LEU* 5.1 3.4 - - - +
520D LEU* 4.9 17.2 - - - +
538D ASP* 5.1 7.0 - - - +
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.5 6.9 + - - -
434C ALA 2.8 23.3 + - - -
436C MET 3.5 1.4 - - - -
437C ARG* 1.3 90.0 + - - +
439C LYS* 1.3 60.8 + - - +
443C GLU* 4.2 0.2 - - - +
467C PHE* 3.4 16.4 - - - -
469C GLY* 3.8 9.9 - - - -
516D LEU* 3.6 17.7 - - - +
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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