Contacts of the helix formed by residues 418 - 438 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D THR* 5.8 0.4 - - - -
414D PRO* 3.5 19.6 + - - +
415D ILE 3.0 10.2 + - - -
417D LYS* 1.3 76.6 - - - +
419D LEU* 1.3 62.8 + - - +
420D HIS 3.3 2.5 - - - -
421D HIS* 3.5 10.1 + - - +
422D LYS* 3.0 24.5 + - - +
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Residues in contact with LEU 419 (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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219C THR* 4.2 19.1 - - + -
415D ILE 3.5 1.4 + - - -
416D ARG* 3.0 55.6 + - + +
417D LYS 3.3 1.0 - - - -
418D GLY* 1.3 76.6 - - - +
420D HIS* 1.3 65.2 + - - +
422D LYS* 3.4 14.7 + - + +
423D ILE* 3.2 39.0 + - + +
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Residues in contact with HIS 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE* 2.9 39.0 - - + +
188C GLY* 3.5 27.1 - - - +
191C ILE* 4.1 5.3 - - + +
219C THR* 3.4 22.9 + - + +
220C ASN* 3.3 23.9 + - - -
223C THR* 2.9 30.8 + - - -
413D HIS 5.6 1.3 - - - +
415D ILE* 3.9 13.2 + - + +
416D ARG* 3.9 17.3 - - + +
418D GLY 3.3 0.6 - - - -
419D LEU* 1.3 78.9 - - - +
421D HIS* 1.3 63.9 + - - +
423D ILE* 3.2 6.4 + - - +
424D LEU* 3.0 22.3 + - - +
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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 ASP* 5.0 2.4 + - - -
188C GLY 5.0 1.7 - - - +
341D ASP* 6.0 0.2 - - - -
407D ILE* 4.4 8.7 - - + -
408D PRO* 2.8 33.8 + - + -
409D VAL 2.9 22.5 + - - -
411D THR* 3.6 43.4 + - + -
413D HIS 5.9 0.4 + - - -
414D PRO* 6.0 0.2 - - + -
418D GLY* 3.5 10.9 + - - +
419D LEU 3.4 0.4 - - - -
420D HIS* 1.3 79.1 - - - +
422D LYS* 1.3 58.0 + - - +
424D LEU* 3.5 28.9 - - + +
425D LEU* 2.8 52.8 + - + +
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Residues in contact with LYS 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C GLU* 2.9 43.0 + - + +
526C PRO* 4.5 2.2 - - - +
528C LEU* 3.4 20.4 - - + +
529C ASP* 2.9 34.3 + - - +
418D GLY 3.0 18.0 + - - +
419D LEU* 3.5 19.0 - - + +
420D HIS 3.2 0.2 - - - -
421D HIS* 1.3 77.9 - - - +
423D ILE* 1.3 61.3 + - + +
425D LEU* 3.3 8.0 + - - -
426D ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE* 3.8 25.8 - - + -
215C GLN* 3.0 40.4 - - + +
216C GLU* 5.5 3.4 - - + -
219C THR* 5.4 3.1 - - + +
525C GLU* 3.4 22.2 - - + +
419D LEU* 3.2 31.6 - - + +
420D HIS* 3.2 6.0 + - - +
422D LYS* 1.3 77.9 - - + +
424D LEU* 1.3 63.8 + - - +
426D ALA* 3.2 5.7 + - - +
427D ASN* 2.8 45.2 + - - +
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Residues in contact with LEU 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASN* 3.9 10.5 - - - +
186C ILE* 3.6 27.1 - - + +
187C ASP* 3.7 24.5 - - + -
340D TYR* 3.5 37.4 - - + +
383D GLY 3.9 3.6 - - - +
384D THR* 3.8 14.4 - - + -
407D ILE* 4.2 6.1 - - + -
420D HIS 3.0 14.3 + - - +
421D HIS* 3.5 33.2 - - + +
423D ILE* 1.3 76.0 - - - +
425D LEU* 1.3 57.1 + - - +
427D ASN* 3.2 5.7 + - - +
428D PHE* 2.9 27.4 + - - +
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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
----------------------------------------------------------
528C LEU* 4.1 11.9 - - + -
548C ILE* 3.6 46.2 - - + -
552C ARG* 6.1 4.7 - - - +
407D ILE* 3.6 29.8 - - + -
408D PRO 4.5 3.1 - - - +
409D VAL* 4.5 5.8 - - - +
421D HIS* 2.8 48.8 + - + +
422D LYS* 3.6 7.4 - - - +
424D LEU* 1.3 73.8 - - - +
426D ALA* 1.3 67.0 + - - +
428D PHE* 3.0 3.5 + - + +
429D LEU* 2.9 30.2 + - + +
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Residues in contact with ALA 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C ALA* 3.8 11.4 - - - +
524C ILE* 4.1 14.6 - - + +
525C GLU* 3.6 34.3 - - + +
528C LEU* 3.9 4.2 - - + +
422D LYS 2.9 14.7 + - - +
423D ILE* 3.4 8.5 - - - +
425D LEU* 1.3 76.1 - - - +
427D ASN* 1.3 61.7 - - - +
429D LEU* 3.5 1.7 + - - +
430D ALA* 2.8 32.4 + - - +
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Residues in contact with ASN 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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186C ILE* 5.5 0.2 - - - +
215C GLN* 4.9 4.9 - - - +
216C GLU* 4.7 8.7 + - - +
517C GLY 5.0 0.5 - - - +
518C LYS* 5.3 3.1 - - - +
521C ALA* 4.0 19.2 - - - +
525C GLU* 5.0 0.6 + - - -
340D TYR* 4.1 5.8 - - + -
384D THR* 4.4 10.2 - - + +
387D GLN* 2.9 33.2 - - - +
423D ILE* 2.8 45.3 + - - +
424D LEU* 3.6 4.2 - - - +
426D ALA* 1.3 76.2 - - - +
428D PHE* 1.3 65.2 + - - +
430D ALA* 4.4 4.7 - - - -
431D GLN* 3.1 34.2 + - - +
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Residues in contact with PHE 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LEU* 4.7 1.3 - - + -
548C ILE* 5.3 3.4 - - + -
340D TYR* 3.8 24.6 - + + -
405D PHE* 3.4 44.8 - - + -
406D LEU 3.5 14.1 - - - -
407D ILE* 3.6 39.3 - - + -
424D LEU 2.9 14.0 + - - +
425D LEU* 3.0 7.6 + - - +
427D ASN* 1.3 77.4 - - - +
429D LEU* 1.3 84.2 + - + +
432D THR* 3.9 19.6 + - - +
475D SER* 4.0 20.2 - - - -
476D ILE 4.4 0.9 - - - -
477D VAL* 3.9 22.9 - - + -
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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
----------------------------------------------------------
524C ILE* 3.9 26.0 - - + -
528C LEU* 4.2 8.5 - - + -
541C THR* 4.5 9.2 + - + +
544C LEU* 3.5 38.1 - - + -
545C ILE* 3.6 27.4 - - + -
548C ILE* 4.0 19.3 - - + -
425D LEU 2.9 18.8 + - - +
426D ALA 3.8 2.7 - - - +
428D PHE* 1.3 94.0 - - + +
430D ALA* 1.3 64.6 + - - +
432D THR* 3.1 19.7 + - - -
433D GLU* 3.2 10.7 + - - +
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Residues in contact with ALA 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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517C GLY 3.5 11.4 - - - +
520C LEU* 3.6 8.7 - - + +
521C ALA* 3.3 34.5 - - + +
524C ILE* 3.7 8.5 - - + +
426D ALA 2.8 22.4 + - - +
427D ASN* 4.2 2.0 - - - +
429D LEU* 1.3 72.8 - - - +
431D GLN* 1.3 56.8 + - - +
433D GLU* 3.3 6.3 + - - +
434D ALA* 2.8 32.0 + - - +
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Residues in contact with GLN 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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514C VAL 5.5 1.8 + - - -
517C GLY* 3.5 29.5 + - - -
518C LYS* 4.4 1.0 - - - +
340D TYR* 3.6 4.9 - - - +
387D GLN* 3.5 35.1 + - - +
391D TYR* 3.1 15.1 - - + -
395D HIS* 2.9 34.4 + - - -
405D PHE* 3.8 20.4 - - + -
427D ASN* 3.1 24.1 + - - +
428D PHE 4.3 0.4 - - - +
430D ALA* 1.3 76.4 - - - +
432D THR* 1.3 57.9 + - - +
434D ALA* 3.3 4.4 + - - +
435D LEU* 2.8 36.0 + - + +
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Residues in contact with THR 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LEU* 4.8 1.7 - - - +
56D LYS* 3.3 25.5 + - - +
405D PHE* 3.5 39.3 - - + -
428D PHE* 3.9 8.0 + - - +
429D LEU* 3.1 15.1 + - - -
431D GLN* 1.3 73.4 - - - +
433D GLU* 1.3 64.9 + - - +
435D LEU* 3.8 8.1 - - - +
436D MET* 3.1 24.6 + - - +
471D ARG 5.1 0.3 - - - +
473D THR* 3.4 25.0 + - - +
475D SER* 3.7 14.1 + - - +
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Residues in contact with GLU 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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520C LEU* 3.5 33.9 - - + +
524C ILE* 3.6 15.6 - - - +
537C HIS* 2.8 35.8 + - - +
538C ASP* 3.8 9.8 + - - +
541C THR* 3.7 17.7 - - - +
56D LYS* 4.3 8.7 - - - +
429D LEU 3.2 10.0 + - - +
430D ALA 3.4 6.5 - - - +
432D THR* 1.3 81.9 + - - +
434D ALA* 1.3 58.4 + - - +
436D MET* 3.2 3.9 + - - +
437D ARG* 2.9 44.0 + - - +
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Residues in contact with ALA 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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516C LEU* 3.7 21.4 - - + +
517C GLY* 4.0 14.1 - - - +
520C LEU* 3.6 13.9 - - + +
395D HIS* 4.0 16.8 - - - +
430D ALA 2.8 18.3 + - - +
431D GLN 3.5 4.5 - - - +
433D GLU* 1.3 74.1 - - - +
435D LEU* 1.3 66.6 + - - +
438D GLY* 2.9 26.8 + - - +
467D PHE* 5.6 0.3 - - - -
469D GLY* 4.6 0.9 - - - -
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Residues in contact with LEU 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D TYR* 5.5 0.9 - - + -
394D ILE* 3.9 23.6 - - + -
395D HIS* 3.4 41.3 - - + +
403D CYS* 6.0 0.2 - - - -
405D PHE* 3.9 25.6 - - + -
431D GLN* 2.8 35.2 + - + +
432D THR* 3.8 6.3 - - - +
434D ALA* 1.3 75.1 - - - +
436D MET* 1.3 57.8 + - - +
469D GLY* 3.3 7.0 - - - -
470D ASN 3.2 7.1 + - - -
471D ARG* 2.9 55.0 + - + +
473D THR* 4.3 9.4 - - + -
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Residues in contact with MET 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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538C ASP* 3.2 37.7 - - + +
25D LEU* 3.4 39.7 - - + +
26D ARG* 4.4 6.6 + - - +
29D PHE* 3.5 37.7 - - + -
56D LYS* 4.1 15.3 - - + -
432D THR 3.1 17.1 + - - +
433D GLU* 3.6 5.4 - - + +
434D ALA 3.0 0.8 - - - -
435D LEU* 1.3 77.4 - - - +
437D ARG* 1.3 89.5 + - + +
470D ASN* 3.0 22.5 + - - -
471D ARG 4.0 2.0 + - - +
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Residues in contact with ARG 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LEU* 5.3 2.0 - - - +
520C LEU* 4.5 23.0 - - - +
538C ASP* 4.9 6.5 - - - +
26D ARG* 2.8 62.7 + - + +
433D GLU* 2.9 28.2 + - - +
434D ALA* 5.3 0.4 - - - -
436D MET* 1.3 101.0 - - + +
438D GLY* 1.3 70.1 + - - +
439D LYS 3.8 0.3 + - - -
443D GLU* 3.8 11.5 + - - -
467D PHE 4.8 0.5 - - - +
468D GLU 5.0 1.9 - - - +
469D GLY* 4.5 3.0 - - - -
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Residues in contact with GLY 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LEU* 3.5 23.7 - - - +
26D ARG* 3.2 9.2 + - - -
434D ALA 2.9 18.3 + - - -
436D MET 3.6 0.8 - - - -
437D ARG* 1.3 86.8 + - - +
439D LYS* 1.3 62.2 + - - +
467D PHE* 3.6 15.7 - - - -
469D GLY* 3.9 7.9 - - - -
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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