Contacts of the helix formed by residues 414 - 438 (chain D) in PDB entry 1EJI
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 LEU 414 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C MET* 5.7 11.4 - - + -
15C TRP* 4.5 12.1 - - + +
330D GLN* 3.3 32.5 - - + +
334D ASN* 3.3 9.9 - - - -
412D GLY 3.3 19.1 - - - +
413D LEU* 1.3 74.1 - - - +
415D GLU* 1.3 75.7 + - - +
416D GLU* 3.4 14.1 - - - +
417D ASP* 2.8 16.8 + - - +
418D PHE* 2.9 20.6 + - - -
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Residues in contact with GLU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C MET* 5.5 8.3 + - - +
330D GLN* 3.1 24.4 + - - +
333D ALA* 4.0 18.2 - - + +
334D ASN* 3.3 6.3 + - - +
337D ALA* 3.9 26.1 - - + +
414D LEU* 1.3 79.2 - - - +
416D GLU* 1.3 66.9 + - + +
418D PHE* 2.9 13.5 + - - +
419D GLN* 2.9 24.7 + - - +
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Residues in contact with GLU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D LEU* 3.4 13.6 - - - +
415D GLU* 1.3 77.1 - - + +
417D ASP* 1.3 67.9 + - - +
419D GLN* 3.3 19.5 + - - +
420D LYS* 3.2 36.4 + - - +
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Residues in contact with ASP 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D LEU* 3.3 25.4 - - + -
414D LEU* 2.8 31.8 + - - +
416D GLU* 1.3 80.2 - - - +
418D PHE* 1.3 60.0 + - - +
420D LYS* 3.1 26.9 + - - +
421D VAL* 2.9 30.8 + - - +
472D PHE* 3.8 7.7 - - + -
476D PHE* 4.0 20.1 - - - -
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Residues in contact with PHE 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 4.2 21.1 - - + -
334D ASN* 3.2 56.5 - - + +
337D ALA* 4.6 2.7 - - + -
338D LEU* 3.8 30.0 - - + +
405D THR* 3.7 30.7 - - + -
408D LEU* 3.7 25.8 - - + -
409D THR* 3.8 2.5 - - - -
413D LEU* 3.9 16.2 - - + -
414D LEU 2.9 13.6 + - - +
415D GLU* 2.9 10.7 + - - +
417D ASP* 1.3 73.6 - - - +
419D GLN* 1.3 61.4 + - - +
421D VAL* 3.2 13.1 - - + +
422D ALA* 2.9 24.9 + - - +
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Residues in contact with GLN 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D ALA* 4.8 10.7 - - + +
341D ALA* 4.4 19.0 - - + +
344D GLU* 5.7 1.2 - - - +
415D GLU* 2.9 21.1 + - - +
416D GLU* 3.4 27.1 - - - +
417D ASP 3.1 0.2 - - - -
418D PHE* 1.3 73.3 - - - +
420D LYS* 1.3 67.9 + - + +
421D VAL 3.0 1.3 - - - -
422D ALA* 2.9 19.6 + - - +
423D HIS* 3.0 12.6 + - - +
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Residues in contact with LYS 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D GLU* 3.3 25.6 - - - +
417D ASP* 3.1 21.4 + - - +
419D GLN* 1.3 76.6 - - + +
421D VAL* 1.3 62.7 + - - +
423D HIS* 3.3 8.7 + - - +
424D PHE* 3.1 32.9 + - + -
472D PHE* 4.1 25.8 - - + -
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Residues in contact with VAL 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.4 16.6 - - + -
50D LEU* 4.0 34.8 - - + -
338D LEU* 4.8 2.2 - - + -
408D LEU* 4.6 2.2 - - + -
413D LEU* 4.2 9.4 - - + -
417D ASP 2.9 20.5 + - - +
418D PHE* 3.2 24.5 - - + +
420D LYS* 1.3 74.7 - - - +
422D ALA* 1.3 68.3 + - - +
424D PHE* 2.9 21.9 + - - +
425D ILE* 3.0 21.3 + - + +
472D PHE* 3.9 19.3 - - + -
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Residues in contact with ALA 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D LEU* 3.7 11.6 - - + +
341D ALA* 3.7 21.5 - - + -
342D LEU* 3.4 30.3 - - + +
345D LEU* 4.4 3.6 - - + -
418D PHE 2.9 13.8 + - - +
419D GLN 2.9 9.6 + - - +
421D VAL* 1.3 76.0 - - - +
423D HIS* 1.3 57.2 + - - +
425D ILE* 3.1 7.8 + - - +
426D HIS* 2.9 27.0 + - - +
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Residues in contact with HIS 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D LEU* 4.4 10.2 - - + +
419D GLN 3.0 11.3 + - - +
420D LYS* 3.6 11.2 - - - +
422D ALA* 1.3 72.3 - - - +
424D PHE* 1.3 67.7 + - + +
426D HIS* 3.0 26.4 + + - +
427D ARG* 2.8 67.8 + - + +
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Residues in contact with PHE 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.1 13.2 - - + -
382D ILE* 4.3 19.1 - - + +
420D LYS* 3.1 29.8 + - + -
421D VAL* 2.9 12.4 + - - +
423D HIS* 1.3 75.8 - - + +
425D ILE* 1.3 58.3 + - + +
427D ARG* 3.3 17.6 + - - +
428D GLY* 3.0 22.9 + - - -
465D LEU* 3.8 15.2 - - + +
468D GLU* 3.4 49.4 - - + -
469D VAL* 3.8 20.6 - - + -
472D PHE* 3.5 33.9 - + + -
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Residues in contact with ILE 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 6.5 0.2 - - + -
50D LEU* 3.6 31.4 - - + -
338D LEU* 4.4 7.0 - - + -
342D LEU* 4.9 6.1 - - + -
347D TYR* 6.4 0.2 - - + -
361D MSE 4.3 23.1 - - + -
377D LEU* 4.1 17.8 - - + +
382D ILE* 4.8 10.1 - - + -
403D LEU* 4.1 19.5 - - + -
421D VAL* 3.0 20.2 + - + +
422D ALA* 3.3 13.0 - - - +
424D PHE* 1.3 75.4 - - + +
426D HIS* 1.3 67.1 + - - +
428D GLY* 2.9 11.3 + - - -
429D ILE* 2.9 25.2 + - + +
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Residues in contact with HIS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 5.5 0.4 - - - +
345D LEU* 3.3 53.5 + - + +
347D TYR* 2.8 40.9 + + + +
422D ALA 2.9 6.0 + - - +
423D HIS* 3.0 23.5 + + - +
425D ILE* 1.3 76.4 - - - +
427D ARG* 1.3 59.0 + - - +
429D ILE 3.3 0.3 + - - -
430D GLU* 2.9 51.4 + - + +
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Residues in contact with ARG 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D HIS* 2.8 61.3 + - + +
424D PHE* 3.3 20.8 - - - +
426D HIS* 1.3 76.5 - - + +
428D GLY* 1.3 57.4 + - - +
430D GLU* 3.0 11.5 - - - +
431D LEU* 3.0 27.4 + - - +
464D THR* 6.2 1.8 - - - +
465D LEU* 3.7 36.4 - - + +
468D GLU* 2.6 33.7 + - - +
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Residues in contact with GLY 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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376D VAL* 3.7 8.7 - - - +
377D LEU* 3.9 16.6 - - - -
380D CYS* 5.7 0.9 - - - -
424D PHE 3.0 9.6 + - - -
425D ILE 2.9 9.4 + - - -
427D ARG* 1.3 75.9 - - - +
429D ILE* 1.3 64.9 + - - -
431D LEU* 3.0 8.4 + - - +
432D THR* 3.0 23.6 + - - -
465D LEU* 4.0 11.6 - - - +
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Residues in contact with ILE 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D TYR* 3.4 44.6 - - + +
361D MSE 4.4 6.3 - - - -
363D LEU* 4.3 18.6 - - + -
366D LYS* 5.6 1.8 - - + -
368D THR* 4.2 15.0 - - + -
373D ALA* 4.9 4.3 - - + -
377D LEU* 4.6 11.4 - - + +
401D LEU* 4.4 6.3 - - + -
425D ILE* 2.9 28.2 + - + +
426D HIS 4.0 0.4 - - - +
428D GLY* 1.3 71.0 - - - +
430D GLU* 1.3 67.3 + - - +
432D THR* 2.9 12.5 + - - -
433D LEU* 2.8 40.5 + - + +
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Residues in contact with GLU 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D TYR* 4.7 1.2 + - - -
426D HIS* 2.9 34.9 + - + +
427D ARG* 3.0 17.7 - - - +
429D ILE* 1.3 77.8 - - - +
431D LEU* 1.3 62.7 + - - +
433D LEU* 3.3 8.3 + - - +
434D GLN* 3.2 39.4 + - - +
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Residues in contact with LEU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D VAL* 4.3 17.5 - - + -
380D CYS* 4.8 5.6 - - - -
427D ARG 3.0 13.0 + - - +
428D GLY 3.0 9.6 + - - +
430D GLU* 1.3 74.0 - - - +
432D THR* 1.3 66.6 + - - +
434D GLN* 3.1 18.8 + - + +
435D ILE* 3.0 38.5 + - + +
452D LEU* 4.4 8.5 - - + -
458D ILE 6.1 0.4 - - - +
461D ALA* 4.3 14.1 - - + -
462D VAL* 4.1 34.3 - - + +
465D LEU* 4.9 7.9 - - + -
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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
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368D THR* 3.5 24.0 - - - +
372D ARG* 4.0 1.6 - - + -
373D ALA* 3.8 20.4 - - - +
376D VAL* 3.1 23.1 - - - +
428D GLY 3.0 12.2 + - - -
429D ILE* 2.9 14.9 + - - -
431D LEU* 1.3 75.7 - - - +
433D LEU* 1.3 64.5 + - - +
435D ILE* 2.9 12.0 - - - +
436D GLN* 2.9 26.4 + - - +
448D PHE* 3.5 20.6 - - + -
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Residues in contact with LEU 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D LYS* 3.2 32.8 - - + +
368D THR* 3.9 16.8 - - + -
429D ILE* 2.8 39.4 + - + +
430D GLU* 3.5 11.4 - - - +
432D THR* 1.3 71.7 - - - +
434D GLN* 1.3 53.0 + - + +
436D GLN* 3.0 24.1 + - - +
437D SER* 2.4 41.8 + - - -
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Residues in contact with GLN 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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430D GLU* 3.4 31.9 + - + +
431D LEU* 3.1 20.6 + - + +
433D LEU* 1.3 73.7 - - + +
435D ILE* 1.3 56.0 + - - +
436D GLN 2.7 14.6 + - - -
437D SER* 2.7 28.9 + - - -
438D HIS* 3.6 6.9 + - - +
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Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D LEU* 3.0 17.9 - - + +
432D THR* 2.9 26.5 - - - +
434D GLN* 1.3 76.0 - - - +
436D GLN* 1.3 55.0 + - - +
438D HIS* 2.8 30.6 + - + -
439D MSE 3.6 11.9 - - - +
448D PHE* 3.3 34.5 - - + -
451D LYS 4.4 4.9 - - - +
452D LEU* 3.4 48.7 - - + +
456D GLU* 4.9 12.3 - - - +
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Residues in contact with GLN 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D LYS 4.2 0.4 + - - -
367D GLY* 3.8 19.4 + - - -
368D THR* 3.1 32.9 + - - -
372D ARG* 4.0 15.3 - - - +
432D THR* 2.9 19.4 + - - +
433D LEU* 3.1 28.9 + - - +
434D GLN 2.7 1.0 + - - -
435D ILE* 1.3 78.8 - - - +
437D SER* 1.3 52.9 + - - +
438D HIS 3.4 0.9 - - - -
439D MSE 3.5 6.5 - - + +
440D ALA* 2.6 47.0 + - + +
448D PHE* 3.8 14.6 - - + -
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Residues in contact with SER 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D LEU* 2.4 26.0 + - - -
434D GLN* 2.7 25.6 + - - -
436D GLN* 1.3 73.4 - - - +
438D HIS* 1.3 61.2 + - - +
440D ALA* 3.4 16.1 - - - +
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Residues in contact with HIS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D GLN 3.7 3.4 + - - +
435D ILE* 2.8 43.6 + - + -
437D SER* 1.3 82.7 + - - +
439D MSE 1.3 76.2 + - + +
440D ALA* 4.8 0.2 - - - -
451D LYS* 5.3 9.8 - - + +
456D GLU* 5.7 10.8 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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