Contacts of the helix formed by residues 427 - 448 (chain C) in PDB entry 3L0I
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 THR 427 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C GLU* 2.8 10.5 + - - -
426C SER* 1.3 80.5 + - - +
428C VAL* 1.3 69.4 + - + +
429C GLU 3.7 0.4 - - - -
430C PRO* 4.1 0.9 - - - -
431C GLY* 3.2 19.6 + - - -
7D GLU* 5.0 6.6 + - - -
34D ASP* 3.3 24.2 + - - +
36D TYR* 3.2 42.9 - - + -
48D PHE* 4.3 4.6 - - - -
61D LYS* 4.1 8.3 + - - -
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Residues in contact with VAL 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLU* 2.4 26.0 + - + +
427C THR* 1.3 70.7 - - + +
429C GLU* 1.3 60.9 + - - +
431C GLY* 3.2 1.2 + - - -
432C LEU* 2.9 43.4 + - + +
483C SER* 4.0 5.2 - - - +
484C LYS 3.5 26.5 - - - +
485C ILE* 3.6 17.0 - - + -
486C TRP 5.8 0.2 - - - +
36D TYR* 3.6 46.4 - - + +
38D GLU* 4.1 0.9 - - - +
41D ILE* 4.6 1.2 - - - +
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Residues in contact with GLU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR* 2.5 35.4 + - + +
420C ALA* 3.6 15.6 - - + +
425C GLU* 3.3 3.2 + - - +
428C VAL* 1.3 75.6 - - - +
430C PRO* 1.4 73.2 - - + +
432C LEU* 3.3 4.8 + - + +
433C VAL* 2.9 29.6 + - + +
475C ILE* 6.2 0.4 - - + -
485C ILE* 3.6 27.7 - - + +
493C LEU* 5.0 0.4 - - - -
494C MSE 3.7 3.0 - - + +
497C LYS* 2.6 30.6 + - - +
522C LYS* 2.7 37.6 + - - +
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Residues in contact with PRO 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C SER* 3.3 34.6 + - - +
420C ALA* 3.7 24.5 - - + +
421C ALA* 3.7 7.0 - - + +
425C GLU* 4.1 1.6 - - - +
426C SER 3.7 29.4 - - - +
427C THR 4.0 0.2 - - - +
428C VAL 3.9 0.2 - - - -
429C GLU* 1.4 93.9 - - + +
431C GLY* 1.3 52.9 + - - +
434C SER* 2.8 40.0 + - - -
48D PHE* 3.6 15.0 - - + -
63D GLN* 4.2 5.4 - - - +
65D TRP* 4.6 0.2 - - + -
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Residues in contact with GLY 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C THR 3.2 13.7 + - - -
428C VAL 3.2 6.6 + - - -
429C GLU 3.1 0.8 - - - -
430C PRO* 1.3 79.3 - - - +
432C LEU* 1.3 62.4 + - - +
434C SER* 3.7 2.1 - - - -
435C ALA* 3.0 23.6 + - - +
41D ILE* 3.7 11.7 - - - -
46D VAL* 3.7 13.9 - - - +
48D PHE* 3.7 14.3 - - - -
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Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C VAL* 2.9 36.9 + - + +
429C GLU* 3.8 3.4 - - - +
431C GLY* 1.3 71.8 - - - +
433C VAL* 1.3 63.0 + - - +
435C ALA* 3.2 4.9 + - - +
436C VAL* 3.2 26.1 + - - +
475C ILE* 4.0 26.9 - - + +
478C VAL* 5.3 1.3 - - + -
479C ALA* 4.6 7.0 - - + -
485C ILE* 4.6 5.4 - - + -
490C THR* 3.8 28.7 - - + -
38D GLU* 3.7 27.6 - - + +
40D TYR* 4.3 16.9 - - + -
41D ILE* 3.5 20.7 - - + +
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA* 3.5 19.4 - - + +
416C TYR* 3.6 46.0 - - + -
417C SER* 3.5 28.0 - - - +
429C GLU* 2.9 26.8 + - + +
430C PRO 3.9 2.9 - - - +
432C LEU* 1.3 76.2 - - + +
434C SER* 1.3 62.5 + - - +
436C VAL* 3.3 6.7 + - - +
437C ASN* 3.1 19.2 + - - +
471C ILE* 4.7 4.5 - - + -
475C ILE* 3.9 14.1 - - + -
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Residues in contact with SER 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C SER* 2.7 26.4 + - - -
430C PRO 2.8 17.1 + - - -
431C GLY 3.7 3.6 - - - -
433C VAL* 1.3 72.2 - - - +
435C ALA* 1.3 52.2 + - - +
437C ASN* 3.1 9.4 + - - +
438C LYS* 2.8 36.0 + - - +
45D GLY 4.6 1.3 - - - -
46D VAL* 4.0 2.0 - - - -
47D ASP* 2.8 40.4 + - - +
48D PHE* 3.3 11.7 - - - -
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Residues in contact with ALA 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C GLY 3.0 13.9 + - - +
432C LEU 3.3 7.4 - - - +
433C VAL 3.2 0.2 - - - -
434C SER* 1.3 73.3 - - - +
436C VAL* 1.3 66.3 + - - +
438C LYS* 3.0 14.4 + - - +
439C MSE 3.0 10.7 + - - +
40D TYR* 3.2 32.6 + - + -
41D ILE* 4.1 7.9 - - + -
44D ILE* 3.5 16.8 - - + +
45D GLY 3.6 15.0 + - - +
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Residues in contact with VAL 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 3.8 26.5 - - + -
409C LEU* 4.8 4.5 - - + -
413C ALA* 5.5 0.7 - - + -
432C LEU 3.2 13.1 + - - +
433C VAL 3.3 8.0 + - - +
435C ALA* 1.3 74.5 - - - +
437C ASN* 1.3 65.0 + - - +
439C MSE 3.1 13.6 + - - +
440C SER* 3.2 12.8 + - - -
471C ILE* 4.4 23.3 - - + -
474C PHE* 3.5 29.4 - - + -
475C ILE* 3.8 21.1 - - + -
40D TYR* 3.4 12.3 + - + +
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Residues in contact with ASN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C LEU* 5.0 5.1 - - - +
410C TRP* 3.8 26.7 - - - +
413C ALA* 4.0 26.9 - - + +
414C SER* 4.9 3.8 + - - -
433C VAL 3.1 12.7 + - - +
434C SER* 3.2 13.9 - - - +
436C VAL* 1.3 77.5 - - - +
438C LYS* 1.3 62.5 + - - +
439C MSE 3.3 0.2 + - - -
440C SER* 3.3 6.1 + - - -
441C ALA* 3.0 20.5 + - - +
47D ASP* 3.5 14.1 - - - +
67D THR* 3.9 8.8 - - - +
68D ALA* 3.1 20.9 + - - +
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Residues in contact with LYS 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C SER 2.8 14.9 + - - +
435C ALA 3.0 8.7 + - - +
437C ASN* 1.3 72.7 - - - +
439C MSE 1.3 53.5 + - - +
441C ALA* 3.1 5.0 + - - +
442C PHE* 2.7 33.8 + - - +
44D ILE* 3.1 32.6 - - + +
45D GLY* 3.1 22.4 - - - +
46D VAL 3.3 26.2 + - - +
47D ASP* 4.5 3.8 - - + +
68D ALA* 3.7 24.4 - - + +
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Residues in contact with MSE 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 3.3 52.5 - - + +
372C ALA* 4.1 14.8 - - + +
373C ASN* 3.5 40.6 - - - +
376C HIS* 4.7 11.9 - - + +
435C ALA 3.0 4.7 + - - +
436C VAL 3.1 9.2 + - - +
438C LYS* 1.3 77.5 - - - +
440C SER* 1.3 63.6 + - - +
442C PHE* 3.0 19.4 + - + +
443C PHE* 3.0 12.1 + - - +
474C PHE* 3.6 11.2 - - + -
40D TYR* 3.3 23.1 - - + +
44D ILE* 4.1 10.3 - - + -
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Residues in contact with SER 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C TYR* 2.5 34.7 + - - -
369C LEU* 5.0 2.0 - - - -
372C ALA* 5.5 0.2 - - - -
406C LEU* 3.3 16.3 + - - +
409C LEU* 4.1 21.5 - - - +
436C VAL 3.2 7.9 + - - -
437C ASN* 3.8 9.4 - - - -
439C MSE 1.3 81.0 - - - +
441C ALA* 1.3 61.8 + - - +
443C PHE* 3.0 15.0 + - - +
444C MSE 3.1 16.1 + - - +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C ASN* 3.0 14.0 + - - +
438C LYS* 3.3 9.9 - - + +
440C SER* 1.3 75.6 - - - +
442C PHE* 1.3 56.8 + - - +
444C MSE 3.4 10.6 + - - +
445C ASP* 2.9 39.0 + - - +
68D ALA* 4.1 7.0 - - + -
69D GLY* 3.7 34.1 - - - +
72D ARG* 5.5 0.4 + - - -
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Residues in contact with PHE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ALA* 5.2 2.5 - - + -
375C LEU* 3.9 14.6 - - + -
376C HIS* 3.5 53.8 - + + +
379C MSE 3.9 21.1 - - + -
384C LEU 5.4 1.6 - - - -
386C GLU* 3.3 44.0 - - + -
438C LYS 2.7 16.5 + - - +
439C MSE 3.1 16.2 - - + +
441C ALA* 1.3 71.9 - - - +
443C PHE* 1.3 65.1 + - - +
445C ASP* 3.1 8.2 + - - +
446C CYS* 3.0 44.3 + - - -
44D ILE* 4.7 3.6 - - + -
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Residues in contact with PHE 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C TRP* 3.0 74.3 + + - +
356C ALA* 3.8 28.0 - - + -
357C ASN* 3.9 22.9 - - + -
360C LEU* 3.7 21.3 - - + -
368C TYR* 3.4 25.6 - + + +
372C ALA* 4.6 7.4 - - + -
375C LEU* 4.8 5.6 - - + -
398C ILE* 3.7 17.9 - - + -
406C LEU* 4.2 7.6 - - + -
439C MSE 3.0 9.4 + - - +
440C SER 3.0 9.5 + - - +
442C PHE* 1.3 83.1 - - + +
444C MSE 1.3 63.1 + - - +
446C CYS* 3.5 6.1 + - - -
447C LYS 3.8 1.4 + - - -
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Residues in contact with MSE 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ILE* 4.3 12.1 - - + -
403C TYR* 3.3 36.1 - - + -
406C LEU* 3.6 28.5 - - + -
440C SER* 3.1 10.8 + - - +
441C ALA* 3.7 11.4 - - - +
443C PHE* 1.3 78.2 - - + +
445C ASP* 1.3 55.6 + - - +
447C LYS* 3.1 4.0 + - - +
448C LEU* 2.8 41.9 + - + +
454C ALA* 3.8 5.4 - - + -
69D GLY* 6.0 0.9 - - - -
72D ARG* 3.7 27.8 - - + +
73D PHE* 3.2 39.9 - - + -
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Residues in contact with ASP 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLU* 3.9 25.0 - - + +
390C ARG* 2.8 34.6 + - - +
441C ALA* 2.9 25.9 + - - +
442C PHE* 3.1 8.6 + - - +
444C MSE 1.3 72.9 - - - +
446C CYS* 1.3 64.8 + - - +
448C LEU 3.2 5.2 - - - +
71D GLU* 4.8 1.9 - - - +
72D ARG* 2.8 26.3 + - - +
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Residues in contact with CYS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C TRP* 3.7 14.4 - - + +
375C LEU* 4.1 8.1 - - - -
379C MSE 4.2 2.9 - - - -
386C GLU* 4.2 15.7 - - - -
389C LEU* 3.8 23.8 - - + -
390C ARG* 3.0 33.1 + - - +
393C LEU* 3.7 4.5 - - - +
442C PHE* 3.0 47.7 + - - -
443C PHE 3.6 11.0 - - - +
444C MSE 3.2 0.2 - - - -
445C ASP* 1.3 77.5 - - - +
447C LYS* 1.3 56.6 + - - +
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Residues in contact with LYS 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C TRP* 3.5 32.5 - - + +
390C ARG* 3.4 15.7 + - - +
393C LEU* 2.7 32.4 + - + +
394C SER* 4.1 8.1 + - - +
396C LYS 2.6 29.4 + - - +
397C THR* 4.3 13.6 - - - +
398C ILE* 4.5 12.8 - - + +
403C TYR* 5.0 1.3 - - - +
443C PHE 4.4 0.9 - - - +
444C MSE 3.1 6.7 + - - +
446C CYS* 1.3 81.4 - - - +
448C LEU* 1.3 76.5 + - + +
452C GLU* 5.1 0.2 - - - +
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Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ARG* 2.8 23.6 + - - -
398C ILE* 5.4 0.2 - - + -
403C TYR* 3.7 34.5 - - + +
444C MSE 2.8 24.3 + - + +
445C ASP 3.2 7.7 + - - +
447C LYS* 1.3 93.4 - - + +
449C SER* 1.3 60.7 + - - +
450C PRO 4.0 0.2 - - - -
452C GLU* 3.8 42.8 - - + +
453C ARG 4.6 7.4 - - - +
454C ALA 5.1 0.2 - - - +
72D ARG* 3.6 33.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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