Contacts of the helix formed by residues 409 - 433 (chain i) in PDB entry 5GAG
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 GLN 409 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403i ALA* 3.9 2.0 - - - -
408i MET* 1.3 85.9 + - + +
410i VAL* 1.3 67.3 + - - +
411i GLN* 3.0 26.9 + - + +
412i ASP* 3.3 34.2 + - - +
413i VAL* 3.3 17.5 + - - +
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Residues in contact with VAL 410 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A C 4.3 16.4 - - - +
486A C 4.1 13.5 - - - +
396i GLY 5.1 0.7 - - - +
399i LYS* 3.6 34.5 - - + +
400i ARG* 4.2 13.7 - - + +
403i ALA* 3.7 19.7 - - + -
408i MET 5.3 0.2 - - - +
409i GLN* 1.3 77.7 + - - +
411i GLN* 1.3 58.0 + - + +
412i ASP 3.5 0.2 - - - -
413i VAL* 3.7 4.1 - - - +
414i ASN* 3.0 30.5 + - - +
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Residues in contact with GLN 411 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A A 6.0 0.7 - - - -
484A C 2.7 57.8 + - - +
485A C 3.6 14.7 + - - +
409i GLN* 3.0 19.8 - - + +
410i VAL* 1.3 82.9 - - + +
412i ASP* 1.3 64.0 + - - +
414i ASN* 3.3 2.8 - - - +
415i ARG* 3.0 29.9 + - - +
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Residues in contact with ASP 412 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375i ARG* 5.8 5.2 - - + -
379i ILE* 4.8 11.2 - - + -
408i MET* 3.4 26.1 - - + +
409i GLN* 3.3 29.2 + - - +
411i GLN* 1.3 76.1 - - - +
413i VAL* 1.3 66.3 + - - +
415i ARG* 2.9 31.7 + - - +
416i LEU* 2.9 33.6 + - + +
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Residues in contact with VAL 413 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379i ILE* 3.7 32.6 - - + +
399i LYS* 4.1 16.6 - - + +
402i ILE* 3.7 30.3 - - + -
403i ALA* 4.1 15.9 - - + +
406i CYS* 5.0 0.2 - - - -
409i GLN 3.3 14.8 + - - +
410i VAL* 3.7 8.5 - - - +
412i ASP* 1.3 74.9 - - - +
414i ASN* 1.3 57.4 - - - +
416i LEU* 3.4 4.1 + - - +
417i LEU* 3.0 53.8 + - + +
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Residues in contact with ASN 414 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A C 2.4 35.3 + - - +
486A C 3.4 22.0 + - - -
399i LYS* 3.2 36.8 + - - +
410i VAL* 3.0 19.9 + - - +
411i GLN 3.3 9.9 - - - +
412i ASP 3.2 0.2 - - - -
413i VAL* 1.3 75.5 - - - +
415i ARG* 1.3 57.8 + - - +
416i LEU 3.2 0.3 + - - -
417i LEU* 3.2 7.9 + - - +
418i LYS* 3.0 27.1 + - - +
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Residues in contact with ARG 415 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372i VAL* 5.2 10.3 - - - +
375i ARG* 3.4 27.9 - - - +
411i GLN 3.0 16.5 + - - +
412i ASP* 2.9 45.1 + - - +
414i ASN* 1.3 74.2 - - - +
416i LEU* 1.3 65.0 + - + +
418i LYS* 3.5 12.8 - - + +
419i GLN* 3.0 49.3 + - - +
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Residues in contact with LEU 416 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331i LEU* 6.0 0.3 - - - +
334i PHE* 5.1 3.3 - - - -
372i VAL* 5.2 5.6 - - + +
375i ARG* 4.4 4.7 - - + +
376i MET* 3.5 39.0 - - + +
379i ILE* 3.6 49.1 - - + -
412i ASP* 2.9 23.2 + - + +
413i VAL 3.7 3.6 - - - +
415i ARG* 1.3 84.0 - - + +
417i LEU* 1.3 61.4 + - + +
418i LYS 3.1 1.3 - - - -
419i GLN* 3.2 23.1 + - - +
420i PHE* 2.9 29.8 + - - +
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Residues in contact with LEU 417 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331i LEU* 4.0 14.1 - - + -
379i ILE* 6.2 0.7 - - + -
383i MET* 3.8 15.3 - - + -
391i PRO* 4.9 4.5 - - + +
394i ILE* 3.6 34.5 - - + -
399i LYS* 3.5 35.0 - - + +
413i VAL* 3.0 36.2 + - + +
414i ASN* 3.7 4.3 - - - +
416i LEU* 1.3 77.2 - - + +
418i LYS* 1.3 57.0 + - - +
420i PHE* 3.9 8.4 - - + +
421i ASP* 3.0 30.3 + - - +
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Residues in contact with LYS 418 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A C 3.7 26.9 + - + +
414i ASN 3.0 16.0 + - - +
415i ARG* 3.5 15.0 - - + +
416i LEU 3.1 0.4 - - - -
417i LEU* 1.3 75.2 - - - +
419i GLN* 1.3 66.3 + - + +
421i ASP* 3.1 9.5 + - - +
422i ASP* 3.0 47.9 + - - +
44k VAL* 4.2 19.9 - - - +
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Residues in contact with GLN 419 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334i PHE* 4.8 1.1 - - - -
372i VAL* 5.5 2.9 - - - +
376i MET* 3.4 12.8 - - + +
415i ARG* 3.0 47.6 + - - +
416i LEU* 3.2 27.1 + - - +
418i LYS* 1.3 76.3 - - + +
420i PHE* 1.3 60.6 + - - +
422i ASP* 3.4 8.1 + - - +
423i MET* 3.0 37.0 + - + +
41k LEU* 3.7 34.9 + - + +
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Residues in contact with PHE 420 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329i PHE* 3.6 28.3 - + - -
330i ASP 3.7 22.7 - - - -
331i LEU* 4.0 15.9 - - + -
334i PHE* 3.9 38.8 - + + -
391i PRO* 3.3 40.4 - - + -
416i LEU 2.9 18.1 + - - +
417i LEU* 4.0 10.5 - - + +
419i GLN* 1.3 77.2 - - - +
421i ASP* 1.3 62.8 + - + +
423i MET 4.6 0.2 - - - +
424i GLN* 2.9 56.2 + - + +
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Residues in contact with ASP 421 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A C 3.4 46.9 + - + +
417i LEU 3.0 17.2 + - - +
418i LYS* 3.1 17.2 + - - +
420i PHE* 1.3 82.8 - - - +
422i ASP* 1.3 54.7 + - - +
424i GLN* 3.6 15.4 - - - +
425i ARG* 2.9 22.5 + - - +
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Residues in contact with ASP 422 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A C 2.6 31.3 + - - +
418i LYS* 3.0 42.3 + - - +
419i GLN* 3.9 6.6 - - - +
420i PHE 3.4 0.2 - - - -
421i ASP* 1.3 75.7 - - - +
423i MET* 1.3 78.0 + - + +
425i ARG* 3.2 13.9 + - - +
426i MET* 2.9 30.7 + - - +
40k LEU* 5.9 2.9 - - + -
44k VAL* 4.3 14.5 - - + +
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Residues in contact with MET 423 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329i PHE* 3.8 4.4 - - + -
334i PHE* 4.2 18.6 - - + -
419i GLN* 3.0 22.3 + - + +
420i PHE 4.3 0.9 - - - +
422i ASP* 1.3 91.0 - - + +
424i GLN* 1.3 60.8 + - - +
426i MET* 3.7 10.7 - - - -
427i MET* 2.9 36.7 + - - +
36k LEU 4.1 13.2 - - - +
37k LEU* 3.6 36.8 - - + +
40k LEU* 3.6 40.8 - - + +
41k LEU* 4.1 16.2 - - + +
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Residues in contact with GLN 424 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329i PHE* 3.5 37.0 + - + -
391i PRO* 4.5 8.6 - - - +
392i GLU* 5.5 3.0 + - - -
420i PHE* 2.9 40.2 + - + +
421i ASP* 3.6 18.5 - - - +
423i MET* 1.3 74.7 - - - +
425i ARG* 1.3 66.5 + - - +
427i MET 3.4 0.7 + - - -
428i LYS* 2.9 50.3 + - + +
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Residues in contact with ARG 425 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A C 3.1 59.0 + - + +
1319A C 4.2 19.8 + - - -
421i ASP 2.9 14.7 + - - +
422i ASP* 3.2 17.2 + - - +
424i GLN* 1.3 75.9 + - - +
426i MET* 1.3 60.6 + - + +
428i LYS* 3.3 7.6 + - - +
429i LYS* 3.0 55.4 + - - +
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Residues in contact with MET 426 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422i ASP 2.9 17.7 + - - +
423i MET* 4.0 13.7 - - - +
424i GLN 3.2 0.2 - - - -
425i ARG* 1.3 78.8 - - + +
427i MET* 1.3 70.1 + - + +
429i LYS* 3.4 23.5 + - + +
430i MET* 2.9 27.5 + - - +
36k LEU* 4.6 28.0 - - + -
40k LEU* 3.7 29.2 - - + -
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Residues in contact with MET 427 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329i PHE* 4.3 34.1 - - + -
337i GLN* 4.5 9.6 - - - +
423i MET* 2.9 22.4 + - - +
424i GLN 4.1 2.2 - - - +
426i MET* 1.3 84.4 - - + +
428i LYS* 1.3 64.1 + - - +
430i MET* 3.7 33.3 - - + +
431i LYS* 3.0 26.3 + - - +
29k GLN* 4.6 9.0 - - - -
32k LEU 4.9 0.4 - - - +
33k ALA* 4.3 12.1 - - - +
36k LEU* 5.4 2.9 - - + -
37k LEU* 3.8 32.3 - - + -
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Residues in contact with LYS 428 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1283A G 5.2 9.0 - - - +
328i GLY* 3.7 8.1 - - - -
329i PHE* 2.9 51.5 + - - +
424i GLN* 2.9 43.0 + - + +
425i ARG* 3.5 7.9 - - - +
426i MET 3.3 0.2 - - - -
427i MET* 1.3 80.6 - - - +
429i LYS* 1.3 58.2 + - + +
430i MET 3.4 0.2 - - - -
431i LYS* 3.6 8.4 - - + +
432i LYS* 3.0 30.3 + - - +
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Residues in contact with LYS 429 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1317A G 4.1 2.9 + - - +
1318A U 3.0 50.3 + - - +
1319A C 5.6 1.0 + - - -
425i ARG* 3.0 42.8 + - - +
426i MET* 3.8 25.0 - - + +
427i MET 3.3 0.2 - - - -
428i LYS* 1.3 78.1 - - + +
430i MET* 1.3 59.1 + - - +
432i LYS* 4.3 4.9 - - - +
433i GLY* 3.6 18.9 + - - +
434i GLY 4.9 1.0 - - - +
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Residues in contact with MET 430 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426i MET* 2.9 15.0 + - + +
427i MET* 3.7 35.2 + - + +
429i LYS* 1.3 73.3 - - - +
431i LYS* 1.3 61.2 + - - +
433i GLY 2.8 19.4 - - - +
434i GLY* 4.5 9.0 - - - +
29k GLN* 3.3 39.7 - - - +
32k LEU* 3.9 28.7 - - + +
36k LEU* 3.8 24.2 - - + -
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Residues in contact with LYS 431 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535A A 5.5 0.2 - - - +
1536A C 4.4 11.1 + - - -
427i MET 3.0 20.9 + - - +
428i LYS* 3.6 12.3 - - + +
429i LYS 3.4 0.2 - - - -
430i MET* 1.3 76.9 - - - +
432i LYS* 1.3 65.0 + - - +
433i GLY 4.2 0.9 - - - +
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Residues in contact with LYS 432 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1317A G 5.2 10.0 + - - -
1318A U 5.0 9.7 + - - -
1536A C 4.2 10.7 + - - -
428i LYS 3.0 20.1 + - - +
429i LYS* 5.0 2.9 - - - -
431i LYS* 1.3 75.9 - - - +
433i GLY* 1.3 62.0 + - - +
434i GLY 4.2 0.2 + - - -
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Residues in contact with GLY 433 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536A C 5.8 0.7 - - - -
429i LYS 3.6 11.9 + - - +
430i MET 2.8 25.1 - - - +
431i LYS 4.1 1.2 - - - +
432i LYS* 1.3 83.1 - - - +
434i GLY* 1.3 67.4 + - - +
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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