Contacts of the helix formed by residues 526 - 551 (chain A) in PDB entry 3QJQ
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 ARG 526 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A LEU 3.8 9.6 - - - +
523A ALA* 3.2 23.3 - - - +
524A MET 2.9 3.2 + - - -
525A ASP* 1.3 74.9 - - - +
527A ILE* 1.3 63.2 + - - +
528A GLY 3.3 2.7 - - - -
529A PHE* 3.3 42.0 + - + +
530A TRP* 2.9 29.3 + - + +
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Residues in contact with ILE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TRP* 3.5 35.4 - - + +
179A THR* 4.1 1.6 - - - +
184A TYR* 3.8 29.6 - - + +
187A VAL* 3.9 15.5 - - + -
188A VAL* 4.7 9.9 - - + -
191A LEU* 3.7 29.4 - - + -
270A LEU* 6.4 0.4 - - + -
273A LEU* 5.0 6.0 - - + +
524A MET 4.1 1.1 - - - +
525A ASP* 3.2 31.3 + - - +
526A ARG* 1.3 73.8 - - - +
528A GLY* 1.3 56.3 + - - +
530A TRP* 4.3 5.1 - - + +
531A PHE* 2.9 28.8 + - - +
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Residues in contact with GLY 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TRP* 5.7 1.2 - - - -
526A ARG 3.3 0.4 - - - -
527A ILE* 1.3 77.9 - - - +
529A PHE* 1.3 55.9 + - - +
531A PHE* 3.3 8.2 + - - +
532A ALA* 2.9 30.2 + - - +
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Residues in contact with PHE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ARG* 3.3 47.7 + - + +
528A GLY* 1.3 74.3 - - - +
530A TRP* 1.3 106.5 + + - +
532A ALA* 3.3 8.5 + - + +
533A VAL* 2.9 44.8 + - + +
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Residues in contact with TRP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.7 35.4 - - + -
273A LEU* 4.4 6.1 - - + -
274A LEU* 3.7 35.7 - - + +
523A ALA* 3.0 33.6 + - + -
524A MET* 3.7 15.6 - - + +
526A ARG* 2.9 30.5 + - + +
527A ILE* 4.3 3.8 - - + +
529A PHE* 1.3 100.8 - + - +
531A PHE* 1.3 61.6 + - - +
533A VAL* 3.6 11.1 - - + +
534A ALA* 3.0 28.8 + - - +
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Residues in contact with PHE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 3.5 60.1 - - + -
194A PHE* 4.4 20.4 - + - -
195A LEU* 4.5 18.8 - - + -
273A LEU* 4.4 13.1 - - + +
527A ILE 2.9 21.3 + - - +
528A GLY* 3.6 6.5 - - - +
530A TRP* 1.3 75.2 - - - +
532A ALA* 1.3 60.0 + - - +
534A ALA* 3.3 7.3 + - + +
535A ALA* 2.9 32.7 + - + +
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Residues in contact with ALA 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLY 2.9 14.7 + - - +
529A PHE* 3.5 12.3 - - + +
531A PHE* 1.3 77.3 - - + +
533A VAL* 1.3 65.5 + - - +
535A ALA* 3.2 7.8 + - - +
536A ILE* 2.9 37.6 + - + +
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Residues in contact with VAL 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.5 13.0 - - + -
529A PHE* 2.9 49.5 + - + +
530A TRP* 3.6 16.4 - - + +
531A PHE 3.4 0.2 - - - -
532A ALA* 1.3 71.9 - - - +
534A ALA* 1.3 54.8 + - - +
536A ILE* 3.0 12.8 + - + +
537A LEU* 2.7 52.9 + - + +
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Residues in contact with ALA 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.8 13.7 - - + -
273A LEU* 3.7 30.3 - - + +
274A LEU* 4.6 4.2 - - - +
530A TRP 3.0 14.5 + - - +
531A PHE* 3.3 13.2 - - + +
532A ALA 3.3 0.2 - - - -
533A VAL* 1.3 77.3 - - - +
535A ALA* 1.3 64.0 + - - +
537A LEU* 3.3 13.6 + - - +
538A VAL* 3.2 24.8 + - - +
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Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.8 22.6 - - + +
531A PHE* 2.9 25.9 + - + +
532A ALA* 3.2 10.1 + - - +
534A ALA* 1.3 71.1 - - - +
536A ILE* 1.3 65.7 + - + +
538A VAL* 3.1 7.8 + - - +
539A VAL* 3.1 24.1 + - + +
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Residues in contact with ILE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A ALA* 2.9 31.4 + - + +
533A VAL* 3.4 10.8 - - + +
535A ALA* 1.3 78.0 - - + +
537A LEU* 1.3 64.4 + - + +
539A VAL* 2.9 11.4 + - + +
540A LEU* 2.9 35.0 + - + +
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 4.0 27.8 - - + +
275A LEU* 5.6 6.3 - - + -
278A PRO* 4.7 18.8 - - + -
301A LEU* 5.1 15.9 - - + -
533A VAL* 2.7 38.5 + - + +
534A ALA* 3.3 12.1 - - - +
536A ILE* 1.3 72.8 - - + +
538A VAL* 1.3 59.2 + - + +
540A LEU* 3.2 19.0 + - + +
541A ALA* 2.9 28.1 + - - +
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.8 25.4 - - + -
230A TRP* 4.0 38.1 - - + -
274A LEU 6.1 0.4 - - - +
277A THR* 3.9 22.0 - - + -
278A PRO* 4.6 14.8 - - + -
534A ALA 3.3 13.0 - - - +
535A ALA 3.1 8.5 + - - +
537A LEU* 1.3 72.3 - - - +
539A VAL* 1.3 67.6 + - + +
541A ALA* 3.1 1.4 + - - +
542A TYR* 3.0 33.2 + - + +
543A GLY 3.8 0.2 + - - -
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ALA* 3.1 15.2 + - + +
536A ILE* 2.9 12.0 + - + +
538A VAL* 1.3 76.4 - - + +
540A LEU* 1.3 59.3 + - - +
543A GLY* 2.7 41.9 + - - +
544A PRO* 3.8 0.9 - - - +
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TRP* 3.3 16.1 - - + -
536A ILE* 2.9 28.4 + - + +
537A LEU* 3.3 21.1 - - + +
539A VAL* 1.3 76.2 - - - +
541A ALA* 1.3 57.6 + - - +
544A PRO* 2.9 27.1 - - - +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PRO* 3.7 24.0 - - + +
281A PHE* 4.4 0.5 - - - -
294A TRP* 3.7 26.3 - - + -
297A ILE* 5.6 2.0 - - + -
298A HIS* 3.6 29.7 - - + +
301A LEU* 5.0 6.5 - - + -
537A LEU 2.9 15.6 + - - +
538A VAL 3.1 1.3 + - - +
540A LEU* 1.3 78.6 - - - +
542A TYR* 1.3 61.2 + - + +
544A PRO* 4.2 2.4 - - - +
545A THR* 4.4 6.4 + - - -
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Residues in contact with TYR 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 4.3 18.2 - - + -
229A TRP* 3.9 0.5 - - - +
230A TRP* 3.3 51.3 + + + -
277A THR* 3.5 20.9 - - + -
278A PRO* 4.1 10.1 - - + -
280A GLY* 2.9 33.1 + - - -
281A PHE* 3.5 31.4 - + - -
284A GLN* 5.0 0.2 - - - -
298A HIS* 3.9 8.3 - - - -
538A VAL* 3.0 21.8 + - + +
541A ALA* 1.3 75.9 - - - +
543A GLY* 1.3 58.0 + - - +
544A PRO 3.6 0.7 - - - -
545A THR* 3.5 3.7 + - - -
546A LEU* 2.9 54.9 + - + +
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Residues in contact with GLY 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL 3.8 0.2 + - - -
539A VAL* 2.7 37.3 + - - +
542A TYR* 1.3 71.9 - - - +
544A PRO* 1.3 65.5 - - - +
546A LEU* 3.9 5.3 - - - +
547A VAL* 3.0 36.2 + - - +
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Residues in contact with PRO 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TRP* 3.4 35.9 - - + +
539A VAL 3.8 1.3 - - - +
540A LEU* 2.9 26.7 - - - +
541A ALA 4.2 1.3 - - - +
542A TYR 3.9 0.7 - - - -
543A GLY* 1.3 81.5 - - - +
545A THR* 1.3 62.6 + - - +
547A VAL* 4.2 3.6 - - + +
548A GLN* 3.2 24.3 + - - +
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Residues in contact with THR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 4.8 5.2 - - + -
281A PHE* 3.5 41.2 - - + -
289A GLY 5.4 0.7 - - - +
290A ILE* 4.5 16.7 - - + +
291A ASP 5.7 1.0 + - - -
294A TRP* 4.1 18.1 - - - +
541A ALA 4.4 1.8 + - - -
542A TYR* 3.5 6.4 + - - -
543A GLY 3.3 0.4 - - - -
544A PRO* 1.3 79.1 - - - +
546A LEU* 1.3 62.5 + - + +
548A GLN* 3.3 13.3 + - - +
549A LEU* 3.1 43.9 + - + +
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 6.4 0.4 - - + -
223A VAL* 5.8 2.7 - - + +
226A THR* 4.6 20.4 - - + -
227A LEU* 4.1 25.8 - - + +
230A TRP* 3.7 28.9 - - + -
542A TYR* 2.9 40.2 + - + +
543A GLY* 3.9 4.9 - - - +
545A THR* 1.3 71.3 - - - +
547A VAL* 1.3 61.6 + - + +
549A LEU* 3.1 8.0 + - + +
550A PHE* 2.9 51.8 + - + -
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A GLY* 3.0 22.4 + - - +
544A PRO* 4.2 4.5 - - + +
546A LEU* 1.3 77.9 - - + +
548A GLN* 1.3 61.8 + - - +
550A PHE* 3.5 6.0 + - - +
551A GLY* 3.4 18.0 + - - -
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Residues in contact with GLN 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A GLY 4.8 5.4 - - - +
290A ILE* 6.0 0.3 - - - -
291A ASP* 5.8 2.0 + - - -
544A PRO 3.2 17.7 + - - +
545A THR* 3.3 12.1 - - - +
547A VAL* 1.3 79.1 - - - +
549A LEU* 1.3 74.0 + - - +
551A GLY 3.7 0.2 + - - -
552A HIS* 3.0 37.4 + - + +
48B GLY 5.3 5.1 + - - +
50B LEU* 4.3 15.6 - - + +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 4.2 16.6 - - + -
223A VAL* 3.9 29.7 - - + +
226A THR* 4.2 22.2 - - + +
289A GLY 4.3 7.2 - - - +
290A ILE* 5.6 1.1 - - + -
545A THR* 3.1 30.8 + - + +
546A LEU* 3.7 9.6 - - + +
548A GLN* 1.3 81.4 - - - +
550A PHE* 1.3 57.1 + - + +
552A HIS 2.8 34.4 + - - +
553A LEU* 3.4 4.5 + - - +
50B LEU* 3.8 35.7 - - + -
52B ARG* 4.9 4.0 - - - +
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Residues in contact with PHE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 6.0 3.4 - - + -
206A LEU* 4.3 18.6 - - + -
207A PHE* 3.8 35.7 - + - -
223A VAL* 4.9 8.7 - - + -
227A LEU* 4.6 14.1 - - + -
546A LEU* 2.9 46.9 + - + +
547A VAL* 4.0 6.3 - - - +
549A LEU* 1.3 80.2 - - + +
551A GLY* 1.3 58.8 + - - +
552A HIS 3.5 0.3 + - - -
553A LEU* 3.7 34.2 - - + +
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Residues in contact with GLY 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A VAL 3.4 11.8 + - - -
548A GLN 3.7 0.6 + - - -
549A LEU 3.2 1.0 - - - -
550A PHE* 1.3 77.3 - - - +
552A HIS* 1.3 76.8 + - - +
553A LEU 3.7 1.4 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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