Contacts of the helix formed by residues 570 - 590 (chain A) in PDB entry 3SJE
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 PHE 570 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.6 21.9 - - + +
70A ILE* 4.3 2.2 - - + -
71A LYS* 3.3 58.1 - - + -
74A LEU* 3.8 31.6 - - + -
559A TYR* 4.3 7.4 - + - -
562A VAL* 4.1 9.9 - - + -
563A GLU* 4.3 11.9 - - + -
567A ASP* 2.9 32.3 + - - -
568A PRO 3.7 10.3 - - - -
569A MET* 1.3 79.4 - - - +
571A LYS* 1.3 59.2 + - - +
573A HIS* 3.6 32.2 + + + +
574A LEU* 3.0 28.1 + - - +
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Residues in contact with LYS 571 (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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67A ALA* 5.0 1.8 - - - -
484A PRO* 2.8 37.5 + - + +
485A ASP 4.7 0.2 - - - -
486A GLU* 4.4 18.6 + - - +
567A ASP* 3.1 9.1 + - - +
569A MET* 3.1 21.1 - - + -
570A PHE* 1.3 78.0 - - - +
572A TYR* 1.3 91.4 + - + +
574A LEU* 3.5 8.7 + - + +
575A THR* 3.0 31.5 + - - -
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Residues in contact with TYR 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ILE* 4.1 16.2 - - + -
458A GLY 5.3 0.2 - - - -
459A ASN* 3.6 39.2 + - + +
484A PRO* 3.7 25.5 + - + -
485A ASP* 3.9 10.0 - - - -
486A GLU* 4.9 2.4 + - - +
537A TYR* 3.5 38.0 - + + -
566A TYR 3.9 7.9 - - - -
567A ASP* 3.1 30.2 + - + +
568A PRO* 6.1 1.1 - - + -
571A LYS* 1.3 98.7 + - - +
573A HIS* 1.3 65.9 + - - +
575A THR* 3.3 4.7 + - - -
576A VAL* 2.9 29.3 + - - +
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Residues in contact with HIS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.8 28.3 - - + -
74A LEU* 4.7 1.2 - - + +
390A SER* 3.1 44.8 - - - -
393A ALA* 5.6 0.4 - - + -
394A VAL* 3.7 7.0 - - + +
455A SER* 3.9 9.0 - - - -
456A ILE* 3.8 20.9 - - + +
562A VAL* 3.6 29.7 - - + +
567A ASP* 2.7 31.3 + - + -
570A PHE* 3.6 22.2 - + + +
571A LYS 3.4 0.2 - - - -
572A TYR* 1.3 73.0 - - - +
574A LEU* 1.3 57.8 + - - +
576A VAL* 3.3 5.3 + - - -
577A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.7 42.4 - - + +
66A LYS* 4.1 1.8 - - - +
67A ALA* 4.1 26.9 - - + +
70A ILE* 3.9 9.3 - - + +
570A PHE 3.0 18.1 + - - +
571A LYS* 3.8 8.7 - - + +
573A HIS* 1.3 76.1 - - - +
575A THR* 1.3 57.4 + - - +
577A ALA* 3.1 3.6 + - + +
578A GLN* 2.9 53.5 + - + +
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Residues in contact with THR 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 5.2 0.9 - - + -
481A LEU* 5.6 0.4 - - + -
482A LYS 4.3 7.1 + - - +
484A PRO* 3.3 24.0 - - + +
493A LEU* 3.6 33.7 - - + -
537A TYR* 3.9 21.5 - - + -
571A LYS 3.0 18.1 + - - -
572A TYR* 3.3 5.1 + - - -
574A LEU* 1.3 74.5 - - - +
576A VAL* 1.3 62.6 + - - +
578A GLN* 3.2 15.5 + - - +
579A VAL* 3.0 23.7 + - + +
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Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 4.9 0.4 - - + -
455A SER* 3.5 33.0 - - - +
462A LEU* 4.6 4.7 - - + -
535A ALA* 3.7 10.5 - - + +
536A ARG* 4.0 2.9 - - - -
537A TYR* 3.7 26.0 - - + +
572A TYR 2.9 17.3 + - - +
573A HIS 3.3 4.0 + - - +
575A THR* 1.3 76.6 - - - +
577A ALA* 1.3 56.0 + - - +
579A VAL* 3.3 5.4 + - - +
580A ARG* 2.9 66.2 + - + +
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Residues in contact with ALA 577 (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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65A LEU* 3.9 21.0 - - + +
70A ILE* 4.0 16.6 - - + -
394A VAL* 3.6 25.3 - - + +
397A GLU* 5.6 0.2 - - + -
398A ILE* 3.7 9.7 - - + +
573A HIS 2.9 13.9 + - - +
574A LEU* 3.4 9.2 - - + +
576A VAL* 1.3 76.0 - - - +
578A GLN* 1.3 57.4 + - - +
581A GLY* 2.8 29.3 + - - -
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Residues in contact with GLN 578 (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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62A LEU* 3.6 27.5 + - + +
65A LEU* 3.9 16.6 + - + -
477A LEU* 4.0 3.3 - - - +
481A LEU* 3.7 35.9 - - + +
482A LYS* 4.8 7.8 + - - +
574A LEU* 2.9 42.6 + - + +
575A THR* 3.2 15.2 + - - +
577A ALA* 1.3 76.6 - - - +
579A VAL* 1.3 57.3 + - - +
582A GLY* 2.8 27.2 + - - -
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Residues in contact with VAL 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 4.4 17.5 - - + -
464A VAL* 5.2 2.7 - - + -
474A VAL* 5.7 2.0 - - + -
477A LEU* 3.4 10.0 - - + +
478A THR* 4.5 7.2 - - + -
481A LEU* 3.6 7.4 - - + -
493A LEU* 3.5 29.8 - - + -
535A ALA* 3.7 27.6 - - + -
575A THR 3.0 21.2 + - - +
576A VAL* 3.8 5.8 - - - +
578A GLN* 1.3 73.7 - - - +
580A ARG* 1.3 65.8 + - - +
583A MET* 3.0 43.4 + - + +
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Residues in contact with ARG 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.6 2.9 - - + -
391A GLY* 3.7 5.7 - - - -
394A VAL* 4.1 11.5 - - - +
398A ILE* 4.1 9.9 - - + -
450A ILE* 4.3 16.6 - - + +
451A ASN 3.8 16.3 + - - +
452A ALA* 3.5 23.5 - - - +
453A ASP 2.9 29.2 + - - -
454A SER 3.1 15.6 + - - -
455A SER* 3.2 18.2 + - - +
535A ALA* 2.8 37.1 + - + +
576A VAL* 2.9 33.7 + - + +
579A VAL* 1.3 72.6 - - - +
581A GLY* 1.3 64.1 + - - +
583A MET* 3.3 6.5 + - - +
584A VAL* 3.0 28.9 + - - +
1754A CL 3.8 10.7 - - - +
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Residues in contact with GLY 581 (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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61A PHE* 3.5 26.7 - - - -
398A ILE* 3.6 15.1 - - - +
402A PHE* 4.1 0.3 - - - -
577A ALA 2.8 17.4 + - - -
580A ARG* 1.3 79.1 - - - +
582A GLY* 1.3 54.7 + - - +
584A VAL* 3.3 5.9 + - - +
585A PHE* 2.8 30.3 + - - +
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Residues in contact with GLY 582 (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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58A MET* 3.7 18.5 - - - +
61A PHE* 3.9 1.8 - - - -
62A LEU* 4.3 4.7 - - - -
477A LEU* 3.7 11.9 - - - -
578A GLN 2.8 21.7 + - - -
581A GLY* 1.3 74.3 - - - +
583A MET* 1.3 63.9 + - - +
585A PHE* 3.4 3.2 + - - +
586A GLU* 3.0 29.8 + - - +
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Residues in contact with MET 583 (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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450A ILE* 3.9 20.9 - - + -
464A VAL* 5.6 2.9 - - + -
466A CYS* 5.3 1.6 - - + -
470A MET* 3.7 29.8 - - + -
473A LEU* 4.3 23.1 - - + +
474A VAL* 3.6 32.1 - - + -
477A LEU* 3.8 13.5 - - + -
533A GLY* 5.1 5.4 - - - -
534A ARG 5.7 3.1 - - - +
535A ALA* 5.2 6.5 - - - -
579A VAL* 3.0 34.9 + - - +
580A ARG* 3.7 6.7 - - - +
581A GLY 3.3 0.2 - - - -
582A GLY* 1.3 74.6 - - - +
584A VAL* 1.3 59.7 + - - +
586A GLU* 3.3 2.3 + - - +
587A LEU* 2.9 36.4 + - - +
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Residues in contact with VAL 584 (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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372A VAL* 4.1 16.9 - - + +
374A LEU* 4.0 28.5 - - + -
402A PHE* 3.8 20.0 - - + -
416A ILE* 3.8 31.2 - - + -
418A PHE* 5.1 0.7 - - + -
450A ILE* 3.9 21.5 - - + -
580A ARG 3.0 18.5 + - - +
581A GLY* 3.6 7.6 - - - +
583A MET* 1.3 75.9 - - - +
585A PHE* 1.3 57.5 + - - +
587A LEU* 3.3 2.8 + - - +
588A ALA* 2.8 29.1 + - - +
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Residues in contact with PHE 585 (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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56A HIS 4.8 0.4 - - - -
57A ASN* 3.5 32.3 - - - -
58A MET* 3.6 37.2 - - + -
61A PHE* 3.7 20.9 - - + -
402A PHE* 3.7 25.6 - + + -
405A LEU* 4.2 4.0 - - + -
410A TRP* 3.6 27.4 - + - -
581A GLY 2.8 20.8 + - - +
582A GLY* 3.7 4.9 - - - +
583A MET 3.3 0.4 - - - -
584A VAL* 1.3 73.1 - - - +
586A GLU* 1.3 64.6 + - - +
588A ALA* 3.2 0.9 + - - -
589A ASN* 2.9 58.8 + - + +
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Residues in contact with GLU 586 (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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58A MET* 2.9 37.3 - - + +
473A LEU* 3.6 31.7 - - + +
477A LEU* 5.7 2.5 - - + -
582A GLY 3.0 12.6 + - - +
583A MET 3.8 0.7 - - - +
585A PHE* 1.3 81.6 - - - +
587A LEU* 1.3 67.3 + - - +
589A ASN* 5.6 0.7 - - - +
590A SER* 3.0 46.9 + - - +
594A PRO* 4.0 8.1 - - + +
1D NAG 5.6 5.0 - - - +
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Residues in contact with LEU 587 (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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372A VAL* 3.7 19.5 - - + +
414A ARG* 2.9 28.6 + - - -
447A VAL* 4.5 4.3 - - + -
448A ALA* 3.8 24.5 - - + -
450A ILE* 3.9 24.0 - - + -
470A MET* 4.6 2.7 - - + -
473A LEU* 4.0 15.3 - - + -
583A MET 2.9 28.0 + - - +
584A VAL 3.8 3.6 - - - +
586A GLU* 1.3 75.9 - - - +
588A ALA* 1.3 58.1 + - - +
593A LEU* 3.7 5.7 - - - +
594A PRO* 3.8 19.3 - - + -
595A PHE* 3.6 32.8 - - + -
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Residues in contact with ALA 588 (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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372A VAL* 3.8 13.0 - - + -
412A PRO* 4.1 0.4 - - + -
413A ARG* 3.3 5.4 + - - +
414A ARG* 2.8 41.2 + - - +
416A ILE* 3.6 34.8 - - + -
584A VAL 2.8 17.9 + - - +
585A PHE 3.2 2.0 + - - +
587A LEU* 1.3 76.8 - - - +
589A ASN* 1.3 65.0 + - - +
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Residues in contact with ASN 589 (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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402A PHE* 5.0 0.6 - - - -
410A TRP* 3.2 33.0 + - - -
411A ARG 4.1 0.7 - - - +
412A PRO* 3.1 13.1 - - - +
413A ARG* 3.0 36.7 + - - +
414A ARG* 4.1 0.7 - - - -
585A PHE* 2.9 46.8 + - + +
586A GLU* 5.1 0.9 - - - +
588A ALA* 1.3 85.2 - - - +
590A SER* 1.3 68.6 + - - +
591A ILE* 3.4 7.8 + - - +
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Residues in contact with SER 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 3.8 0.7 - - - -
414A ARG* 2.7 28.7 + - - +
586A GLU* 3.0 36.5 + - - +
589A ASN* 1.3 77.9 - - - +
591A ILE* 1.3 65.9 + - - +
592A VAL* 2.6 26.7 + - - +
594A PRO* 4.2 11.0 - - - +
1D NAG 5.9 2.3 - - - +
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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