Contacts of the helix formed by residues 583 - 601 (chain A) in PDB entry 1OY6
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 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581A GLY 5.1 3.1 - - - +
582A ALA* 1.3 77.0 - - - +
584A GLN* 1.3 64.0 + - - +
585A GLU* 3.2 11.7 - - - +
586A ARG* 3.8 24.8 + - - +
587A THR* 3.3 14.9 + - - +
622A GLN* 3.1 32.0 - - - +
781A MET* 6.5 0.9 - - + -
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Residues in contact with GLN 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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275A TYR* 3.1 19.9 + - - +
276A ASP* 2.9 29.3 + - - +
278A ILE* 4.1 25.2 - - + +
583A THR* 1.3 74.2 - - - +
585A GLU* 1.3 59.5 + - - +
586A ARG 3.5 0.2 - - - -
587A THR* 3.8 7.0 - - - -
588A GLN* 3.2 15.0 + - + +
613A ASN* 2.9 35.2 + - - +
622A GLN* 3.2 25.5 - - + +
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Residues in contact with GLU 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A THR* 3.2 8.4 - - - +
584A GLN* 1.3 78.5 - - - +
586A ARG* 1.3 65.7 + - - +
588A GLN* 3.6 4.9 + - - +
589A LYS* 3.5 17.5 + - - +
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Residues in contact with ARG 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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578A LEU* 3.8 23.3 - - + -
579A PRO* 4.0 18.3 - - - +
580A ALA 4.8 3.4 + - - -
581A GLY 4.6 6.3 + - - -
582A ALA* 3.5 30.2 - - + +
583A THR* 3.6 23.9 + - - +
584A GLN 3.5 0.2 - - - -
585A GLU* 1.3 80.9 + - - +
587A THR* 1.3 61.3 + - - +
589A LYS* 3.3 24.1 + - + +
590A VAL* 3.6 9.2 + - + +
660A ASP* 5.5 4.7 - - - +
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Residues in contact with THR 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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576A VAL* 4.3 3.5 - - - +
578A LEU* 3.3 31.2 - - - +
583A THR 3.3 8.8 + - - +
584A GLN* 3.5 2.7 - - - +
586A ARG* 1.3 77.0 - - - +
588A GLN* 1.3 65.7 - - - +
590A VAL* 3.3 4.1 + - - +
591A LEU* 3.2 28.8 + - - +
613A ASN* 3.1 34.3 - - - +
622A GLN 3.2 24.7 - - - +
623A ASN 3.5 6.8 + - - -
624A THR 3.6 7.0 + - - +
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Residues in contact with GLN 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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278A ILE* 3.5 9.9 - - + +
280A GLU* 3.0 40.0 + - - +
584A GLN* 3.2 17.9 + - + +
585A GLU* 3.8 7.2 - - - +
586A ARG 3.2 0.8 - - - -
587A THR* 1.3 79.0 - - - +
589A LYS* 1.3 59.3 + - - +
591A LEU* 3.6 11.9 + - - +
592A ASN* 2.7 48.2 + - - +
611A ALA* 6.0 1.0 - - - +
613A ASN* 3.4 27.0 - - - +
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Residues in contact with LYS 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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585A GLU 3.5 9.1 + - - +
586A ARG* 3.3 15.2 + - + +
587A THR 3.3 0.2 - - - -
588A GLN* 1.3 79.6 - - - +
590A VAL* 1.3 64.6 + - + +
592A ASN* 3.5 12.0 + - - +
593A GLU* 3.4 46.2 + - - +
660A ASP* 5.8 4.0 - - - +
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Residues in contact with VAL 590 (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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576A VAL* 4.2 8.7 - - + -
578A LEU* 4.0 27.6 - - + -
586A ARG* 3.6 14.8 - - + +
587A THR 3.3 5.8 + - - +
588A GLN 3.2 0.6 - - - -
589A LYS* 1.3 80.2 - - + +
591A LEU* 1.3 63.9 + - - +
593A GLU* 3.2 13.3 + - - +
594A VAL* 3.2 28.4 + - + +
659A LYS* 4.6 17.3 - - + -
660A ASP* 5.5 6.3 - - - +
661A ALA* 5.2 7.4 - - + -
663A VAL* 4.0 26.7 - - + -
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Residues in contact with LEU 591 (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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576A VAL* 4.0 14.1 - - + -
587A THR* 3.2 29.0 + - - +
588A GLN* 3.9 12.8 - - - +
589A LYS 3.5 0.2 - - - -
590A VAL* 1.3 78.4 - - - +
592A ASN* 1.3 54.1 + - - +
594A VAL* 3.8 9.4 - - + +
595A THR* 2.6 38.9 + - - -
611A ALA* 4.2 11.2 - - + -
612A VAL 3.5 13.0 - - - +
613A ASN* 3.5 36.3 - - + +
625A GLY* 4.8 4.0 - - - -
626A ILE 3.3 35.0 - - - +
627A ALA* 4.8 4.0 - - + -
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Residues in contact with ASN 592 (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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280A GLU* 3.7 9.2 - - - +
283A GLY* 5.6 2.3 - - - -
588A GLN* 2.7 44.1 + - - +
589A LYS* 3.5 12.5 - - - +
590A VAL 3.1 0.4 - - - -
591A LEU* 1.3 75.6 - - - +
593A GLU* 1.3 63.2 + - + +
595A THR* 4.5 2.9 - - - -
596A HIS* 3.1 48.2 + - + +
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Residues in contact with GLU 593 (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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589A LYS* 3.4 42.1 + - - +
590A VAL* 3.2 11.3 + - - +
592A ASN* 1.3 76.7 - - + +
594A VAL* 1.3 57.6 + - - +
596A HIS* 4.0 3.5 - - - +
597A TYR* 3.2 26.3 + - - +
658A ILE* 3.8 14.5 - - + +
659A LYS* 3.5 40.0 + - - +
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Residues in contact with VAL 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A THR* 4.4 15.3 - - + +
576A VAL* 5.3 5.6 - - + -
590A VAL* 3.2 27.7 + - + +
591A LEU* 3.8 9.4 - - + +
592A ASN 3.2 0.2 - - - -
593A GLU* 1.3 74.7 - - - +
595A THR* 1.3 65.1 + - - +
596A HIS 3.1 2.5 + - - -
597A TYR* 3.4 10.9 + - - +
598A TYR* 3.7 25.9 + - + -
627A ALA* 4.7 10.5 - - + -
655A PHE* 3.5 40.8 - - + -
659A LYS* 5.0 2.5 - - - +
663A VAL* 4.2 13.2 - - + -
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Residues in contact with THR 595 (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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280A GLU* 6.3 0.2 - - + -
282A ASN* 4.3 1.8 - - - +
283A GLY* 4.2 17.0 - - - +
591A LEU 2.6 21.8 + - - -
592A ASN* 4.1 1.7 - - - -
594A VAL* 1.3 79.0 - - - +
596A HIS* 1.3 67.9 + - - +
598A TYR* 3.6 7.2 - - - +
599A LEU* 3.3 35.5 + - + +
609A VAL* 3.6 34.5 - - + +
611A ALA* 3.4 23.0 - - + +
627A ALA* 5.2 1.6 - - - +
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Residues in contact with HIS 596 (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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282A ASN 5.0 0.7 - - - -
283A GLY* 4.5 15.0 - - - -
592A ASN* 3.1 34.6 + - + +
593A GLU* 4.3 4.3 - - - +
594A VAL 3.1 0.4 - - - -
595A THR* 1.3 91.6 - - + +
597A TYR* 1.3 59.6 + - - +
598A TYR 3.1 1.6 - - - -
599A LEU* 3.4 24.4 - - + +
600A THR* 2.9 40.7 + - + +
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Residues in contact with TYR 597 (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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593A GLU 3.2 17.9 + - - +
594A VAL 3.4 6.9 + - - +
596A HIS* 1.3 77.8 - - - +
598A TYR* 1.3 73.7 + + - +
600A THR* 4.7 1.3 - - - -
601A LYS* 3.4 57.8 + - + +
602A GLU* 3.4 20.1 - - - +
650A ARG* 2.9 38.6 + - - +
651A ALA* 3.7 18.4 - - + -
654A ALA* 3.3 27.7 - - + +
655A PHE* 4.4 13.0 - + + -
658A ILE* 5.7 4.5 - - + -
659A LYS* 5.4 3.6 - - - +
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Residues in contact with TYR 598 (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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572A PHE* 3.5 25.3 - + - -
574A THR* 3.1 29.2 - - + +
594A VAL* 3.7 17.0 + - + -
595A THR 3.6 6.7 + - - +
596A HIS 3.1 0.2 - - - -
597A TYR* 1.3 104.3 - + - +
599A LEU* 1.3 59.2 + - - +
602A GLU* 2.9 40.7 - - + +
603A LYS* 4.4 0.5 - - - -
606A VAL* 3.7 25.8 - - + +
609A VAL* 3.9 26.5 - - + -
627A ALA* 5.2 0.7 - - + -
629A VAL* 3.3 27.1 - - + -
647A ILE* 5.5 0.9 - - + -
651A ALA* 4.4 6.9 - - + +
655A PHE* 3.8 18.8 - + - -
665A ALA* 4.7 0.3 - - - +
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Residues in contact with LEU 599 (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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282A ASN* 3.6 42.0 - - + +
595A THR* 3.3 29.8 + - + +
596A HIS* 3.3 31.1 + - + +
598A TYR* 1.3 79.3 - - - +
600A THR* 1.3 58.4 + - - +
603A LYS* 3.1 23.6 - - - +
606A VAL* 5.9 2.0 - - + -
607A GLU 6.5 0.2 - - - -
609A VAL* 4.4 7.2 - - + -
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Residues in contact with THR 600 (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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596A HIS* 2.9 30.2 + - + +
597A TYR* 4.7 0.9 - - - -
599A LEU* 1.3 79.7 - - - +
601A LYS* 1.3 74.0 + - + +
602A GLU 3.4 5.0 + - - -
603A LYS* 3.2 25.5 + - - +
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Residues in contact with LYS 601 (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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597A TYR* 3.4 41.2 + - + +
600A THR* 1.3 92.9 - - + +
602A GLU* 1.3 76.0 + - - +
650A ARG* 5.7 1.0 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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