Contacts of the helix formed by residues 619 - 640 (chain A) in PDB entry 5YDJ
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 619 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A LYS* 3.8 38.6 - - + +
617A GLY 5.0 2.5 - - - +
618A TYR* 1.3 77.6 - - - +
620A GLU* 1.3 59.8 + - - +
621A ASP* 3.6 6.5 + - - +
622A GLU* 2.8 44.7 + - - +
623A LYS* 3.2 27.6 + - - +
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Residues in contact with GLU 620 (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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619A THR* 1.3 72.9 - - - +
621A ASP* 1.3 65.7 + - - +
623A LYS* 3.3 24.0 + - - +
624A ASP* 3.0 39.9 + - - +
627A ARG* 4.6 12.6 + - - -
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Residues in contact with ASP 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A THR* 3.5 6.3 + - - +
620A GLU* 1.3 80.7 - - - +
622A GLU* 1.3 60.5 + - - +
624A ASP* 3.5 12.3 + - - +
625A PHE* 2.9 28.9 + - - +
669A LEU* 4.0 25.2 - - + +
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Residues in contact with GLU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A HIS* 3.6 17.5 + - + +
587A SER* 3.4 7.3 - - - -
588A LYS* 2.8 33.8 + - - +
606A TYR* 3.3 31.6 + - + +
611A PRO* 3.9 3.2 - - - +
617A GLY 4.8 0.3 - - - +
618A TYR* 3.4 19.4 - - + -
619A THR* 2.8 49.8 + - - +
621A ASP* 1.3 75.0 - - - +
623A LYS* 1.3 58.9 + - - +
625A PHE* 4.1 5.8 - - - -
626A SER* 3.0 25.6 + - - -
669A LEU* 4.5 2.7 - - + -
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Residues in contact with LYS 623 (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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611A PRO* 3.4 37.7 - - + +
612A LEU* 4.0 7.7 - - + +
614A PRO* 4.3 23.2 - - - +
616A LEU 5.6 0.2 - - - -
618A TYR* 3.6 21.4 + - - +
619A THR 3.2 12.6 + - - +
620A GLU* 3.5 28.7 + - - +
621A ASP 3.3 0.4 - - - -
622A GLU* 1.3 75.1 - - - +
624A ASP* 1.3 61.9 + - - +
626A SER* 3.5 2.8 + - - -
627A ARG* 3.2 42.6 + - - +
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Residues in contact with ASP 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A GLU* 3.0 29.3 + - - +
621A ASP* 3.7 14.1 - - - +
623A LYS* 1.3 76.7 - - - +
625A PHE* 1.3 56.9 + - - +
627A ARG* 2.7 36.4 + - - +
628A LYS* 3.0 27.8 + - - +
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Residues in contact with PHE 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A TYR* 3.6 29.4 - + - -
585A HIS* 3.9 20.9 - + + -
606A TYR* 3.6 23.8 - + - -
621A ASP 2.9 18.9 + - - +
622A GLU* 3.6 7.2 - - - +
623A LYS 3.3 0.2 - - - -
624A ASP* 1.3 75.4 - - - +
626A SER* 1.3 63.2 + - - +
628A LYS* 3.4 18.2 - - + +
629A ILE* 3.1 40.9 + - + +
667A LEU* 3.6 26.2 - - + -
668A GLY* 3.2 33.2 - - - -
669A LEU* 4.3 11.2 - - + +
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Residues in contact with SER 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A TYR* 2.8 34.8 + - - +
609A GLY* 3.4 20.3 - - - -
611A PRO* 3.8 17.5 - - - +
612A LEU* 4.1 6.4 - - - +
622A GLU 3.0 17.2 + - - -
623A LYS 3.7 4.7 - - - -
624A ASP 3.4 0.2 - - - -
625A PHE* 1.3 73.1 - - - +
627A ARG* 1.3 61.0 + - - +
629A ILE* 3.3 1.1 + - - +
630A MET* 2.8 37.6 + - - +
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Residues in contact with ARG 627 (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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299A GLU* 3.4 30.7 + - + +
300A GLU* 4.3 4.6 - - - +
612A LEU* 4.1 16.2 - - + +
620A GLU* 4.6 10.5 + - - -
623A LYS* 3.2 27.8 + - - +
624A ASP* 2.7 37.7 + - - +
626A SER* 1.3 77.7 - - - +
628A LYS* 1.3 60.9 + - - +
630A MET* 3.8 8.0 + - - +
631A ARG* 3.3 27.5 + - - +
651A PHE* 4.2 5.9 - - + -
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Residues in contact with LYS 628 (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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624A ASP 3.0 19.3 + - - +
625A PHE* 3.4 21.3 - - + +
626A SER 3.1 0.2 - - - -
627A ARG* 1.3 77.7 - - - +
629A ILE* 1.3 63.5 + - + +
631A ARG* 3.4 6.1 + - - +
632A TYR* 3.4 37.4 + - + -
650A GLU 3.6 18.3 + - - +
651A PHE* 3.7 19.3 - - + -
652A PRO* 4.0 25.3 - - - +
665A LEU* 6.3 0.4 - - - -
666A GLU 5.9 0.6 + - - -
667A LEU* 5.5 4.5 - - - +
668A GLY 3.9 14.6 + - - +
669A LEU 4.5 6.6 + - - +
671A THR 3.6 22.2 + - - -
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Residues in contact with ILE 629 (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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583A TYR* 4.8 10.5 - - + -
603A GLU* 4.1 3.4 - - + +
606A TYR* 3.4 33.0 - - + +
607A VAL* 3.5 28.0 - - + +
625A PHE* 3.1 40.5 + - + +
626A SER 3.7 8.1 - - - +
628A LYS* 1.3 75.2 - - + +
630A MET* 1.3 63.3 + - - +
631A ARG 3.2 0.2 - - - -
632A TYR* 3.5 8.0 + - + -
633A TRP* 3.0 48.6 + - + +
667A LEU* 4.4 21.8 - - + -
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Residues in contact with MET 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 3.5 29.6 - - + +
296A LEU* 3.7 19.7 - - + +
299A GLU* 3.8 18.6 - - + -
300A GLU* 3.4 16.8 - - + +
606A TYR 3.5 5.4 - - - +
607A VAL* 3.4 21.8 - - - +
609A GLY* 3.5 16.6 - - - -
612A LEU* 4.6 7.2 - - + -
626A SER* 2.8 40.4 + - - +
627A ARG* 4.0 5.6 - - - +
629A ILE* 1.3 78.4 - - - +
631A ARG* 1.3 56.1 + - - +
633A TRP* 3.7 5.9 + - - +
634A SER* 2.9 29.5 + - - -
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Residues in contact with ARG 631 (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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299A GLU* 3.4 21.6 + - - +
300A GLU* 2.8 34.6 + - - +
301A ASN* 6.1 0.4 - - - +
627A ARG* 3.3 13.0 + - - +
628A LYS 3.6 0.7 - - - +
629A ILE 3.2 0.6 - - - -
630A MET* 1.3 75.7 - - - +
632A TYR* 1.3 58.3 + - - +
634A SER* 3.0 3.6 + - - -
635A ASN* 2.6 67.4 + - - +
638A LYS* 5.5 3.6 - - - +
644A PRO* 6.2 0.4 - - + -
651A PHE* 3.4 42.9 - - + -
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Residues in contact with TYR 632 (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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479A LEU* 4.2 0.6 - - - +
628A LYS* 3.4 27.9 + - + -
629A ILE* 3.5 11.6 + - + +
631A ARG* 1.3 77.5 - - - +
633A TRP* 1.3 65.2 + - + +
635A ASN* 5.7 0.4 - - - -
636A PHE* 3.1 19.8 + - - +
642A PRO* 3.2 40.0 - - + +
643A ASN* 4.9 1.3 - - - -
644A PRO* 4.8 5.6 - - + -
651A PHE* 4.3 21.8 - + + -
652A PRO* 2.8 49.6 + - - +
654A TRP* 3.7 31.0 - + + -
665A LEU* 3.8 22.2 - - + +
667A LEU* 4.0 15.3 - - + -
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Residues in contact with TRP 633 (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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273A MET* 4.2 10.5 - - + -
296A LEU* 5.4 3.1 - - + -
357A PHE* 4.5 10.5 - + - -
383A ILE* 3.7 31.5 - - + +
385A GLN* 3.0 29.6 + - + -
479A LEU* 3.8 18.8 - - + -
581A TYR* 3.8 35.4 - + - -
603A GLU* 5.8 2.0 - - + -
607A VAL* 3.5 29.5 - - + +
629A ILE* 3.0 42.5 + - + +
630A MET* 3.8 6.7 - - - +
632A TYR* 1.3 83.4 - - + +
634A SER* 1.3 57.5 + - - +
636A PHE* 3.5 4.6 + - - +
637A ALA* 3.1 26.0 + - - +
654A TRP* 3.8 21.8 - + - -
667A LEU* 3.8 17.3 - - + -
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Residues in contact with SER 634 (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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273A MET* 4.1 19.0 - - - +
296A LEU* 5.2 0.2 - - - -
300A GLU* 2.9 44.9 + - - -
302A VAL* 4.4 7.8 - - - +
630A MET 2.9 16.4 + - - -
631A ARG* 3.0 7.1 + - - -
633A TRP* 1.3 73.2 - - - +
635A ASN* 1.3 62.4 + - - +
637A ALA* 3.2 2.6 + - - +
638A LYS* 2.9 39.1 + - - +
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Residues in contact with ASN 635 (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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631A ARG* 2.6 52.0 + - - +
634A SER* 1.3 73.9 + - - +
636A PHE* 1.3 55.9 + - - +
638A LYS* 3.8 13.7 + - - +
639A THR* 3.0 36.7 + - - +
641A ASN 3.1 6.5 - - - +
642A PRO 3.2 25.4 + - - +
643A ASN 3.7 10.6 + - - +
644A PRO* 3.8 16.8 - - - +
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Residues in contact with PHE 636 (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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355A THR* 4.8 0.4 - - + -
381A ARG* 3.4 16.8 - - + -
382A ALA 3.4 20.2 - - - -
383A ILE* 3.7 22.0 - - + -
477A GLU* 3.6 26.7 - - + -
478A ILE 3.4 21.5 - - - -
479A LEU* 3.4 34.5 - - + -
579A TYR* 4.3 4.0 - + - -
632A TYR 3.1 20.4 + - - +
633A TRP 3.6 2.5 - - - +
635A ASN* 1.3 75.4 - - - +
637A ALA* 1.3 64.1 + - - +
640A GLY* 2.8 46.5 + - - -
641A ASN 3.4 8.7 + - - -
642A PRO* 3.8 15.9 - - + -
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Residues in contact with ALA 637 (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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271A ALA* 4.2 11.5 - - + +
273A MET* 3.8 24.2 - - + -
302A VAL* 5.6 0.4 - - + -
353A ARG* 4.7 2.8 - - - +
355A THR* 3.1 43.0 + - + +
380A GLN* 4.3 1.2 - - - +
381A ARG* 2.9 17.5 + - - +
633A TRP 3.1 14.5 + - - +
634A SER* 3.2 7.8 + - - +
636A PHE* 1.3 75.8 - - - +
638A LYS* 1.3 57.9 + - - +
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Residues in contact with LYS 638 (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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271A ALA* 3.8 17.3 - - + -
300A GLU* 2.7 30.2 + - - +
301A ASN* 3.9 13.2 + - - +
302A VAL* 3.9 9.0 - - + -
353A ARG* 3.7 28.5 + - - +
381A ARG* 2.8 20.9 + - - -
631A ARG* 5.5 3.6 - - - +
634A SER* 2.9 28.3 + - - +
635A ASN* 3.8 13.1 + - - +
637A ALA* 1.3 76.3 - - - +
639A THR* 1.3 64.8 + - + +
802A SO4 3.5 26.1 + - - +
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Residues in contact with THR 639 (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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353A ARG* 5.7 0.7 - - - +
381A ARG* 3.2 12.6 + - - +
477A GLU* 5.0 1.0 - - - +
635A ASN* 3.0 15.6 + - - +
638A LYS* 1.3 84.7 - - + +
640A GLY* 1.3 61.8 + - - +
641A ASN* 3.6 15.5 + - - +
643A ASN 5.3 1.0 + - - -
802A SO4 5.3 4.9 - - - +
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Residues in contact with GLY 640 (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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381A ARG* 3.1 26.6 - - - -
477A GLU* 3.6 23.0 - - - +
577A ASN* 5.3 1.6 + - - +
579A TYR* 3.8 9.0 + - - -
636A PHE* 2.8 33.0 + - - -
639A THR* 1.3 71.4 - - - +
641A ASN* 1.3 59.4 + - - +
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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
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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