Contacts of the helix formed by residues 619 - 640 (chain B) in PDB entry 5X61
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B LYS* 3.7 34.3 - - + +
617B GLY 5.2 2.5 - - - +
618B TYR* 1.3 76.0 - - - +
620B GLU* 1.3 60.6 + - - +
621B ASP* 3.6 7.0 + - - +
622B GLU* 3.1 43.0 + - - +
623B LYS* 2.9 26.2 + - - +
669B LEU* 5.3 1.2 - - - +
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Residues in contact with GLU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B TYR 3.9 0.8 + - - -
619B THR* 1.3 72.3 - - - +
621B ASP* 1.3 66.3 + - - +
623B LYS* 3.3 29.0 + - - +
624B ASP* 3.2 35.5 + - - +
627B ARG* 5.4 3.5 + - - -
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Residues in contact with ASP 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B THR* 3.3 6.4 + - - +
620B GLU* 1.3 81.0 - - - +
622B GLU* 1.3 58.5 + - - +
624B ASP* 3.3 9.6 + - - +
625B PHE* 2.9 22.5 + - - +
669B LEU* 3.4 31.5 - - + +
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Residues in contact with GLU 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B HIS* 3.5 20.8 - - + +
587B SER* 4.0 1.3 + - - -
588B LYS* 2.8 35.1 + - - +
606B TYR* 3.2 33.1 + - + +
611B PRO* 3.9 1.9 - - - +
618B TYR* 3.3 18.9 - - + -
619B THR* 3.1 41.8 + - - +
621B ASP* 1.3 74.5 - - - +
623B LYS* 1.3 60.3 + - - +
625B PHE* 3.3 8.0 + - - +
626B SER* 3.0 26.3 + - - -
669B LEU* 4.3 6.1 - - + +
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Residues in contact with LYS 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B PRO* 3.5 33.4 - - + +
612B LEU* 3.7 13.4 - - + +
614B PRO* 4.4 24.4 - - - +
617B GLY* 6.1 0.4 - - - -
618B TYR* 3.4 21.5 - - + +
619B THR 2.9 14.3 + - - +
620B GLU* 3.4 34.4 + - - +
622B GLU* 1.3 77.6 - - - +
624B ASP* 1.3 60.4 + - - +
626B SER 3.6 0.5 + - - -
627B ARG* 3.3 40.1 + - - +
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Residues in contact with ASP 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B GLU* 3.2 24.0 + - - +
621B ASP* 3.7 11.5 - - - +
622B GLU 3.3 0.2 - - - -
623B LYS* 1.3 74.1 - - - +
625B PHE* 1.3 59.4 + - - +
627B ARG* 3.0 25.5 + - - +
628B LYS* 2.9 28.3 + - - +
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Residues in contact with PHE 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B TYR* 3.5 26.7 - + - -
585B HIS* 3.6 23.8 - + + -
606B TYR* 3.5 22.2 - + + -
621B ASP 2.9 17.9 + - - +
622B GLU* 3.3 6.5 + - - +
624B ASP* 1.3 76.6 - - - +
626B SER* 1.3 60.3 + - - +
628B LYS* 3.3 21.3 + - + +
629B ILE* 3.1 41.0 + - + +
667B LEU* 3.2 26.5 - - + -
668B GLY 3.2 32.5 - - - -
669B LEU* 3.8 15.5 - - + -
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Residues in contact with SER 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B TYR* 2.8 32.0 + - - +
609B GLY* 3.3 20.4 - - - -
611B PRO* 3.5 29.5 - - - +
612B LEU* 4.0 4.0 - - - -
622B GLU 3.0 8.7 + - - -
623B LYS 3.8 5.4 - - - -
624B ASP 3.3 0.2 - - - -
625B PHE* 1.3 74.1 - - - +
627B ARG* 1.3 59.8 + - - +
629B ILE* 3.3 1.1 + - - +
630B MET* 2.8 35.0 + - - +
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Residues in contact with ARG 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 3.8 25.2 + - + +
300B GLU* 4.3 5.1 - - - +
612B LEU* 4.0 29.2 - - + +
620B GLU* 5.4 3.2 + - - -
623B LYS* 3.3 30.7 + - - +
624B ASP* 3.0 38.2 + - - +
626B SER* 1.3 77.7 - - - +
628B LYS* 1.3 59.9 + - - +
630B MET* 4.0 7.0 - - - +
631B ARG* 3.2 24.4 + - - +
651B PHE* 4.2 5.8 - - + -
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Residues in contact with LYS 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ASP 2.9 13.8 + - - +
625B PHE* 3.3 26.2 - - + +
626B SER 3.1 0.4 - - - -
627B ARG* 1.3 78.2 - - - +
629B ILE* 1.3 58.5 + - + +
631B ARG* 3.5 4.5 + - - +
632B TYR* 3.2 46.8 + - + -
650B GLU 4.1 8.9 + - - +
651B PHE* 3.7 25.2 - - + -
652B PRO* 3.6 36.2 - - - +
665B LEU* 5.8 1.7 - - - +
666B GLU 5.6 3.2 + - - -
667B LEU* 5.2 6.1 - - - +
668B GLY 4.5 9.9 + - - +
669B LEU 5.3 2.6 + - - -
671B THR 4.0 15.8 + - - -
672B SER* 5.5 0.4 - - - +
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Residues in contact with ILE 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B TYR* 4.7 10.1 - - + -
603B GLU* 4.3 2.7 - - + +
606B TYR* 3.5 31.6 - - + +
607B VAL* 3.5 29.2 - - + +
625B PHE* 3.1 39.7 + - + +
626B SER 3.7 8.3 - - - +
628B LYS* 1.3 77.1 - - + +
630B MET* 1.3 67.5 + - - +
631B ARG 3.2 0.4 - - - -
632B TYR* 3.9 6.7 - - + -
633B TRP* 3.1 42.9 + - + +
667B LEU* 4.3 22.7 - - + -
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Residues in contact with MET 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 3.7 3.8 - - - +
296B LEU* 3.5 33.8 - - + +
299B GLU* 3.4 35.7 - - + -
300B GLU* 3.6 13.9 - - + +
606B TYR 3.7 2.9 - - - +
607B VAL 3.2 24.2 - - - +
609B GLY* 3.3 29.2 - - - -
612B LEU* 4.7 8.7 - - + -
626B SER* 2.8 24.8 + - - +
627B ARG* 4.0 5.2 - - - +
628B LYS 3.4 0.2 - - - -
629B ILE* 1.3 77.9 - - - +
631B ARG* 1.3 57.6 + - - +
633B TRP* 3.8 4.8 - - - +
634B SER* 2.9 30.1 + - - -
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Residues in contact with ARG 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 4.1 10.1 + - - +
300B GLU* 2.6 35.3 + - - +
627B ARG 3.2 20.3 + - - +
628B LYS 3.6 0.2 - - - +
629B ILE 3.2 0.2 - - - -
630B MET* 1.3 74.3 - - - +
632B TYR* 1.3 67.1 + - - +
634B SER* 2.8 2.4 + - - -
635B ASN* 2.7 58.8 + - - +
638B LYS* 5.7 3.4 - - - +
642B PRO 5.4 0.2 - - - +
644B PRO* 5.2 3.1 - - + -
651B PHE* 3.5 36.8 - - + -
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Residues in contact with TYR 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B LEU* 4.9 0.4 - - - -
628B LYS* 3.2 33.6 + - + -
629B ILE* 3.7 12.3 - - + +
630B MET 3.6 0.2 - - - -
631B ARG* 1.3 75.4 - - - +
633B TRP* 1.3 73.3 + + + +
635B ASN* 3.0 15.7 - - - +
636B PHE* 3.2 16.3 + - - +
642B PRO* 3.4 25.1 - - + +
643B ASN* 5.0 2.7 - - - -
644B PRO* 5.2 0.9 - - + -
651B PHE* 4.6 14.6 - + + -
652B PRO* 3.0 44.0 + - + +
654B TRP* 3.7 30.7 - + + -
665B LEU* 3.6 18.8 - - + +
667B LEU* 3.7 26.9 - - + -
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Residues in contact with TRP 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MET* 4.4 9.4 - - + -
296B LEU* 5.7 2.9 - - + -
357B PHE* 4.3 7.6 - + - -
383B ILE* 3.5 34.9 - - + +
385B GLN* 2.8 32.1 + - + -
479B LEU* 3.8 12.6 - - + -
581B TYR* 3.6 41.3 - + - -
603B GLU* 5.7 2.0 - - + -
607B VAL* 3.9 28.6 - - + +
629B ILE* 3.1 36.8 + - + +
630B MET* 3.8 5.8 - - - +
632B TYR* 1.3 85.7 - - + +
634B SER* 1.3 62.8 + - - +
636B PHE* 3.3 4.7 + - - +
637B ALA* 3.1 22.3 + - - +
654B TRP* 3.9 21.1 - + - -
667B LEU* 3.9 17.5 - - + -
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Residues in contact with SER 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B MET* 4.3 14.8 - - - -
300B GLU* 3.2 38.9 + - - +
302B VAL* 4.3 3.7 - - - +
630B MET 2.9 20.1 + - - -
631B ARG* 2.8 8.3 + - - -
633B TRP* 1.3 71.0 - - - +
635B ASN* 1.3 57.8 + - - +
637B ALA* 2.9 21.5 + - - +
638B LYS* 2.9 32.4 + - - +
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Residues in contact with ASN 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B ARG* 2.7 55.3 + - - +
632B TYR 3.0 6.8 - - - +
634B SER* 1.3 70.3 + - - +
636B PHE* 1.3 57.7 + - - +
638B LYS* 3.7 19.3 - - + +
639B THR* 2.6 43.1 + - + -
641B ASN 2.8 4.5 - - - +
642B PRO 2.7 30.2 + - - +
643B ASN 4.1 8.9 + - - +
644B PRO* 4.1 14.8 - - - +
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Residues in contact with PHE 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B THR* 5.6 0.2 - - - -
381B ARG* 3.4 17.6 - - + -
382B ALA 3.5 18.6 - - - -
383B ILE* 3.6 24.5 - - + -
477B GLU* 3.6 23.8 - - + -
478B ILE* 3.6 4.7 - - - -
479B LEU* 3.4 38.8 - - + -
579B TYR* 3.8 20.6 - + - -
632B TYR 3.2 20.2 + - - +
633B TRP 3.5 2.9 - - - +
634B SER 3.1 0.6 - - - -
635B ASN* 1.3 74.5 - - - +
637B ALA* 1.3 64.7 + - - +
638B LYS 3.1 1.3 - - - -
640B GLY* 2.8 51.4 + - - -
641B ASN 3.7 7.2 - - - +
642B PRO* 4.0 4.9 - - + -
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Residues in contact with ALA 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ALA* 4.1 13.1 - - + +
272B VAL 5.3 0.2 - - - +
273B MET* 3.8 22.9 - - + -
302B VAL* 6.0 0.7 - - + -
353B ARG* 4.7 2.4 + - - +
355B THR* 3.3 40.4 - - + +
380B GLN* 4.3 0.9 - - - +
381B ARG* 2.8 20.2 + - - -
383B ILE* 4.9 0.9 - - + -
633B TRP 3.1 11.8 + - - +
634B SER 2.9 10.9 + - - +
636B PHE* 1.3 80.3 - - - +
638B LYS* 1.3 53.3 + - - +
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Residues in contact with LYS 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ALA* 4.1 11.2 - - + -
300B GLU* 3.0 28.7 + - - +
301B ASN* 4.3 5.4 + - - +
302B VAL* 3.6 11.4 - - + -
353B ARG* 3.4 25.5 + - - +
381B ARG* 3.3 15.2 + - - -
631B ARG* 5.7 4.0 - - - +
634B SER* 2.9 29.2 + - - +
635B ASN* 3.9 15.3 - - + +
637B ALA* 1.3 78.3 - - - +
639B THR* 1.3 66.6 + - + +
802B SO4 3.6 34.9 + - - +
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Residues in contact with THR 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.3 14.8 + - - +
477B GLU* 5.6 0.3 - - - -
635B ASN* 2.6 28.5 + - + +
638B LYS* 1.3 82.6 - - + +
640B GLY* 1.3 58.9 + - - +
641B ASN* 2.8 22.4 + - - +
643B ASN 4.9 2.6 + - - +
645B ASN* 6.2 2.0 - - - +
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Residues in contact with GLY 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.3 18.7 - - - -
477B GLU* 3.6 19.9 - - - +
577B ASN* 5.2 1.2 + - - +
579B TYR* 3.3 19.4 + - - -
636B PHE* 2.8 27.6 + - - -
639B THR* 1.3 77.9 - - - +
641B ASN* 1.3 59.5 + - - +
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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