Contacts of the helix formed by residues 614 - 630 (chain B) in PDB entry 5JO3
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 ASN 614 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606B TYR* 3.7 15.9 - - - -
607B ARG 3.6 20.4 - - - +
608B LYS* 4.4 11.8 + - - +
610B VAL 2.9 21.1 + - - +
611B ALA* 3.1 20.2 + - - +
612B TYR 2.8 9.9 + - - +
613B HIS* 1.3 75.1 - - - +
615B TRP* 1.3 66.3 + - - +
616B ARG* 2.9 27.0 + - - +
617B HIS* 3.0 14.0 + - - +
618B ALA 3.4 7.1 + - - -
781B LEU* 5.6 2.0 - - - +
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Residues in contact with TRP 615 (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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568B ASP* 4.7 4.0 - - - -
571B THR* 2.9 33.2 + - - -
572B ALA* 4.8 1.6 - - - -
575B THR* 3.9 10.1 - - + -
599B ILE* 4.5 15.0 - - + -
602B VAL* 3.9 20.9 - - + -
603B LYS* 3.5 51.3 - - + +
606B TYR* 3.3 32.5 - + + +
608B LYS* 6.6 0.2 - - + -
614B ASN* 1.3 75.1 - - - +
616B ARG* 1.3 76.9 + - + +
618B ALA* 3.1 4.6 + - + -
619B PHE* 2.8 49.6 + + + +
651B LEU* 3.8 27.4 - - + -
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Residues in contact with ARG 616 (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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563B ASP* 2.8 61.6 + - - +
564B PHE* 4.7 2.8 + - - +
566B LEU 2.8 22.6 + - - -
567B SER* 3.4 10.5 - - - +
568B ASP* 2.9 28.5 + - - -
571B THR* 3.7 19.5 - - - +
614B ASN* 2.9 13.9 + - - +
615B TRP* 1.3 90.3 - - + +
617B HIS* 1.3 57.2 + - - +
619B PHE* 3.5 4.0 + - - +
620B ASN* 2.9 37.8 + - - +
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Residues in contact with HIS 617 (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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612B TYR* 3.2 54.1 + + + +
613B HIS* 3.8 12.4 - + - -
614B ASN* 3.0 8.2 + - - +
616B ARG* 1.3 75.0 - - - +
618B ALA* 1.3 62.9 + - - +
620B ASN* 3.3 7.1 + - - +
621B THR* 2.8 43.3 + - - -
653B HIS* 3.2 5.1 + + - -
654B ASP* 3.0 19.7 - - + -
764B ASP* 3.0 32.3 - - - -
901B ZN 2.1 24.8 - - - -
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Residues in contact with ALA 618 (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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606B TYR* 3.3 42.2 - - + +
614B ASN 3.4 2.6 + - - -
615B TRP* 3.1 12.4 + - + +
617B HIS* 1.3 79.4 - - - +
619B PHE* 1.3 63.1 + - - +
621B THR* 3.2 6.2 + - - -
622B ALA* 2.9 24.9 + - - +
650B ALA 3.7 8.7 - - - +
651B LEU* 3.4 15.0 - - - +
653B HIS* 4.4 5.2 - - + -
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Residues in contact with PHE 619 (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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561B PHE* 3.7 34.3 - + - -
563B ASP* 3.9 15.9 - - + -
566B LEU* 4.4 0.9 - - + -
571B THR* 3.2 48.7 - - + -
574B CYS* 3.5 26.0 - - + -
575B THR* 3.5 18.2 - - - -
578B MET* 3.7 15.0 - - + -
615B TRP* 2.8 35.2 + + + +
616B ARG* 3.7 5.8 - - - +
618B ALA* 1.3 76.5 - - - +
620B ASN* 1.3 57.4 + - - +
622B ALA* 3.3 2.1 + - - +
623B GLN* 2.8 28.1 + - + +
651B LEU* 4.5 9.0 - - + -
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Residues in contact with ASN 620 (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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561B PHE* 3.8 28.6 - - - +
562B SER* 5.2 0.2 - - - -
563B ASP* 2.9 32.6 + - - +
616B ARG* 2.9 28.5 + - - +
617B HIS* 3.8 7.9 - - - +
619B PHE* 1.3 75.7 - - - +
621B THR* 1.3 56.5 + - - +
623B GLN* 3.3 8.0 + - - +
624B CYS* 2.9 29.5 + - - +
766B SER* 4.4 5.5 + - - +
770B LYS* 5.1 9.7 + - - -
777B ARG* 5.4 0.4 - - - +
778B ILE* 5.0 13.5 - - - +
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Residues in contact with THR 621 (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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617B HIS* 2.8 41.6 + - - -
618B ALA 3.2 5.8 + - - -
620B ASN* 1.3 75.7 - - - +
622B ALA* 1.3 56.9 + - - +
624B CYS* 3.3 4.2 + - - +
625B MET* 3.0 26.7 + - - +
650B ALA* 4.1 12.3 - - + -
653B HIS* 3.4 24.8 - - + +
760B MET* 4.9 4.5 - - + +
763B CYS* 3.7 17.0 + - + +
764B ASP* 3.8 25.8 - - + +
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Residues in contact with ALA 622 (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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578B MET* 3.9 9.9 - - + +
618B ALA 2.9 7.4 + - - +
619B PHE 3.6 5.2 - - - +
621B THR* 1.3 73.1 - - - +
623B GLN* 1.3 60.9 + - - +
625B MET* 3.1 4.9 + - - +
626B PHE* 2.9 28.2 + - - +
647B LEU* 4.0 12.5 - - + +
650B ALA* 3.7 15.4 - - + +
651B LEU* 3.4 39.9 - - + -
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Residues in contact with GLN 623 (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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556B ILE* 2.8 32.0 + - + +
558B ASP 2.9 23.1 + - - +
559B PHE* 4.9 0.3 - - - +
561B PHE* 3.4 47.1 - - + +
578B MET* 3.7 23.5 - - + +
619B PHE* 2.8 18.4 + - + +
620B ASN* 3.6 7.9 - - - +
622B ALA* 1.3 77.9 - - - +
624B CYS* 1.3 61.0 + - - +
626B PHE* 3.2 3.3 + - - +
627B ALA* 2.9 29.4 + - - +
770B LYS* 3.6 13.3 + - - -
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Residues in contact with CYS 624 (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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559B PHE* 4.8 4.7 - - - +
620B ASN 2.9 13.4 + - - +
621B THR 3.3 5.6 + - - +
623B GLN* 1.3 82.7 + - - +
625B MET* 1.3 52.4 + - - +
627B ALA* 3.3 4.5 + - - +
628B ALA* 2.8 34.3 + - - +
762B ALA 4.5 0.4 - - - -
763B CYS* 3.8 18.8 - - + +
766B SER* 3.4 39.0 - - - +
770B LYS* 5.8 2.9 - - - +
842B LEU* 4.1 26.9 - - - -
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Residues in contact with MET 625 (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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621B THR 3.0 13.3 + - - +
622B ALA* 3.1 13.7 + - - +
624B CYS* 1.3 75.9 - - - +
626B PHE* 1.3 57.0 + - - +
628B ALA* 3.3 2.9 + - - +
629B LEU* 2.9 49.7 + - + +
646B LEU* 3.8 38.1 - - + +
647B LEU* 4.8 6.5 - - + +
650B ALA* 4.4 4.7 - - + -
759B LEU* 3.8 31.9 - - + +
760B MET* 3.6 30.5 - - - -
763B CYS* 3.5 24.1 - - + -
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Residues in contact with PHE 626 (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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551B ALA* 4.4 4.7 - - + -
556B ILE* 3.3 42.2 - - + -
557B THR* 3.7 22.4 - - - -
578B MET* 3.8 46.2 - - + -
581B ASP* 4.0 22.9 - - + -
582B LEU* 3.9 16.2 - - + -
622B ALA 2.9 13.3 + - - +
623B GLN* 3.5 7.6 - - - +
625B MET* 1.3 76.3 - - - +
627B ALA* 1.3 56.1 + - - +
629B LEU* 3.2 8.1 + - - +
630B LYS* 2.8 59.6 + - + +
647B LEU* 5.4 1.3 - - + +
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Residues in contact with ALA 627 (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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556B ILE 4.3 2.2 - - - -
557B THR* 3.6 24.5 - - - +
558B ASP 4.2 2.0 - - - +
559B PHE* 3.6 24.0 - - + -
623B GLN* 2.9 31.0 + - - +
624B CYS* 3.8 3.1 - - - +
626B PHE* 1.3 78.0 - - - +
628B ALA* 1.3 59.0 + - - +
630B LYS* 4.7 0.2 - - - -
631B ALA* 2.9 29.5 + - - +
632B GLY 2.9 6.2 + - - -
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Residues in contact with ALA 628 (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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559B PHE* 3.6 18.0 - - + -
624B CYS* 2.8 21.4 + - - +
625B MET* 3.7 6.1 - - - +
627B ALA* 1.3 71.8 - - - +
629B LEU* 1.3 60.5 + - + +
632B GLY* 3.1 27.4 - - - -
634B ILE* 3.1 27.4 + - + +
759B LEU* 4.2 14.1 - - + -
763B CYS* 4.8 2.5 - - - -
839B CYS* 4.6 4.3 - - - -
842B LEU* 5.2 5.2 - - + -
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Residues in contact with LEU 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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582B LEU* 3.8 39.7 - - + -
625B MET* 2.9 41.8 + - + +
626B PHE* 3.6 3.8 - - - +
628B ALA* 1.3 78.6 - - + +
630B LYS* 1.3 60.7 + - - +
633B LYS* 3.6 2.1 + - - -
634B ILE* 3.3 13.2 + - + -
635B GLN* 3.0 48.4 + - + +
638B LEU* 3.8 27.4 - - + -
643B ILE* 4.1 17.3 - - + +
646B LEU* 4.9 3.6 - - + -
647B LEU* 6.1 0.7 - - + -
759B LEU* 5.1 0.4 - - + -
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Residues in contact with LYS 630 (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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557B THR* 3.7 19.1 - - + +
581B ASP* 2.9 31.3 + - - -
582B LEU* 3.9 10.3 - - + -
626B PHE* 2.8 46.1 + - + +
627B ALA 4.2 0.2 - - - +
629B LEU* 1.3 74.7 - - - +
631B ALA* 1.3 67.3 + - - +
632B GLY 3.2 0.4 - - - -
633B LYS* 3.0 28.9 + - - +
635B GLN* 2.8 31.7 + - - +
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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
------------------------------------------------------------
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