Contacts of the helix formed by residues 606 - 627 (chain A) in PDB entry 6OD3
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 606 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A PRO* 3.1 14.5 + - + +
605A GLN* 1.3 75.4 - - - +
607A LYS* 1.3 66.2 + - - +
608A LEU* 3.6 8.1 + - - +
609A LEU* 3.2 22.7 + - - +
610A ILE* 3.0 27.5 + - - +
4W A 3.7 40.8 - - - +
5W C 3.3 12.1 - - - -
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Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A VAL* 5.3 3.8 + - - +
584A ILE* 4.6 8.0 - - - +
585A ASN* 5.2 7.1 - - - +
588A PHE* 3.5 46.7 - - + -
606A THR* 1.3 73.4 - - - +
608A LEU* 1.3 63.1 + - - +
610A ILE* 3.4 1.2 + - + -
611A LEU* 3.1 30.1 + - - +
580B ARG* 4.6 3.7 - - - +
584B ILE* 3.9 21.1 - - + -
703B CL 3.5 23.5 - - + +
5W C 2.6 33.8 + - - +
6W A 2.8 37.9 + - - -
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Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A THR* 3.3 7.2 + - - +
607A LYS* 1.3 77.7 - - - +
609A LEU* 1.3 62.7 + - - +
611A LEU* 3.3 4.4 + - - +
612A HIS* 3.0 51.4 + - + +
580B ARG* 6.0 4.7 - - + -
583B ASP* 3.4 51.8 - - + +
584B ILE* 4.1 14.5 - - + +
587B ALA* 3.7 9.4 - - + -
5W C 5.0 1.0 + - - +
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LYS* 3.7 23.1 - - + +
604A PRO 3.4 25.6 - - - +
605A GLN* 4.1 4.7 - - - -
606A THR* 3.2 21.7 + - - +
608A LEU* 1.3 77.5 - - - +
610A ILE* 1.3 53.3 + - - +
612A HIS* 3.2 11.4 + - + -
613A GLN* 2.7 70.5 + - + +
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Residues in contact with ILE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 3.7 37.7 - - + +
589A LYS* 5.5 1.1 - - - -
591A LEU* 3.8 29.4 - - + -
592A GLY* 3.7 21.1 - - - +
595A VAL* 4.7 2.1 - - + +
605A GLN* 3.8 32.5 - - + +
606A THR 3.0 22.3 + - - +
607A LYS* 3.8 4.3 - - + +
609A LEU* 1.3 74.6 - - - +
611A LEU* 1.3 58.0 + - - +
613A GLN* 3.3 7.5 + - - +
614A ALA* 2.8 28.9 + - - +
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Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 3.8 19.5 - - + -
591A LEU* 4.9 0.7 - - + -
607A LYS 3.1 18.5 + - - +
608A LEU* 3.7 5.8 - - - +
610A ILE* 1.3 78.2 - - - +
612A HIS* 1.3 62.6 + - - +
614A ALA* 3.4 5.0 + - - +
615A VAL* 3.2 28.7 + - - +
584B ILE* 3.7 13.5 - - + +
587B ALA* 3.7 31.4 - - + +
588B PHE* 3.6 43.7 - - + +
591B LEU* 3.7 24.8 - - + +
611B LEU* 4.0 4.5 - - + -
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Residues in contact with HIS 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A LEU* 3.0 40.4 + - + +
609A LEU* 3.7 12.1 - - + +
611A LEU* 1.3 75.1 - - - +
613A GLN* 1.3 64.9 + - + +
615A VAL* 3.4 8.8 + - - +
616A ALA* 3.2 21.4 + - - +
583B ASP 5.1 0.2 - - - -
587B ALA* 3.6 29.9 - - + +
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Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 3.4 13.4 - - + +
599A LEU* 3.7 27.0 - - + +
601A SER* 6.2 2.2 - - - +
602A ASP 6.1 0.8 - - - +
603A LYS* 5.4 4.4 + - - +
605A GLN* 3.1 32.4 + - - +
609A LEU* 2.7 56.7 + - + +
610A ILE* 3.8 4.7 - - - +
612A HIS* 1.3 71.0 - - + +
614A ALA* 1.3 59.4 + - - +
616A ALA* 3.2 7.3 + - - +
617A VAL* 2.8 34.1 + - - +
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Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A LEU* 4.0 30.1 - - + -
595A VAL* 3.8 10.3 - - + +
610A ILE 2.8 18.1 + - - +
611A LEU 3.7 5.2 - - - +
612A HIS 3.3 0.2 - - - -
613A GLN* 1.3 77.8 - - - +
615A VAL* 1.3 61.7 + - - +
617A VAL* 3.4 1.5 + - - +
618A ILE* 3.0 30.4 + - + +
591B LEU* 3.8 19.1 - - + -
614B ALA* 4.8 0.9 - - + -
618B ILE* 4.7 3.4 - - + -
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Residues in contact with VAL 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU 3.2 15.1 + - - +
612A HIS* 3.7 10.1 - - - +
614A ALA* 1.3 76.4 - - - +
616A ALA* 1.3 58.5 + - - +
618A ILE* 3.4 2.6 + - - +
619A LEU* 2.9 40.5 + - + +
587B ALA 4.9 1.1 - - - +
590B GLU* 4.2 18.6 - - + +
591B LEU* 3.8 36.6 - - + +
594B MET* 3.7 26.9 - - + +
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A LEU* 5.4 9.9 - - + -
612A HIS 3.2 14.1 + - - +
613A GLN* 3.2 9.8 + - - +
615A VAL* 1.3 76.3 - - - +
617A VAL* 1.3 58.6 + - + +
619A LEU* 4.4 0.4 - - - -
620A SER* 2.9 25.6 + - - -
702A EDO 2.9 40.0 + - - +
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Residues in contact with VAL 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 4.0 17.0 - - + -
598A HIS* 3.9 30.3 - - + -
599A LEU* 3.9 29.6 - - + -
613A GLN 2.8 21.1 + - - +
614A ALA 3.9 3.6 - - - +
616A ALA* 1.3 73.6 - - - +
618A ILE* 1.3 59.5 + - - +
620A SER* 3.2 5.8 + - - -
621A LEU* 2.8 49.0 + - + +
618B ILE* 4.0 15.5 - - + -
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Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ALA 3.0 17.6 + - - +
615A VAL 3.9 3.4 - - - +
617A VAL* 1.3 75.7 - - - +
619A LEU* 1.3 63.2 + - - +
621A LEU* 3.3 1.8 + - - -
622A GLU* 2.9 50.0 + - - +
591B LEU* 4.0 14.1 - - + -
594B MET* 3.7 17.3 - - + -
595B VAL* 4.0 27.4 - - + -
598B HIS* 4.2 2.5 - - + +
614B ALA* 4.5 4.0 - - + +
617B VAL* 4.0 17.0 - - + -
618B ILE* 3.7 23.8 - - + -
621B LEU* 3.9 16.4 - - + +
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A VAL* 2.9 34.2 + - + +
618A ILE* 1.3 77.7 - - - +
620A SER* 1.3 60.9 + - - +
622A GLU* 3.7 12.6 - - - +
623A GLN* 3.3 34.9 + - + +
702A EDO 3.7 30.1 - - - +
594B MET* 3.6 23.6 - - + -
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Residues in contact with SER 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A LEU* 6.4 1.6 - - - -
616A ALA 2.9 17.8 + - - -
617A VAL* 3.7 7.0 - - - -
619A LEU* 1.3 77.9 - - - +
621A LEU* 1.3 62.1 + - - +
623A GLN* 3.3 10.9 + - - +
624A GLN* 3.2 40.2 + - - +
702A EDO 3.5 12.5 + - - -
703A EDO 5.4 7.9 - - - -
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Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A HIS* 3.8 26.2 - - + +
617A VAL* 2.8 38.2 + - + +
620A SER* 1.3 73.7 - - - +
622A GLU* 1.3 66.3 + - - +
624A GLN* 3.3 26.5 + - - +
625A VAL* 3.1 27.4 + - - +
618B ILE* 3.9 25.6 - - + +
621B LEU* 3.7 35.7 - - + +
622B GLU* 4.5 2.2 - - + -
625B VAL* 4.6 10.3 - - + +
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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
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618A ILE* 2.9 30.0 + - - +
619A LEU* 3.7 20.3 - - - +
620A SER 3.3 0.2 - - - -
621A LEU* 1.3 77.7 - - - +
623A GLN* 1.3 62.4 + - + +
625A VAL* 3.4 5.1 + - - +
626A ARG* 3.1 28.4 + - + +
594B MET* 4.0 9.6 - - - +
597B LEU* 4.8 11.4 - - - +
598B HIS* 2.4 47.7 + - + +
621B LEU* 3.9 5.8 - - + -
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Residues in contact with GLN 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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619A LEU* 3.3 27.2 + - + +
620A SER* 3.3 10.8 + - - +
621A LEU 3.3 0.4 - - - -
622A GLU* 1.3 77.7 - - + +
624A GLN* 1.3 59.8 + - + +
626A ARG* 3.2 5.0 + - - -
627A GLU* 2.8 44.6 + - + +
702A EDO 5.0 6.9 + - - -
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Residues in contact with GLN 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A SER* 3.2 32.6 + - - +
621A LEU* 3.3 29.1 + - - +
623A GLN* 1.3 76.8 - - + +
625A VAL* 1.3 62.9 + - - +
627A GLU* 3.6 29.9 + - - +
625B VAL* 4.1 26.8 - - + +
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Residues in contact with VAL 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A LEU 3.1 17.1 + - - +
622A GLU* 3.4 5.8 + - - +
624A GLN* 1.3 76.1 - - - +
626A ARG* 1.3 66.9 + - + +
627A GLU 3.6 4.0 + - - +
628A ARG* 5.7 0.9 - - - +
621B LEU* 4.1 12.1 - - + +
624B GLN* 3.4 44.2 - - + +
625B VAL* 3.8 21.8 - - + +
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Residues in contact with ARG 626 (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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622A GLU* 3.1 21.2 + - + +
623A GLN* 3.2 5.6 + - - +
625A VAL* 1.3 82.7 - - + +
627A GLU* 1.3 62.9 + - - +
628A ARG* 3.2 9.5 + - - +
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Residues in contact with GLU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A GLN* 2.8 29.6 + - + +
624A GLN* 3.8 25.2 + - - +
625A VAL 3.3 4.9 - - - +
626A ARG* 1.3 73.8 - - - +
628A ARG* 1.3 62.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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