Contacts of the helix formed by residues 609 - 627 (chain A) in PDB entry 5QSY
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 MET 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A GLU* 3.7 28.5 - - + +
572A ILE* 3.7 19.7 - - + -
573A ILE* 3.6 37.9 - - + -
603A ILE* 4.0 20.9 - - - +
604A TYR* 3.6 24.8 + - - +
607A GLY* 3.8 21.3 - - - +
608A ARG* 1.3 71.6 - - - +
610A GLU* 1.3 63.7 + - - +
611A LYS* 3.1 4.3 - - - +
612A HIS* 2.9 31.4 + - + +
613A LEU 3.4 7.4 + - - -
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Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A TYR 3.2 16.7 - - - +
605A SER* 3.6 17.2 + - - +
608A ARG* 3.3 12.5 - - - +
609A MET* 1.3 85.0 + - - +
611A LYS* 1.3 63.2 + - - +
612A HIS 3.2 0.5 + - - -
613A LEU* 3.3 11.0 + - + +
614A ASP* 3.2 18.0 + - - +
649A THR* 6.0 0.2 - - - -
650A ILE* 4.8 6.6 - - - +
653A ARG* 3.2 46.7 + - - +
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Residues in contact with LYS 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ARG 4.8 10.4 + - - +
609A MET 3.1 3.4 + - - +
610A GLU* 1.3 77.8 - - - +
612A HIS* 1.3 88.5 + - + +
614A ASP* 3.4 10.5 - - - +
615A ALA* 3.2 23.6 + - - +
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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
----------------------------------------------------------
572A ILE* 3.4 28.8 - - + +
573A ILE* 3.6 41.8 - - + +
576A PRO* 4.0 4.1 - - + +
604A TYR* 4.0 3.5 - - - -
609A MET* 2.9 27.2 + - + +
611A LYS* 1.3 106.1 - - + +
613A LEU* 1.3 64.8 + - - +
615A ALA* 3.2 12.6 + - + +
616A LEU* 3.0 22.2 + - - +
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Residues in contact with LEU 613 (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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604A TYR* 3.4 30.8 - - + +
609A MET 3.4 3.2 + - - +
610A GLU* 3.3 14.9 + - + +
612A HIS* 1.3 75.9 - - - +
614A ASP* 1.3 65.8 + - - +
616A LEU* 3.2 4.5 + - + +
617A LEU* 3.1 32.2 + - + +
643A LEU* 4.2 24.7 - - + -
650A ILE* 3.6 41.3 - - + -
653A ARG* 4.0 22.4 - - - +
654A VAL* 4.2 19.1 - - + -
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Residues in contact with ASP 614 (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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610A GLU 3.2 5.4 + - - +
611A LYS* 3.4 13.4 - - - +
613A LEU* 1.3 79.7 - - - +
615A ALA* 1.3 56.6 + - - +
617A LEU* 3.3 12.9 + - - +
618A LYS* 3.0 28.7 + - - +
653A ARG* 2.8 42.2 + - - +
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Residues in contact with ALA 615 (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 PRO* 3.7 20.6 - - + -
611A LYS 3.2 11.7 + - - +
612A HIS* 3.6 14.8 - - + +
613A LEU 3.2 0.4 - - - -
614A ASP* 1.3 77.1 - - - +
616A LEU* 1.3 66.6 + - - +
618A LYS* 3.2 19.1 + - - +
619A GLN* 2.9 26.6 + - + +
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Residues in contact with LEU 616 (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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575A LEU* 3.7 17.3 - - + -
576A PRO* 3.7 13.4 - - + +
579A LEU* 3.4 32.1 - - + -
593A LEU* 4.9 2.0 - - + -
596A PRO* 4.4 18.8 - - + -
599A PHE* 4.9 0.2 - - + -
604A TYR* 3.5 23.6 - - + +
612A HIS 3.0 13.2 + - - +
613A LEU* 3.2 7.8 + - + +
615A ALA* 1.3 75.3 - - - +
617A LEU* 1.3 51.9 + - - +
619A GLN* 3.1 2.8 + - - -
620A ILE* 2.7 49.8 + - + +
639A THR* 4.6 0.2 - - + -
643A LEU* 3.9 24.7 - - + -
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Residues in contact with LEU 617 (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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613A LEU* 3.1 30.5 + - + +
614A ASP* 3.7 17.9 - - - +
616A LEU* 1.3 72.5 - - - +
618A LYS* 1.3 65.8 + - - +
620A ILE* 4.0 5.9 - - + +
621A LYS* 3.0 25.5 + - - +
640A TYR* 4.1 18.3 + - + -
643A LEU* 4.0 25.1 - - + -
653A ARG* 4.5 13.9 - - + +
654A VAL* 4.0 23.6 - - + -
657A ALA* 3.9 24.6 - - + +
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Residues in contact with LYS 618 (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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614A ASP 3.0 12.9 + - - +
615A ALA* 3.4 19.3 - - - +
617A LEU* 1.3 76.2 - - - +
619A GLN* 1.3 76.2 + - - +
621A LYS* 3.2 8.2 + - + +
622A PHE* 3.0 54.2 + - + -
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Residues in contact with GLN 619 (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 PRO* 3.4 22.9 - - + +
579A LEU* 4.0 23.1 - - + +
580A SER* 3.5 36.7 + - - +
583A SER* 4.8 3.6 + - - -
615A ALA* 2.9 19.2 + - + +
616A LEU* 3.6 4.7 - - - +
618A LYS* 1.3 98.1 - - - +
620A ILE* 1.3 63.7 + - - +
622A PHE* 3.3 24.4 + - - +
623A VAL* 3.1 28.5 + - - +
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Residues in contact with ILE 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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579A LEU* 4.9 0.7 - - + -
593A LEU* 4.1 18.6 - - + -
616A LEU* 2.7 42.8 + - + +
617A LEU* 4.0 8.1 - - + +
619A GLN* 1.3 70.8 - - - +
621A LYS* 1.3 64.4 + - - +
623A VAL* 3.1 8.1 + - - +
624A VAL* 2.9 22.7 + - + +
636A CYS* 4.1 21.3 - - + +
639A THR* 3.4 31.9 - - + -
640A TYR* 3.5 34.8 - - + +
643A LEU* 4.4 7.4 - - + -
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Residues in contact with LYS 621 (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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617A LEU 3.0 18.4 + - - +
618A LYS* 3.5 8.1 - - + +
620A ILE* 1.3 77.2 - - - +
622A PHE* 1.3 62.7 + - - +
624A VAL* 3.4 5.1 + - - +
625A GLU* 3.0 46.0 + - - +
640A TYR* 4.0 8.9 + - - +
657A ALA* 4.6 9.4 - - - +
660A GLN* 4.0 12.7 - - - +
661A LEU* 4.1 33.2 - - + +
664A GLU* 2.9 41.2 + - - -
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Residues in contact with PHE 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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583A SER* 4.6 9.2 - - - +
618A LYS* 3.0 45.0 + - + -
619A GLN* 3.6 31.6 - - - +
620A ILE 3.3 0.2 - - - -
621A LYS* 1.3 75.9 - - - +
623A VAL* 1.3 62.4 + - - +
625A GLU* 3.4 16.6 + - - +
626A LYS* 3.1 41.4 + - + +
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Residues in contact with VAL 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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579A LEU* 4.8 10.1 - - + -
583A SER* 4.2 19.1 - - - +
589A VAL* 3.6 27.4 - - + -
593A LEU* 5.2 1.1 - - + -
619A GLN* 3.1 17.0 + - - +
620A ILE* 3.1 9.8 + - - +
622A PHE* 1.3 73.4 - - - +
624A VAL* 1.3 66.3 + - - +
626A LYS 3.1 0.7 + - - -
627A HIS* 3.0 34.4 + - + +
632A VAL* 3.4 29.8 - - + -
636A CYS* 3.6 13.0 - - - -
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Residues in contact with VAL 624 (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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620A ILE* 2.9 23.6 + - + +
621A LYS 3.4 4.0 + - - +
623A VAL* 1.3 75.2 - - - +
625A GLU* 1.3 57.8 + - - +
627A HIS 3.4 5.0 - - - +
633A LEU* 4.1 11.7 - - + -
636A CYS* 3.5 30.1 - - + -
661A LEU* 4.3 16.4 - - + -
665A PHE* 4.2 13.0 - - + -
697A ARG* 2.9 55.8 + - + -
701A PHE* 4.1 18.2 - - + -
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Residues in contact with GLU 625 (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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621A LYS* 3.0 42.9 + - + +
622A PHE* 3.7 22.2 - - - +
623A VAL 3.2 0.2 - - - -
624A VAL* 1.3 78.9 - - - +
626A LYS* 1.3 71.9 + - - +
661A LEU* 4.9 2.0 - - + +
664A GLU* 3.7 18.0 - - - +
665A PHE* 4.0 23.5 - - + -
668A ARG* 5.1 9.8 + - - +
697A ARG* 2.8 16.8 + - - +
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Residues in contact with LYS 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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583A SER* 5.2 6.7 - - - +
584A ALA* 6.0 1.8 - - + -
622A PHE* 3.1 31.1 + - + +
623A VAL* 3.1 0.8 + - - -
625A GLU* 1.3 96.0 + - - +
627A HIS* 1.3 76.1 + - + +
628A VAL* 4.5 1.6 + - - +
697A ARG* 4.1 2.5 - - - -
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Residues in contact with HIS 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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583A SER 2.7 26.3 + - - -
584A ALA* 3.2 31.2 - - - -
586A ALA* 3.7 17.9 - - + +
589A VAL* 5.0 1.0 - - - +
623A VAL* 3.0 32.8 + - + +
624A VAL 3.4 14.0 - - - +
625A GLU 3.6 0.6 - - - -
626A LYS* 1.3 90.5 + - + +
628A VAL* 1.3 64.8 + - - +
629A GLU* 2.8 24.7 + - - +
632A VAL* 3.7 18.8 - - + -
633A LEU* 3.4 12.9 - - - +
697A ARG* 3.4 5.7 + - - -
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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
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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