Contacts of the helix formed by residues 598 - 617 (chain A) in PDB entry 6AH0
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 LEU 598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A MET 6.1 0.2 - - - -
592A TYR* 4.9 10.1 - - - +
595A LYS 3.0 11.7 + - - -
596A TYR 2.7 5.9 + - - -
597A LYS* 1.6 49.5 - - - +
599A MET* 1.3 63.2 + - - +
600A ARG 2.9 2.9 - - - +
601A GLN* 2.9 15.2 + - - +
602A ILE* 3.2 8.1 + - - -
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Residues in contact with MET 599 (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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592A TYR* 5.6 0.4 - - - +
596A TYR 2.7 13.8 + - - -
597A LYS 2.5 9.7 + - - -
598A LEU* 1.3 72.7 - - - +
600A ARG* 1.3 54.7 + - - +
602A ILE* 3.0 4.1 + - - +
603A ARG* 2.9 29.6 + - - -
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Residues in contact with ARG 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LYS 2.7 12.9 + - - -
598A LEU 4.1 0.2 - - - -
599A MET* 1.3 78.5 - - - +
601A GLN* 1.3 59.5 + - - +
603A ARG* 3.9 1.3 + - - +
604A MET* 3.5 14.2 + - - -
29B A 5.3 9.0 - - - -
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Residues in contact with GLN 601 (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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598A LEU* 2.9 9.0 + - - +
600A ARG* 1.3 74.0 - - - +
602A ILE* 1.3 66.4 + - - +
604A MET* 3.1 3.4 + - - +
605A CYS* 2.9 19.6 + - - -
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Residues in contact with ILE 602 (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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586A GLY* 6.0 7.6 - - - +
598A LEU 3.2 8.8 + - - -
599A MET* 3.0 8.3 + - - +
601A GLN* 1.3 75.9 - - - +
603A ARG* 1.3 57.5 + - - +
605A CYS* 3.2 3.3 + - - +
606A LYS* 2.9 24.8 + - - -
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Residues in contact with ARG 603 (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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599A MET 2.9 14.1 + - - -
600A ARG 4.3 1.1 - - - -
602A ILE* 1.3 76.0 - - - +
604A MET* 1.3 62.0 + - - +
606A LYS* 3.2 3.4 + - - +
607A ASP* 3.1 19.1 + - - -
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Residues in contact with MET 604 (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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600A ARG 3.5 10.5 + - - -
601A GLN* 3.1 8.1 + - - +
603A ARG* 1.3 75.6 - - - +
605A CYS* 1.3 58.0 + - - +
607A ASP* 3.4 1.7 + - - +
608A LEU* 3.0 24.4 + - - -
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Residues in contact with CYS 605 (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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582A PHE 5.2 4.0 - - - -
583A ALA* 4.7 24.3 - - - +
601A GLN 2.9 13.4 + - - -
602A ILE* 3.2 3.8 + - - +
604A MET* 1.3 73.2 - - - +
606A LYS* 1.3 59.6 + - - +
608A LEU* 3.8 1.1 - - - +
609A LYS* 2.9 26.2 + - - -
633A GLY* 6.6 0.2 - - - -
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Residues in contact with LYS 606 (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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602A ILE 2.9 14.0 + - - -
603A ARG* 3.2 5.1 + - - +
605A CYS* 1.3 77.4 - - - +
607A ASP* 1.3 56.1 + - - +
609A LYS* 3.3 2.7 + - - +
610A HIS* 3.1 22.0 + - - -
3000A IHP 5.2 8.0 + - - -
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Residues in contact with ASP 607 (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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446A SER* 4.9 17.2 - - - +
603A ARG 3.1 13.0 + - - -
604A MET* 3.4 3.3 + - - +
605A CYS 3.2 0.2 - - - -
606A LYS* 1.3 72.5 - - - +
608A LEU* 1.3 60.8 + - - +
610A HIS* 3.2 3.0 + - - +
611A LEU* 2.9 24.8 + - - -
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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
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604A MET 3.0 16.7 + - - -
605A CYS* 3.9 1.6 - - - +
607A ASP* 1.3 76.5 - - - +
609A LYS* 1.3 56.7 + - - +
611A LEU* 3.2 2.0 + - - +
612A ILE* 2.9 28.2 + - - -
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Residues in contact with LYS 609 (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 ALA* 6.1 3.1 - - - +
605A CYS 2.9 18.2 + - - -
606A LYS* 3.7 3.1 - - - +
607A ASP 3.2 0.2 - - - -
608A LEU* 1.3 76.4 - - - +
610A HIS* 1.3 54.7 + - - +
613A TYR* 2.9 29.2 + - - +
3000A IHP 5.4 11.7 - - - -
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Residues in contact with HIS 610 (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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443A VAL* 6.4 1.8 - - - +
606A LYS 3.1 13.2 + - - -
607A ASP* 3.2 3.8 + - - +
609A LYS* 1.3 73.3 - - - +
611A LEU* 1.3 65.3 + - - +
613A TYR* 5.2 0.2 - - - +
614A TYR* 3.0 21.3 + - - -
3000A IHP 5.2 5.7 + - - -
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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
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607A ASP 2.9 14.3 + - - -
608A LEU* 3.2 3.6 + - - +
610A HIS* 1.3 79.4 - - - +
612A ILE* 1.3 60.8 + - - +
614A TYR* 3.9 0.9 - - - -
615A ARG* 3.3 17.5 + - - -
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Residues in contact with ILE 612 (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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608A LEU 2.9 14.1 + - - -
609A LYS* 5.4 0.2 - - - +
611A LEU* 1.3 73.9 - - - +
613A TYR* 1.3 60.2 + - - +
615A ARG* 3.2 2.3 + - - -
616A PHE* 2.8 28.1 + - - -
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Residues in contact with TYR 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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609A LYS 2.9 18.7 + - - -
610A HIS* 5.2 0.2 - - - +
612A ILE* 1.3 76.3 - - - +
614A TYR* 1.3 62.0 - - - +
616A PHE* 3.4 7.9 + - - +
617A ASN* 3.6 8.5 + - - -
3000A IHP 5.5 9.1 + - - -
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Residues in contact with TYR 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 HIS 3.0 17.7 + - - -
611A LEU 3.9 1.1 - - - -
613A TYR* 1.3 78.4 - - - +
615A ARG* 1.3 57.3 + - - +
617A ASN 2.9 25.3 - - - +
618A THR* 5.1 0.2 - - - -
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Residues in contact with ARG 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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611A LEU 3.3 9.8 + - - -
612A ILE 3.2 6.2 + - - -
614A TYR* 1.3 73.9 - - - +
616A PHE* 1.3 66.3 + - - +
617A ASN 3.2 6.1 + - - -
618A THR* 4.2 2.6 + - - -
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Residues in contact with PHE 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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152A ARG* 4.9 14.2 - - - +
612A ILE 2.8 15.1 + - - -
613A TYR* 3.4 3.1 + - - +
614A TYR 3.2 0.8 - - - -
615A ARG* 1.3 78.5 - - - +
617A ASN* 1.3 57.4 + - - +
618A THR 3.9 1.7 + - - -
621A VAL* 4.0 6.6 - - - +
622A GLY 4.8 1.6 - - - -
627A CYS* 6.0 5.6 - - - +
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Residues in contact with ASN 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 TYR 3.6 6.4 + - - -
614A TYR 2.9 22.2 + - - +
615A ARG 3.9 1.3 - - - -
616A PHE* 1.3 74.9 - - - +
618A THR* 1.3 59.0 + - - +
621A VAL 2.6 23.8 - - - -
622A GLY* 3.6 15.5 + - - -
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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
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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