Contacts of the helix formed by residues 606 - 617 (chain A) in PDB entry 3AR2
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 GLU 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604A ARG* 3.4 27.5 + - - +
605A LYS* 1.3 82.5 + - + +
607A VAL* 1.3 58.1 + - - +
608A MET 3.4 0.7 - - - -
609A GLY* 4.1 2.9 - - - +
610A SER* 2.6 37.0 + - - -
738A ASP 3.8 3.5 - - - +
739A ASN* 3.0 26.3 - - - +
740A PHE* 3.3 16.6 + - + +
741A SER* 3.1 29.8 - - - +
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Residues in contact with VAL 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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356A LEU* 3.4 43.3 - - + +
604A ARG* 3.3 35.9 - - + +
605A LYS 3.3 1.8 - - - -
606A GLU* 1.3 78.8 - - - +
608A MET* 1.3 65.0 + - - +
610A SER* 3.7 4.6 - - - -
611A ILE* 3.0 43.8 + - + +
639A ILE* 4.1 17.0 - - + -
740A PHE* 4.1 20.6 - - + -
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Residues in contact with MET 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 ARG 4.6 1.6 + - - +
605A LYS 4.2 7.2 + - - +
606A GLU 3.4 0.8 - - - -
607A VAL* 1.3 81.4 - - - +
609A GLY* 1.3 67.3 + - - +
611A ILE* 3.2 2.9 + - - +
612A GLN* 3.2 18.4 + - + +
637A ARG 4.7 2.0 - - - +
638A ARG 3.6 23.8 - - - +
639A ILE* 3.3 34.7 + - + +
640A GLY* 3.8 10.5 - - - +
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Residues in contact with GLY 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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605A LYS 4.8 1.6 + - - -
606A GLU* 3.6 5.6 + - - -
608A MET* 1.3 79.9 - - - +
610A SER* 1.3 64.2 + - - +
612A GLN* 2.9 19.6 + - - +
613A LEU* 3.0 24.0 + - - +
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Residues in contact with SER 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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606A GLU 2.6 25.7 + - - -
607A VAL 3.7 3.1 - - - -
609A GLY* 1.3 73.0 - - - +
611A ILE* 1.3 57.3 + - - +
613A LEU* 3.4 9.9 + - - +
614A CYS* 3.0 33.1 + - - -
740A PHE* 3.8 21.1 - - - -
741A SER* 3.1 32.1 + - - -
744A VAL* 3.7 16.5 - - - +
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Residues in contact with ILE 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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356A LEU* 4.8 1.6 - - + -
607A VAL* 3.0 41.6 + - + +
608A MET 3.7 4.5 - - - +
609A GLY 3.2 0.2 - - - -
610A SER* 1.3 76.1 - - - +
612A GLN* 1.3 58.2 + - - +
614A CYS* 3.0 9.8 + - - +
615A ARG* 2.8 38.1 + - - +
621A VAL* 4.0 32.7 - - + +
639A ILE* 3.8 15.7 - - + +
640A GLY 4.3 16.6 - - - +
641A ILE* 3.6 29.8 - - + -
740A PHE* 4.8 7.2 - - + -
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Residues in contact with GLN 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 MET* 3.2 11.8 + - + +
609A GLY* 2.9 13.3 + - - +
611A ILE* 1.3 77.6 - - - +
613A LEU* 1.3 61.5 + - + +
615A ARG* 3.2 40.6 + - - +
616A ASP* 3.1 38.8 + - - +
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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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609A GLY* 3.0 22.2 + - - +
610A SER* 3.5 12.6 - - - +
612A GLN* 1.3 79.2 - - + +
614A CYS* 1.3 60.8 + - - +
616A ASP* 3.3 12.9 + - - +
617A ALA* 3.0 27.9 + - - +
744A VAL* 4.0 28.5 - - + -
817A MET* 4.8 2.6 - - + +
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Residues in contact with CYS 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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348A ILE* 3.8 26.5 - - - -
610A SER* 3.0 23.2 + - - -
611A ILE* 3.0 9.6 + - - +
613A LEU* 1.3 74.2 - - - +
615A ARG* 1.3 59.3 + - - +
617A ALA* 3.2 4.9 + - - +
618A GLY 3.2 5.0 + - - -
619A ILE* 2.7 56.1 + - + +
621A VAL* 4.0 13.2 - - + -
740A PHE* 5.9 4.3 - - - -
744A VAL* 3.7 20.2 - - - -
747A VAL* 6.0 0.2 - - - -
817A MET* 6.3 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 ILE* 2.8 22.1 + - - +
612A GLN* 3.2 38.0 + - - +
614A CYS* 1.3 76.5 - - - +
616A ASP* 1.3 64.7 + - - +
618A GLY* 3.0 14.7 + - - -
619A ILE 3.6 8.6 + - - +
640A GLY 2.9 27.8 + - - -
641A ILE* 3.6 18.2 + - - +
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Residues in contact with ASP 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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612A GLN* 3.1 27.2 + - - +
613A LEU* 3.6 15.3 - - - +
615A ARG* 1.3 79.7 - - - +
617A ALA* 1.3 56.5 + - - +
618A GLY 3.0 4.0 + - - -
817A MET 3.9 10.1 - - - +
818A ASP* 3.8 30.0 - - - +
819A ARG 4.4 0.7 - - - +
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Residues in contact with ALA 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 3.0 17.2 + - - +
614A CYS* 3.2 2.0 + - - +
616A ASP* 1.3 75.3 - - - +
618A GLY* 1.3 61.1 + - - +
619A ILE* 3.7 16.1 - - + +
751A ARG* 2.8 42.5 + - - +
817A MET* 3.7 26.7 + - + +
819A ARG 3.1 14.2 - - - +
820A PRO* 4.3 0.2 - - - -
821A PRO* 3.4 2.9 - - - +
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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