Contacts of the helix formed by residues 610 - 623 (chain s) in PDB entry 6QX2
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 ASP 610 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13r ASN* 5.3 0.4 - - - +
15r THR* 5.0 0.9 + - - -
608s LEU* 3.9 3.6 - - - +
609s GLU* 1.3 76.9 - - + +
611s ALA* 1.3 57.3 + - - +
612s ILE* 3.1 25.2 + - - +
613s GLU* 3.4 33.0 + - + +
614s ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 611 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525s TYR* 3.0 8.0 + - - -
529s ARG* 3.2 35.9 - - - +
608s LEU* 4.0 12.0 - - + +
609s GLU 4.0 3.8 + - - -
610s ASP* 1.3 70.2 + - - +
612s ILE* 1.3 57.9 + - + +
615s ASP* 2.9 38.6 + - - +
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Residues in contact with ILE 612 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610s ASP* 3.1 11.7 + - - +
611s ALA* 1.3 77.8 - - + +
613s GLU* 1.3 62.0 + - - +
615s ASP* 3.3 10.8 + - - +
616s GLN* 3.2 44.9 + - - +
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Residues in contact with GLU 613 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13r ASN* 5.0 2.8 + - - +
15r THR* 3.7 29.7 + - - +
610s ASP* 3.4 33.3 + - - +
612s ILE* 1.3 76.2 - - - +
614s ALA* 1.3 59.9 + - - +
616s GLN* 3.5 15.2 + - - +
617s THR* 3.0 36.3 + - - +
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Residues in contact with ALA 614 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14r ILE* 4.6 6.3 - - + -
15r THR* 3.9 15.4 + - - +
525s TYR* 3.4 29.2 - - + +
608s LEU* 3.8 11.0 - - + -
610s ASP 3.0 17.3 + - - +
611s ALA 3.6 1.1 - - - +
612s ILE 3.3 0.2 - - - -
613s GLU* 1.3 73.2 - - - +
615s ASP* 1.3 63.9 + - - +
617s THR* 3.1 3.8 + - - -
618s PHE* 3.0 35.4 + - + -
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Residues in contact with ASP 615 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525s TYR* 3.0 14.8 + - - -
526s ARG* 3.1 35.1 + - - +
529s ARG* 4.2 10.2 + - - -
611s ALA* 2.9 26.0 + - - +
612s ILE* 3.3 11.7 + - - +
614s ALA* 1.3 74.1 - - - +
616s GLN* 1.3 62.5 + - + +
619s GLU* 3.3 24.8 + - - +
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Residues in contact with GLN 616 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612s ILE* 3.2 32.4 + - - +
613s GLU* 3.8 17.7 - - - +
614s ALA 3.2 0.6 - - - -
615s ASP* 1.3 76.7 - - + +
617s THR* 1.3 59.6 + - - +
619s GLU* 3.5 15.0 + - - +
620s MET* 3.0 30.4 + - - +
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Residues in contact with THR 617 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15r THR* 4.0 21.0 - - + +
18r MET* 4.2 14.1 - - + -
19r ARG* 4.0 23.1 + - + +
613s GLU* 3.0 20.1 + - - +
614s ALA* 3.1 5.8 + - - -
616s GLN* 1.3 73.6 - - - +
618s PHE* 1.3 61.8 + - + +
620s MET* 3.7 10.4 - - + +
621s LEU* 3.0 55.7 + - + +
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Residues in contact with PHE 618 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14r ILE* 3.9 19.7 - - + -
15r THR* 6.0 0.9 - - - -
18r MET* 3.6 34.8 - - + -
465s GLU* 3.9 6.0 - - - +
521s LEU 3.8 4.0 - - - -
522s THR* 3.2 50.5 - - + -
525s TYR* 3.6 44.2 - + + -
526s ARG* 3.8 19.3 - - - +
614s ALA* 3.0 31.2 + - + +
617s THR* 1.3 73.8 - - + +
619s GLU* 1.3 58.9 + - - +
621s LEU* 5.0 0.2 - - - -
622s MET* 2.8 39.5 + - + +
623s GLY 3.5 0.5 + - - -
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Residues in contact with GLU 619 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465s GLU* 3.4 17.4 + - - +
526s ARG* 4.4 2.2 - - - +
615s ASP 3.3 17.1 + - - +
616s GLN* 3.7 17.7 - - - +
617s THR 3.4 0.2 - - - -
618s PHE* 1.3 77.4 - - - +
620s MET* 1.3 58.1 + - - +
623s GLY* 3.1 26.9 + - - +
625s VAL* 5.4 3.8 + - - +
628s ASN* 6.4 0.2 - - - -
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Residues in contact with MET 620 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19r ARG* 5.1 7.2 - - - +
616s GLN 3.0 17.7 + - - +
617s THR* 3.7 14.1 - - + +
618s PHE 3.2 0.2 - - - -
619s GLU* 1.3 77.8 + - - +
621s LEU* 1.3 87.2 + - + +
625s VAL 4.3 3.3 - - - +
628s ASN* 3.9 33.2 - - + +
629s ARG* 3.5 27.2 + - - +
632s PHE* 3.7 33.4 - - + -
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Residues in contact with LEU 621 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18r MET* 3.8 39.3 - - + +
19r ARG* 4.1 4.7 - - + -
22r PHE* 3.7 28.1 - - + -
617s THR* 3.0 33.5 + - + +
620s MET* 1.3 89.7 - - + +
622s MET* 1.3 69.2 + - + +
629s ARG* 2.8 33.3 + - + +
632s PHE* 3.3 38.6 - - + -
2016w C 4.6 1.2 + - - -
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Residues in contact with MET 622 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18r MET* 4.1 15.0 - - + -
22r PHE* 3.8 19.3 - - + -
463s ASN* 3.1 32.3 + - - +
465s GLU* 3.2 25.7 - - + +
466s LYS* 3.4 5.5 - - - +
515s HIS* 5.0 0.2 - - - +
518s THR* 3.7 20.0 - - - +
519s LEU* 3.7 26.9 - - + -
522s THR* 3.2 28.7 - - + +
618s PHE* 2.8 20.2 + - + +
621s LEU* 1.3 82.6 - - + +
623s GLY* 1.3 64.1 + - - +
629s ARG* 4.0 0.9 - - - +
2016w C 4.1 6.7 - - - +
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Residues in contact with GLY 623 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465s GLU* 3.7 13.9 - - - -
466s LYS* 3.4 5.7 - - - -
618s PHE 3.5 1.6 + - - -
619s GLU* 3.1 25.4 + - - -
621s LEU 3.6 1.2 - - - -
622s MET* 1.3 79.6 - - - +
624s ASP* 1.3 60.5 + - - -
625s VAL 3.3 3.4 - - - -
629s ARG* 2.8 28.8 + - - +
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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