Contacts of the helix formed by residues 611 - 624 (chain C) in PDB entry 1DQ8
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 611 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607C ALA* 3.3 16.8 - - + +
608C TRP* 2.7 25.0 + - + +
610C GLU* 1.3 82.1 - - - +
612C SER* 1.3 62.9 + - - +
613C GLU* 3.6 15.1 + - - +
614C GLY* 3.0 15.8 + - - -
615C PHE* 3.2 22.5 + - - +
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Residues in contact with SER 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C GLU 4.0 0.6 + - - -
611C THR* 1.3 72.9 - - - +
613C GLU* 1.3 78.2 + - - +
615C PHE* 4.0 5.5 - - - +
616C ALA* 3.0 26.0 + - - +
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Residues in contact with GLU 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C TRP* 5.2 3.4 - - - +
611C THR* 3.6 17.4 - - - +
612C SER* 1.3 87.3 + - - +
614C GLY* 1.3 66.0 + - - +
616C ALA* 3.2 7.6 + - - +
617C VAL* 3.1 27.5 + - + +
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Residues in contact with GLY 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C TRP* 3.6 46.5 - - - -
609C LEU* 4.6 1.8 - - - -
611C THR* 3.0 8.8 + - - -
613C GLU* 1.3 78.7 - - - +
615C PHE* 1.3 61.4 - - - +
617C VAL* 3.0 19.6 - - - +
618C ILE* 3.2 11.5 + - - +
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Residues in contact with PHE 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C LEU* 3.7 14.3 + - - +
610C GLU 5.4 0.2 - - - -
611C THR 3.2 19.7 + - - +
612C SER* 4.1 5.4 - - - +
614C GLY* 1.3 74.1 - - - +
616C ALA* 1.3 60.0 + - - +
618C ILE* 3.5 5.4 + - + +
619C LYS* 2.9 55.6 + - + +
631C LEU* 4.1 24.0 - - + -
632C GLN 3.7 21.5 - - - -
633C LYS* 4.0 12.6 - - - -
634C LEU* 4.0 35.0 - - + -
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Residues in contact with ALA 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C SER 3.0 20.2 + - - +
613C GLU* 3.4 7.4 - - - +
615C PHE* 1.3 80.4 - - - +
617C VAL* 1.3 63.9 + - + +
619C LYS* 3.3 8.4 + - - +
620C GLU* 3.0 25.1 + - - +
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Residues in contact with VAL 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C TRP* 3.1 31.6 - - + -
613C GLU* 3.1 10.8 + - + +
614C GLY 3.0 22.7 - - - +
616C ALA* 1.3 76.9 - - + +
618C ILE* 1.3 63.3 + - + +
620C GLU* 3.2 11.6 + - - +
621C ALA* 3.1 21.0 + - - +
670C LYS* 4.4 12.6 - - + +
674C TYR* 3.8 26.7 - - + +
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Residues in contact with ILE 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C TRP* 3.6 23.8 - - + -
609C LEU* 4.1 17.0 - - + -
614C GLY 3.2 15.4 + - - +
615C PHE* 4.0 8.1 - - + +
617C VAL* 1.3 79.3 - - + +
619C LYS* 1.3 57.9 + - - +
621C ALA* 3.7 6.8 - - - +
622C PHE* 2.8 30.8 + - - +
631C LEU* 3.4 16.8 - - + -
634C LEU* 4.3 10.5 - - + -
647C PHE* 3.2 36.8 - - + -
667C ALA* 3.8 18.0 - - + +
670C LYS* 5.0 2.7 - - + -
671C LEU* 4.8 9.2 - - + +
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Residues in contact with LYS 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C PHE* 2.9 39.4 + - + +
616C ALA* 3.6 7.0 - - - +
618C ILE* 1.3 74.5 - - - +
620C GLU* 1.3 58.5 + - - +
623C ASP* 2.7 70.5 + - - +
630C ARG* 3.9 10.3 - - - +
631C LEU* 3.0 48.7 + - + +
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Residues in contact with GLU 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C ALA 3.0 13.1 + - - +
617C VAL* 3.4 13.2 - - - +
619C LYS* 1.3 75.8 - - - +
621C ALA* 1.3 65.9 + - - +
623C ASP* 3.5 3.9 + - - +
624C SER* 3.1 26.0 + - - -
670C LYS* 5.8 3.6 - - - -
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Residues in contact with ALA 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C VAL 3.1 9.8 + - - +
618C ILE 3.7 6.7 - - - +
620C GLU* 1.3 81.6 - - - +
622C PHE* 1.3 62.3 + - - +
624C SER* 2.7 24.1 + - - -
625C THR* 3.9 7.8 - - - +
666C LYS* 4.1 13.2 - - + +
667C ALA* 4.0 9.4 - - - -
670C LYS* 3.8 31.9 - - + -
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Residues in contact with PHE 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C ILE 2.8 22.3 + - - +
619C LYS 3.7 3.6 - - - +
621C ALA* 1.3 74.8 - - - +
623C ASP* 1.3 72.3 + - - +
624C SER 3.1 1.0 + - - -
625C THR* 2.9 26.7 + - - +
629C ALA* 3.8 19.0 - - + +
631C LEU* 4.0 16.6 - - + -
647C PHE* 3.6 33.9 - + + -
649C SER* 3.7 31.2 - - - -
660C ILE* 3.9 27.1 - - + -
663C GLY* 3.2 36.5 - - - +
664C THR* 3.7 7.0 - - - -
667C ALA* 4.2 2.4 - - + +
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Residues in contact with ASP 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C LYS* 2.7 53.6 + - - +
620C GLU* 4.1 4.0 - - - +
622C PHE* 1.3 76.5 - - - +
624C SER* 1.3 57.4 + - - +
625C THR 3.2 0.7 - - - -
626C SER 2.9 24.0 - - - +
629C ALA 2.9 19.5 - - - +
630C ARG* 3.4 21.5 + - - +
631C LEU* 2.8 24.0 + - - +
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Residues in contact with SER 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C GLU* 3.1 14.3 + - - -
621C ALA* 2.7 22.4 + - - -
622C PHE 3.1 0.2 + - - -
623C ASP* 1.3 75.1 - - - +
625C THR* 1.3 61.5 + - - +
626C SER 3.2 2.3 + - - -
666C LYS* 4.3 11.5 - - - +
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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