Contacts of the helix formed by residues 701 - 710 (chain C) in PDB entry 5Y3R
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 TYR 701 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676C ASN* 4.4 14.1 - - + -
677C ALA* 5.3 0.7 - - - -
680C ILE* 3.7 24.4 - - + +
700C LYS* 1.3 119.8 + - + +
702C SER* 1.3 57.6 + - - +
704C PHE* 2.7 42.8 + + - +
705C ALA* 3.0 8.5 + - - +
1442C GLN* 3.9 23.1 + - - -
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Residues in contact with SER 702 (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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680C ILE* 4.2 7.4 - - - +
700C LYS 4.6 0.6 - - - +
701C TYR* 1.3 75.6 - - - +
703C CYS* 1.3 60.6 + - - +
705C ALA* 2.7 29.3 + - - +
706C LEU* 2.9 21.5 + - - +
1384C PHE* 5.9 3.6 - - - -
1385C ASN* 4.7 13.7 - - - -
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Residues in contact with CYS 703 (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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639C ALA* 4.8 13.0 - - + +
640C GLU* 5.0 10.3 - - - -
642C PHE* 5.1 2.5 - - + -
643C GLU* 2.9 33.5 - - + +
700C LYS* 2.5 41.3 - - - +
701C TYR 3.0 0.2 - - - -
702C SER* 1.3 77.2 - - - +
704C PHE* 1.3 50.3 + - + -
706C LEU* 4.2 6.3 - - - +
707C PHE* 2.4 39.2 + - - +
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Residues in contact with PHE 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C GLN* 5.8 2.2 - - + -
639C ALA* 5.0 12.3 - - + -
672C ILE* 3.3 32.3 - - + -
673C THR* 3.8 24.2 - - + +
676C ASN* 4.1 16.6 - - + -
677C ALA* 3.5 22.0 - - + -
680C ILE* 6.0 0.2 - - + -
700C LYS* 2.6 50.7 + - + -
701C TYR* 2.7 42.9 + + - +
703C CYS* 1.3 73.9 - - + +
705C ALA* 1.3 54.6 + - - +
707C PHE* 3.0 13.5 - + + +
708C VAL* 2.8 32.5 + - - +
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Residues in contact with ALA 705 (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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677C ALA* 4.8 4.9 - - - +
680C ILE* 5.1 16.8 - - + -
701C TYR 3.0 5.1 + - - +
702C SER* 2.7 28.2 + - - +
704C PHE* 1.3 67.9 - - - +
706C LEU* 1.3 62.8 + - + +
708C VAL* 2.8 16.2 - - - +
709C LYS* 2.8 24.3 + - - +
1385C ASN* 5.1 8.5 - - - +
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Residues in contact with LEU 706 (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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643C GLU* 5.5 2.2 - - + +
647C TYR* 4.3 20.2 - - + +
702C SER* 2.9 18.4 + - - +
703C CYS* 4.2 5.8 - - - +
705C ALA* 1.3 72.9 - - - +
707C PHE* 1.3 54.0 + - - +
708C VAL 2.8 3.6 - - - -
709C LYS* 2.2 43.4 + - + +
710C PHE* 2.9 20.8 + - + -
1384C PHE* 5.1 6.3 - - + -
1385C ASN* 3.3 54.3 - - + +
1388C ASP* 4.3 13.2 - - - +
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Residues in contact with PHE 707 (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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639C ALA* 6.5 0.7 - - - -
642C PHE* 3.6 43.9 - + + -
664C SER* 4.7 9.4 - - - -
670C LEU* 4.8 2.2 - - + -
673C THR* 3.2 37.5 - - + -
677C ALA* 5.3 0.9 - - + -
703C CYS 2.4 25.9 + - - +
704C PHE* 3.0 25.8 - + + +
706C LEU* 1.3 73.1 - - - +
708C VAL* 1.3 61.0 + - + +
710C PHE* 2.8 29.0 - - - -
740C ILE* 3.5 30.5 - - + -
741C ILE* 5.6 4.1 - - + +
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Residues in contact with VAL 708 (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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677C ALA* 4.0 20.4 - - + +
681C LYS* 5.1 9.2 - - + +
704C PHE 2.8 21.9 + - - +
705C ALA* 2.8 13.5 - - - +
706C LEU 2.8 3.4 - - - -
707C PHE* 1.3 80.1 - - + +
709C LYS* 1.3 57.4 + - + +
710C PHE* 2.4 20.1 + - - +
711C GLY* 3.2 10.9 + - - +
741C ILE* 4.8 17.3 - - + +
744C ASP* 4.4 26.0 - - + +
748C TYR* 4.9 8.3 - - - +
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Residues in contact with LYS 709 (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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705C ALA 2.8 11.7 + - - +
706C LEU* 2.2 45.6 + - + +
708C VAL* 1.3 74.0 - - - +
710C PHE* 1.3 58.8 + - - -
711C GLY 2.7 3.9 + - - +
712C LYS 4.4 1.2 + - - -
713C GLU* 2.5 46.1 + - - +
1385C ASN* 4.0 19.9 + - + +
1386C ILE* 4.4 19.8 - - + +
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Residues in contact with PHE 710 (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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642C PHE* 3.4 17.0 - + - -
646C VAL* 3.4 45.5 - - + -
649C PHE* 6.3 0.7 - - + -
706C LEU* 2.9 28.8 + - + -
707C PHE* 2.8 36.6 - - - -
708C VAL 2.4 14.6 + - - +
709C LYS* 1.3 68.9 - - - +
711C GLY* 1.3 66.3 + - - +
713C GLU* 2.8 22.5 + - - +
714C VAL* 2.9 36.6 + - + -
734C LEU* 6.2 1.3 - - + -
737C PRO* 6.2 4.3 - - + -
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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