Contacts of the helix formed by residues 744 - 764 (chain C) in PDB entry 5Y7K
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 SER 744 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738C GLU* 2.5 38.0 + - - -
742C ILE 3.4 0.4 - - - -
743C ALA* 1.3 77.2 - - - +
745C SER* 1.3 59.3 + - - +
746C THR* 4.4 6.1 - - - -
747C ALA* 3.8 10.5 - - - -
748C HIS* 2.7 35.5 + - - +
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Residues in contact with SER 745 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743C ALA 3.5 3.1 + - - -
744C SER* 1.3 73.4 - - - +
746C THR* 1.3 68.0 + - - +
748C HIS* 4.0 3.8 - - - +
749C GLN* 3.3 38.2 + - - +
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Residues in contact with THR 746 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C SER* 4.6 5.0 - - - -
745C SER* 1.3 78.8 - - - +
747C ALA* 1.3 68.0 + - - +
749C GLN* 3.7 11.0 + - - +
750C HIS* 3.1 23.2 + - - +
724D VAL* 3.4 23.4 - - - +
725D ASP* 3.3 39.5 + - + +
727D GLY* 5.8 0.7 - - - -
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Residues in contact with ALA 747 (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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735C TYR* 4.2 7.6 - - + -
738C GLU* 3.5 41.1 - - + +
742C ILE* 4.0 9.0 - - + -
744C SER* 3.4 5.8 + - - -
746C THR* 1.3 78.0 + - - +
748C HIS* 1.3 67.3 + - - +
750C HIS* 3.0 1.5 + - - +
751C ILE* 2.8 28.6 + - - +
724D VAL* 3.6 16.4 - - + -
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Residues in contact with HIS 748 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 3.4 23.7 + - - -
49C LEU* 3.9 24.0 - - + +
629C TRP* 6.1 0.8 - - - -
742C ILE 3.8 15.8 + - - +
743C ALA* 4.5 6.3 - - - +
744C SER 2.7 23.2 + - - +
745C SER* 4.0 4.3 - - - +
747C ALA* 1.3 71.6 - - - +
749C GLN* 1.3 68.6 + - + +
751C ILE* 3.1 20.5 - - - +
752C TYR* 3.3 44.2 + + - +
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Residues in contact with GLN 749 (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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49C LEU* 3.7 38.7 - - + +
50C LYS* 3.2 38.7 - - - +
745C SER* 3.3 32.4 + - - +
746C THR* 4.0 10.3 - - - +
747C ALA 3.3 0.4 - - - -
748C HIS* 1.3 79.9 - - + +
750C HIS* 1.3 54.9 + - - +
753C THR* 2.6 37.9 + - - +
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Residues in contact with HIS 750 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733C MET* 4.4 9.0 - - + -
735C TYR* 2.7 30.2 + + + +
746C THR 3.1 18.6 + - - +
747C ALA 3.0 5.8 + - - +
749C GLN* 1.3 79.6 - - - +
751C ILE* 1.3 57.0 + - - +
753C THR* 3.4 4.9 + - - -
754C HIS* 2.9 26.9 + - + +
724D VAL* 3.8 29.6 - - + +
727D GLY* 4.8 6.5 - - - -
728D VAL 3.3 32.8 + - - -
729D ASP* 3.9 20.2 - - + +
730D PHE* 3.5 25.6 - + - -
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Residues in contact with ILE 751 (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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629C TRP* 4.2 6.5 - - + -
653C VAL* 3.9 13.7 - - + -
703C ILE* 3.7 37.7 - - + -
735C TYR* 3.1 20.2 + - + +
742C ILE* 3.8 28.0 - - + +
747C ALA 2.8 14.3 + - - +
748C HIS* 3.1 18.6 - - - +
750C HIS* 1.3 76.9 - - - +
752C TYR* 1.3 81.2 + - + +
754C HIS* 3.2 3.0 + - - +
755C MET* 2.8 41.9 + - + +
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Residues in contact with TYR 752 (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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45C LEU* 4.3 3.8 - - + +
48C TYR* 3.6 15.6 + + + -
49C LEU* 4.0 15.9 - - + -
563C TRP* 3.4 51.8 + + + -
627C TRP* 4.0 12.1 - + - -
629C TRP* 4.0 21.6 - + - -
748C HIS* 3.3 51.7 + + - +
751C ILE* 1.3 88.9 - - + +
753C THR* 1.3 56.7 - - - +
755C MET* 3.5 21.5 - - + -
756C SER* 2.7 35.9 + - - -
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Residues in contact with THR 753 (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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45C LEU* 4.0 14.6 - - + +
49C LEU* 3.6 14.2 - - - +
749C GLN* 2.6 25.3 + - - +
750C HIS* 3.7 5.8 - - - -
752C TYR* 1.3 75.9 - - - +
754C HIS* 1.3 64.8 + - - +
756C SER* 3.2 11.1 + - - -
757C HIS* 3.3 36.8 + - + +
729D ASP* 5.2 8.3 - - + -
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Residues in contact with HIS 754 (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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701C LEU* 4.2 31.0 - - + +
703C ILE* 5.0 4.0 - - + -
731C GLN* 5.9 1.4 + - - +
732C ALA 4.8 2.2 + - - -
733C MET* 3.7 23.6 - - + +
735C TYR* 4.4 6.7 - - - +
750C HIS* 2.9 20.0 + - - +
751C ILE* 3.2 4.9 + - - +
753C THR* 1.3 75.7 - - - +
755C MET* 1.3 62.3 + - + +
757C HIS* 3.5 4.6 + - + +
758C PHE* 3.2 20.1 + - + +
729D ASP* 2.6 33.1 + - - +
730D PHE 3.1 23.3 + - - -
731D GLN* 3.6 21.0 + - - -
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Residues in contact with MET 755 (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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563C TRP* 4.0 12.3 - - + -
627C TRP* 4.1 16.4 - - + -
629C TRP* 5.2 1.1 - - + -
651C ILE* 3.9 34.3 - - + +
653C VAL* 4.0 15.3 - - + -
701C LEU* 4.3 1.3 - - + -
703C ILE* 3.8 18.6 - - + -
751C ILE* 2.8 36.8 + - + +
752C TYR* 3.5 41.3 - - + +
753C THR 3.3 0.2 - - - -
754C HIS* 1.3 73.9 - - - +
756C SER* 1.3 65.2 + - - +
758C PHE* 3.4 4.0 + - - +
759C ILE* 3.1 28.6 + - - +
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Residues in contact with SER 756 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 3.8 12.1 - - - +
563C TRP* 3.1 23.7 + - - -
566C TYR* 3.6 24.9 - - - -
567C LEU* 5.5 0.7 - - - -
752C TYR 2.7 22.2 + - - -
753C THR 3.2 6.5 + - - -
755C MET* 1.3 74.5 - - - +
757C HIS* 1.3 64.0 + - - +
759C ILE* 3.4 2.7 + - - +
760C LYS* 2.9 39.4 + - - +
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Residues in contact with HIS 757 (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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753C THR* 3.3 32.0 + - + +
754C HIS* 3.9 6.0 - - + +
756C SER* 1.3 80.7 - - - +
758C PHE* 1.3 57.7 + - - +
760C LYS* 4.0 13.4 - - + +
761C GLN* 2.9 36.3 + - - +
729D ASP* 3.1 30.6 + - + +
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Residues in contact with PHE 758 (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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649C CYS* 3.8 22.2 - - + -
650C GLY 3.7 20.2 - - - -
651C ILE* 3.5 21.8 - - + -
699C GLU* 3.5 37.0 - - + -
700C TYR 4.4 0.9 - - - -
701C LEU* 3.6 32.8 - - + -
731C GLN* 4.0 22.2 - - + -
754C HIS* 3.2 12.8 + - + +
755C MET 3.7 7.0 - - - +
756C SER 3.3 0.2 - - - -
757C HIS* 1.3 79.9 - - - +
759C ILE* 1.3 60.8 + - + +
761C GLN* 3.9 6.0 - - - +
762C CYS* 3.0 28.3 + - + +
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Residues in contact with ILE 759 (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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543C LEU* 4.2 15.9 - - + -
563C TRP* 4.0 15.3 - - + -
567C LEU* 4.6 7.6 - - + -
573C ILE* 3.8 14.1 - - + -
625C ALA* 4.2 23.6 - - + -
626C ILE 6.0 0.2 - - - +
627C TRP* 5.7 0.2 - - + -
649C CYS* 4.7 2.0 - - - -
650C GLY* 6.0 0.7 - - - -
651C ILE* 3.8 24.2 - - + -
755C MET 3.1 17.3 + - - +
756C SER* 3.9 4.3 - - - +
758C PHE* 1.3 81.8 - - + +
760C LYS* 1.3 61.4 + - + +
762C CYS* 3.0 5.2 + - - +
763C PHE* 2.9 54.1 + - + +
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Residues in contact with LYS 760 (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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566C TYR* 3.9 10.4 + - - +
567C LEU* 5.9 1.1 - - + -
571C GLU* 3.5 45.0 + - + +
573C ILE* 5.6 2.7 - - + -
756C SER* 2.9 27.1 + - - +
757C HIS* 4.0 13.2 - - + +
759C ILE* 1.3 78.1 - - + +
761C GLN* 1.3 58.3 + - - +
763C PHE* 3.3 5.6 + - - +
764C SER* 2.9 31.2 + - - -
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Residues in contact with GLN 761 (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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648C LYS* 5.0 1.6 + - - -
699C GLU* 5.1 9.6 + - - +
757C HIS* 2.9 20.5 + - - +
758C PHE* 3.9 6.2 - - - +
760C LYS* 1.3 76.9 - - - +
762C CYS* 1.3 61.6 + - - +
764C SER* 3.5 14.7 + - - +
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Residues in contact with CYS 762 (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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623C ARG* 4.7 1.4 - - - +
648C LYS* 3.1 48.4 + - - +
649C CYS* 2.0 52.9 - - + -
699C GLU* 4.8 8.7 - - - +
758C PHE* 3.0 19.3 + - + +
759C ILE 3.0 4.2 + - - +
761C GLN* 1.3 77.8 - - - +
763C PHE* 1.3 67.1 + - - +
764C SER* 3.5 2.1 + - - -
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Residues in contact with PHE 763 (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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541C PRO* 3.5 22.9 - - + -
542C LEU 3.8 14.4 - - - -
543C LEU* 4.7 1.8 - - + -
573C ILE* 3.4 36.6 - - + -
623C ARG* 3.0 66.3 + - + +
624C ILE 4.2 0.2 - - - -
625C ALA* 3.7 31.0 - - + -
649C CYS* 4.7 0.2 - - - -
759C ILE* 2.9 30.6 + - + +
760C LYS* 4.1 4.5 - - - +
762C CYS* 1.3 89.0 - - - +
764C SER* 1.3 72.3 + - - +
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Residues in contact with SER 764 (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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623C ARG* 5.0 4.3 + - - -
648C LYS* 5.8 2.1 + - - -
760C LYS 2.9 16.9 + - - -
761C GLN* 3.5 12.3 + - - +
762C CYS 4.7 2.1 + - - -
763C PHE* 1.3 85.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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