Contacts of the helix formed by residues 755 - 762 (chain C) in PDB entry 6DBT
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 755 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746C THR* 3.2 24.0 - - + +
747C TYR* 4.0 33.0 - - + +
748C ILE* 4.0 3.5 - - - +
753C ASP 4.7 0.2 - - - +
754C SER* 1.3 78.1 - - - +
756C ARG* 1.3 66.5 + - - +
757C ALA* 3.6 9.0 + - - +
758C GLU* 2.5 32.9 + - - +
759C ALA* 3.2 19.8 + - - +
796C ASP* 4.8 6.5 - - - +
799C LYS* 4.9 1.6 - - - +
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Residues in contact with ARG 756 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744C GLY 5.6 1.4 + - - -
745C SER 4.5 11.0 + - - -
746C THR* 3.0 23.5 + - + +
748C ILE* 3.6 39.1 - - - +
755C THR* 1.3 79.6 - - - +
757C ALA* 1.3 57.9 + - + +
759C ALA* 3.4 3.5 + - - +
760C SER* 2.9 26.0 + - - -
952C GLY 4.1 11.9 - - - +
953C LYS* 4.7 8.7 - - - +
954C ILE* 2.9 32.4 + - - +
955C THR* 5.5 1.4 - - - +
956C ASN 5.6 0.2 - - - +
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Residues in contact with ALA 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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746C THR* 5.5 0.4 - - - +
755C THR* 3.5 5.1 + - - +
756C ARG* 1.3 79.6 - - + +
758C GLU* 1.3 57.0 + - - +
760C SER* 2.7 20.7 + - - -
761C GLN* 2.9 20.0 + - - +
952C GLY* 3.6 21.8 - - - +
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Residues in contact with GLU 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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753C ASP 4.1 1.7 - - - +
754C SER* 3.0 21.1 + - - -
755C THR* 2.5 52.6 + - - +
757C ALA* 1.3 76.1 - - - +
759C ALA* 1.3 59.0 + - - +
761C GLN* 3.7 18.5 + - - +
762C ASN* 3.8 8.1 + - - +
766C HIS* 4.5 4.7 - - - -
799C LYS* 4.4 5.8 + - - -
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Residues in contact with ALA 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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748C ILE* 4.3 13.7 - - + -
754C SER* 4.3 8.7 - - - -
755C THR 3.2 20.2 + - - +
756C ARG 3.4 4.4 + - - +
757C ALA 3.1 0.6 - - - -
758C GLU* 1.3 77.9 - - - +
760C SER* 1.3 61.2 + - - +
762C ASN 2.7 23.2 - - - +
763C MET* 4.0 2.9 - - - -
766C HIS* 4.3 8.5 + - - +
954C ILE* 3.3 16.0 - - + +
959C HIS* 4.6 19.1 - - + +
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Residues in contact with SER 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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756C ARG 2.9 9.1 + - - -
757C ALA 2.7 18.2 + - - -
759C ALA* 1.3 71.8 - - - +
761C GLN* 1.3 65.5 + - - +
763C MET* 4.2 12.1 - - - +
947C LYS* 5.8 1.7 - - - -
950C TYR 2.7 35.7 + - - +
951C ASP 3.2 6.3 + - - +
952C GLY* 3.3 28.0 - - - -
953C LYS 3.4 4.3 + - - -
954C ILE* 3.4 17.5 - - - +
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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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757C ALA* 2.9 14.6 + - - +
758C GLU* 3.9 13.9 - - - +
759C ALA 3.3 0.4 - - - -
760C SER* 1.3 79.4 - - - +
762C ASN* 1.3 59.8 + - + +
763C MET* 5.1 1.4 - - - +
943C SER* 5.2 6.1 + - - -
947C LYS* 4.7 27.1 + - - +
951C ASP* 2.8 27.0 + - - +
952C GLY* 5.0 0.2 - - - -
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Residues in contact with ASN 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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758C GLU 3.8 4.2 + - - +
759C ALA 2.7 19.5 - - - +
761C GLN* 1.3 80.7 - - + +
763C MET* 1.3 72.9 + - - +
764C VAL* 3.1 18.1 + - - +
765C LEU* 3.3 39.7 + - - +
766C HIS* 3.2 18.9 + - + -
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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