Contacts of the helix formed by residues 760 - 767 (chain A) in PDB entry 3T06
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 PHE 760 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755A VAL* 4.1 7.4 - - + -
756A LEU* 2.9 18.1 + - + +
759A ILE* 1.3 95.8 - - + +
761A TYR* 1.3 68.9 + - - +
762A GLN 3.4 1.6 - - - -
763A ARG* 3.2 3.3 + - - +
764A MET* 2.8 55.6 + - + +
779A PHE* 4.2 10.3 - - + -
856A PHE* 4.4 1.1 - + - -
857A MET* 4.2 13.5 - - + -
860A ALA* 3.7 22.4 - - + -
861A GLU* 4.1 22.4 - - + -
866A CYS* 4.1 7.4 - - - -
871A LEU* 4.0 31.9 - - + -
874A LEU* 3.8 22.7 - - + -
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Residues in contact with TYR 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A LEU 2.9 9.3 + - - -
757A ASP* 3.5 14.8 - - - +
760A PHE* 1.3 74.8 - - - +
762A GLN* 1.3 88.3 + - - +
764A MET* 3.1 3.6 + - - +
765A LYS* 2.9 52.1 + - - +
775A LEU* 4.1 22.2 - - + -
779A PHE* 3.4 48.7 + + + -
780A PRO 5.7 0.2 + - - -
782A LEU* 3.8 24.0 - - + -
783A PRO* 4.4 22.6 - - + +
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Residues in contact with GLN 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A ASP* 2.8 44.6 + - - +
758A LEU* 4.1 10.1 - - + +
761A TYR* 1.3 101.3 - - - +
763A ARG* 1.3 58.3 + - + +
765A LYS* 3.2 19.7 + - - +
766A LYS* 2.9 34.1 + - - +
783A PRO* 5.8 1.6 - - - +
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Residues in contact with ARG 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A LEU 3.6 13.8 + - - +
759A ILE* 3.5 20.9 + - - +
760A PHE 3.2 4.5 + - - +
762A GLN* 1.3 76.9 - - + +
764A MET* 1.3 63.9 + - - +
766A LYS* 4.9 4.7 - - - -
767A GLU* 3.2 51.1 + - - +
769A LEU* 4.4 0.2 - - - +
856A PHE* 3.7 33.8 - - + -
859A GLU* 3.0 31.3 + - - +
860A ALA* 3.7 30.3 - - - +
863A HIS* 5.8 2.2 + - - +
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Residues in contact with MET 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760A PHE* 2.8 47.7 + - + +
761A TYR 3.7 3.1 - - - +
763A ARG* 1.3 73.8 - - - +
765A LYS* 1.3 61.2 + - - +
768A ASN* 3.2 17.2 + - - -
769A LEU* 3.2 25.5 + - + +
770A MET* 3.5 31.7 + - + +
775A LEU* 4.1 20.6 - - + +
778A LEU* 4.8 2.5 - - + -
779A PHE* 4.5 11.0 - - + -
843A ILE* 6.1 0.4 - - + -
853A PHE* 4.9 1.1 - - + -
856A PHE* 3.5 16.3 - - + -
857A MET* 3.1 32.1 - - + -
871A LEU* 4.8 9.6 - - + -
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Residues in contact with LYS 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761A TYR* 2.9 55.4 + - + +
762A GLN* 3.5 21.0 + - - +
764A MET* 1.3 73.0 - - - +
766A LYS* 1.3 62.8 + - + +
767A GLU 3.0 9.4 + - - -
768A ASN* 3.2 8.1 + - - +
772A ARG* 3.1 48.8 + - - +
775A LEU* 3.9 18.8 - - + +
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Residues in contact with LYS 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A GLN* 2.9 17.8 + - - +
763A ARG* 4.6 4.0 - - + +
765A LYS* 1.3 81.3 - - + +
767A GLU* 1.3 69.9 + - + +
768A ASN* 3.7 5.2 + - - -
772A ARG* 5.1 1.8 - - - +
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Residues in contact with GLU 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763A ARG* 3.2 46.6 + - - +
765A LYS 3.1 0.6 - - - -
766A LYS* 1.3 91.7 - - + +
768A ASN* 1.3 76.6 + - - +
769A LEU* 3.5 11.0 - - + +
852A ARG* 3.0 25.8 + - - +
856A PHE* 4.2 16.8 - - - -
768E ASN* 3.9 4.4 + - - -
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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