Contacts of the helix formed by residues 771 - 778 (chain A) in PDB entry 1T65
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 ASN 771 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695A ASP* 5.8 0.6 + - - -
760A ARG 5.6 0.4 - - - -
761A MET* 4.1 22.9 - - + +
769A VAL 3.8 3.4 + - - -
770A PHE* 1.3 75.8 - - - +
772A GLU* 1.3 63.9 - - - +
773A TYR* 3.3 13.0 + - - +
774A ARG* 2.9 32.6 + - - +
775A MET* 3.1 23.3 + - - +
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Residues in contact with GLU 772 (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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771A ASN* 1.3 74.7 - - - +
773A TYR* 1.3 63.4 + - - +
775A MET* 3.2 19.2 + - + +
776A HIS* 3.0 23.2 + - - +
781A TYR* 3.0 34.5 + - + -
785A VAL* 4.7 0.5 - - - +
788A ARG* 2.7 39.5 + - - +
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Residues in contact with TYR 773 (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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695A ASP* 3.8 35.1 + - + -
771A ASN* 3.2 15.3 + - - +
772A GLU* 1.3 77.4 - - - +
774A ARG* 1.3 59.5 + - - +
776A HIS* 3.3 15.0 + + + +
777A LYS* 3.0 47.7 + - + +
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Residues in contact with ARG 774 (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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689A HIS* 4.1 8.6 + - - -
691A ASN* 3.0 35.9 + - - +
693A GLN 5.5 1.0 + - - -
695A ASP* 3.0 43.0 + - + +
700A LEU* 4.0 15.4 - - + +
768A LEU* 4.5 8.5 - - - +
769A VAL* 3.0 37.2 + - - +
770A PHE* 3.8 24.6 - - + +
771A ASN* 2.9 25.7 + - - +
773A TYR* 1.3 74.8 - - + +
775A MET* 1.3 65.6 + - - +
777A LYS* 3.8 7.2 - - - +
778A SER* 3.0 25.8 + - - -
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Residues in contact with MET 775 (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 ARG 5.4 1.6 - - - +
761A MET* 5.1 2.9 - - - -
762A LEU* 4.4 14.4 - - + +
770A PHE* 3.7 32.1 - - + +
771A ASN* 3.1 20.5 + - - +
772A GLU* 3.4 31.9 - - + +
774A ARG* 1.3 75.9 - - - +
776A HIS* 1.3 60.3 + - - +
778A SER* 2.7 22.5 + - - -
779A ARG 3.8 0.2 + - - -
781A TYR* 3.5 33.0 + - + -
784A CYS* 3.6 37.2 - - + +
785A VAL* 4.7 3.4 - - - -
788A ARG* 4.7 16.6 - - - +
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Residues in contact with HIS 776 (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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772A GLU 3.0 11.3 + - - +
773A TYR* 3.5 18.2 - + + +
774A ARG 3.2 0.2 - - - -
775A MET* 1.3 75.6 - - - +
777A LYS* 1.3 72.9 + - + +
779A ARG* 3.2 16.8 + - - +
781A TYR* 4.0 19.4 - - + +
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Residues in contact with LYS 777 (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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695A ASP* 3.7 21.1 + - + -
696A SER* 3.4 16.6 - - - +
697A PHE* 3.3 50.5 - - - +
700A LEU* 5.4 4.9 - - + -
773A TYR* 3.0 38.3 + - + +
774A ARG* 3.3 9.6 + - - +
776A HIS* 1.3 83.8 - - + +
778A SER* 1.3 60.4 + - - +
779A ARG* 3.2 5.9 + - - +
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Residues in contact with SER 778 (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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697A PHE* 3.3 12.6 - - - -
700A LEU* 5.4 4.2 - - - +
701A LEU* 3.7 20.4 - - - +
770A PHE* 3.8 20.1 - - - -
774A ARG 3.0 13.1 + - - -
775A MET* 2.7 23.0 + - - -
777A LYS* 1.3 74.6 - - - +
779A ARG* 1.3 68.7 + - - +
780A MET* 3.1 24.6 + - - +
784A CYS* 4.2 0.9 - - - -
876A PHE* 3.6 8.3 - - - -
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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