Contacts of the helix formed by residues 769 - 778 (chain A) in PDB entry 1HU3
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 MSE 769 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767A PRO 3.9 1.6 + - - +
768A GLN* 1.3 75.2 - - - +
770A PHE* 1.3 69.3 + - - +
771A ASN* 4.4 25.1 - - + +
772A GLN* 3.0 24.7 + - + +
773A LEU* 3.0 20.3 + - - +
811A ASN* 6.0 1.1 - - - +
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Residues in contact with PHE 770 (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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769A MSE 1.3 74.9 - - + +
771A ASN* 1.3 68.4 + - - +
773A LEU* 2.6 36.6 + - - +
774A MSE 3.0 37.8 + - + +
811A ASN* 3.9 35.8 - - + +
814A ARG* 3.5 44.4 - - + -
815A CYS* 3.8 17.0 - - - -
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Residues in contact with ASN 771 (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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769A MSE 3.6 22.5 - - + +
770A PHE* 1.3 92.1 - - - +
772A GLN* 1.3 63.9 + - - +
774A MSE 3.1 15.7 + - - +
775A LYS* 3.3 11.5 + - - +
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Residues in contact with GLN 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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764A LYS* 5.9 3.0 - - - +
766A THR 5.5 0.8 + - - -
767A PRO 5.1 0.2 - - - +
768A GLN* 2.8 33.5 - - + +
769A MSE 3.0 42.4 + - + +
771A ASN* 1.3 78.0 - - - +
773A LEU* 1.3 57.1 + - - +
775A LYS* 3.4 17.2 + - + +
776A GLN* 3.0 46.7 + - - +
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Residues in contact with LEU 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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761A ILE* 4.5 6.7 - - + +
768A GLN* 3.5 37.2 - - + +
769A MSE 3.0 11.4 + - - +
770A PHE* 2.6 22.8 + - - +
772A GLN* 1.3 73.1 - - - +
774A MSE 1.3 53.5 + - - +
776A GLN* 3.3 11.8 + - - +
777A VAL* 2.8 35.7 + - + +
808A ALA* 3.8 6.5 - - + +
811A ASN* 3.6 20.0 - - + +
812A MSE 3.6 48.5 - - + +
815A CYS* 3.8 7.9 - - - -
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Residues in contact with MSE 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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770A PHE* 3.0 40.8 + - + +
771A ASN* 3.1 9.8 + - - +
773A LEU* 1.3 75.9 - - - +
775A LYS* 1.3 61.8 + - - +
777A VAL* 3.7 3.6 + - - +
778A SER* 3.2 23.2 + - - -
814A ARG 5.5 0.4 - - - +
815A CYS* 3.6 35.4 - - - +
818A THR* 4.9 15.5 - - + +
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Residues in contact with LYS 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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771A ASN 3.3 7.6 + - - +
772A GLN* 3.6 20.9 - - + +
773A LEU 3.3 0.4 - - - -
774A MSE 1.3 76.6 - - - +
776A GLN* 1.3 70.8 + - + +
778A SER* 2.7 24.5 + - - +
779A GLY* 3.6 3.3 + - - -
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Residues in contact with GLN 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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761A ILE* 3.8 35.8 - - + +
764A LYS* 5.3 11.8 - - - +
768A GLN* 4.2 3.0 - - - +
772A GLN* 3.0 42.6 + - - +
773A LEU* 3.5 29.1 - - - +
775A LYS* 1.3 83.4 - - + +
777A VAL* 1.3 56.9 + - - +
779A GLY* 2.9 22.5 + - - -
780A LEU* 3.7 8.0 - - - +
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Residues in contact with VAL 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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761A ILE* 5.0 3.4 - - + -
773A LEU* 2.8 24.6 + - + +
774A MSE 4.2 3.8 - - - +
776A GLN* 1.3 73.4 - - + +
778A SER* 1.3 56.3 + - - +
779A GLY 3.0 0.4 - - - -
780A LEU* 3.2 35.5 + - + +
812A MSE 4.2 18.8 - - - -
815A CYS* 3.8 32.8 - - + +
816A LEU* 3.5 32.1 - - + -
819A LEU* 4.7 15.2 - - + +
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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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774A MSE 3.2 15.8 + - - -
775A LYS* 2.7 19.2 + - - -
776A GLN 3.1 1.2 - - - -
777A VAL* 1.3 76.6 - - - +
779A GLY* 1.3 57.1 + - - +
780A LEU 3.2 6.1 + - - +
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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