Contacts of the helix formed by residues 805 - 817 (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 PHE 805 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764A LYS 5.9 0.4 - - - -
765A LEU* 4.5 11.9 - - + -
767A PRO* 3.3 43.7 - - + -
802A GLU* 3.0 34.8 + - + +
803A PRO 3.1 1.4 - - - -
804A SER* 1.3 89.5 - - - +
806A SER* 1.3 59.4 + - - +
807A VAL* 3.1 3.4 - - - -
808A ALA* 2.8 23.3 + - + +
809A TYR* 3.1 36.8 + - + +
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Residues in contact with SER 806 (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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799A ALA* 5.1 0.9 - - - -
803A PRO* 2.5 24.4 + - - -
804A SER 3.2 1.2 - - - -
805A PHE* 1.3 75.0 - - - +
807A VAL* 1.3 60.1 + - - +
809A TYR* 3.8 12.3 - - - -
810A ALA* 2.9 31.5 + - - +
894A LYS* 3.4 26.6 + - - +
895A PHE* 3.7 35.1 - - - -
898A GLU* 3.5 6.6 + - - +
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Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A SER 4.7 5.6 + - - +
805A PHE* 3.1 1.7 - - - -
806A SER* 1.3 79.4 + - - +
808A ALA* 1.3 60.3 + - - +
810A ALA* 3.3 2.8 + - - +
811A ASN* 2.9 47.5 + - - +
894A LYS* 5.8 4.5 - - - +
898A GLU* 3.5 33.7 - - - +
902A LEU* 5.5 0.2 - - - +
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Residues in contact with ALA 808 (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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767A PRO* 4.1 26.9 - - + -
768A GLN 4.2 15.0 - - - +
773A LEU* 3.8 4.3 - - + +
805A PHE* 2.8 13.9 + - + +
807A VAL* 1.3 81.6 - - - +
809A TYR* 1.3 63.7 + - + +
811A ASN* 2.9 12.2 + - - +
812A MSE 2.8 27.8 + - - +
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Residues in contact with TYR 809 (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 LEU* 3.7 39.7 + - + -
767A PRO* 5.5 1.0 - - + +
795A VAL* 3.9 9.8 - - + +
798A LYS* 3.4 29.2 - - + +
799A ALA* 3.6 26.0 - - + -
802A GLU* 3.4 38.9 + - - -
805A PHE* 3.1 34.9 + - + -
806A SER* 3.8 3.1 - - - +
808A ALA* 1.3 79.6 - - + +
810A ALA* 1.3 57.7 + - - +
812A MSE 3.0 9.9 - - + +
813A CYS* 2.9 30.5 + - - -
895A PHE* 3.7 17.9 - - + -
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Residues in contact with ALA 810 (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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806A SER 2.9 19.9 + - - +
807A VAL 3.6 4.0 - - - +
809A TYR* 1.3 74.2 - - - +
811A ASN* 1.3 62.4 + - - +
813A CYS* 3.2 3.6 + - - +
814A ARG* 2.9 26.5 + - - +
895A PHE* 3.8 2.4 - - + -
898A GLU* 3.8 27.8 - - + -
899A LEU* 3.8 22.9 - - + -
902A LEU* 4.0 10.3 - - + -
904A MSE 3.7 4.9 - - - +
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Residues in contact with ASN 811 (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 6.0 1.0 - - - +
770A PHE* 3.9 28.7 - - + +
773A LEU* 3.6 15.5 - - + -
807A VAL* 2.9 39.3 + - - +
808A ALA* 2.9 10.8 + - - +
810A ALA* 1.3 76.5 - - - +
812A MSE 1.3 62.7 + - - +
814A ARG* 3.1 11.7 + - - +
815A CYS* 3.0 25.3 + - - -
902A LEU* 4.1 14.8 - - - +
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Residues in contact with MSE 812 (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 VAL* 3.9 19.5 - - + -
761A ILE* 3.7 25.4 - - + -
762A LEU* 3.5 39.7 - - + -
773A LEU* 3.6 23.8 - - + +
777A VAL* 4.2 17.3 - - - -
780A LEU* 5.8 2.2 - - + -
791A VAL* 5.6 0.2 - - + -
795A VAL* 4.2 9.0 - - + -
808A ALA 2.8 10.6 + - - +
809A TYR* 3.0 17.5 - - + +
811A ASN* 1.3 76.0 - - - +
813A CYS* 1.3 54.5 + - - +
815A CYS* 2.8 26.5 + - - +
816A LEU* 3.1 39.0 + - + +
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Residues in contact with CYS 813 (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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792A ILE* 5.8 3.4 - - - -
795A VAL* 4.0 23.6 - - - -
796A PHE* 5.2 1.3 - - - -
809A TYR 2.9 15.0 + - - -
810A ALA 3.2 8.0 + - - +
812A MSE 1.3 76.2 - - - +
814A ARG* 1.3 64.3 + - - +
816A LEU* 3.1 20.7 + - - +
817A VAL* 3.1 15.2 + - - +
833A PHE* 3.8 13.2 - - + -
837A LEU* 4.3 15.0 - - - -
895A PHE* 4.3 5.6 - - - -
899A LEU* 3.6 26.0 - - + -
904A MSE 3.8 6.9 - - - +
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Residues in contact with ARG 814 (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* 3.5 38.2 - - + -
774A MSE 5.5 0.7 - - - +
810A ALA 2.9 13.1 + - - +
811A ASN* 3.1 19.0 + - - +
813A CYS* 1.3 76.8 - - - +
815A CYS* 1.3 58.8 + - - +
817A VAL* 3.3 20.3 - - + +
818A THR* 4.0 4.9 + - - -
902A LEU* 4.2 33.8 + - + +
904A MSE 3.7 17.4 - - + -
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Residues in contact with CYS 815 (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* 3.8 8.5 - - - -
773A LEU* 3.8 15.0 - - - -
774A MSE 3.6 53.9 - - - +
777A VAL* 3.8 27.9 - - + +
811A ASN 3.0 14.3 + - - -
812A MSE 2.8 12.7 + - - +
814A ARG* 1.3 77.6 - - - +
816A LEU* 1.3 61.2 + - - +
818A THR* 3.3 21.2 + - - -
819A LEU* 4.7 0.9 - - - +
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Residues in contact with LEU 816 (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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777A VAL* 3.5 28.5 - - + -
780A LEU* 4.5 10.5 - - + -
782A VAL* 5.0 3.8 - - + -
788A LEU* 5.1 6.4 - - + +
791A VAL* 4.3 24.0 - - + -
792A ILE* 5.7 2.0 - - + -
795A VAL* 4.8 7.2 - - + -
812A MSE 3.1 49.8 + - + +
813A CYS* 3.1 8.0 + - - +
815A CYS* 1.3 72.6 - - - +
817A VAL* 1.3 58.2 + - - +
818A THR 2.9 11.6 + - - -
819A LEU* 3.2 33.1 + - + +
833A PHE* 3.5 28.3 - - + -
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Residues in contact with VAL 817 (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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813A CYS 3.1 9.2 + - - +
814A ARG* 3.3 23.6 - - + +
815A CYS 3.2 0.8 - - - -
816A LEU* 1.3 74.6 - - - +
818A THR* 1.3 58.9 + - - +
819A LEU 3.2 8.5 + - - +
833A PHE* 3.3 41.9 - - + +
834A ARG* 4.2 36.3 - - + +
904A MSE 4.5 7.6 - - + -
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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