Contacts of the helix formed by residues 809 - 828 (chain A) in PDB entry 5V87
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 809 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801A GLU* 5.3 1.2 + - - -
802A LEU* 3.9 3.6 - - - +
807A GLY 3.8 8.2 + - - +
808A PHE* 1.3 85.5 - - - +
810A GLN* 1.3 64.1 + - - +
811A HIS* 4.2 6.3 - - - +
812A VAL* 3.5 27.7 + - - +
813A TYR* 3.1 23.7 + - - +
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Residues in contact with GLN 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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808A PHE* 4.1 13.1 - - + -
809A THR* 1.3 74.4 - - - +
811A HIS* 1.3 57.2 + - - +
813A TYR* 3.9 5.0 - - - +
814A HIS* 2.8 34.6 + - + +
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Residues in contact with HIS 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A THR* 3.2 6.3 + - - +
810A GLN* 1.3 81.1 - - - +
812A VAL* 1.3 64.7 + - + +
814A HIS* 3.6 5.5 + - - +
815A LYS* 3.4 20.8 + - - +
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Residues in contact with VAL 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A PRO* 4.6 12.1 - - + -
801A GLU* 4.1 30.1 - - - +
802A LEU* 3.6 27.4 - - + -
809A THR* 3.5 20.1 + - - +
810A GLN 3.3 0.2 - - - -
811A HIS* 1.3 80.5 - - + +
813A TYR* 1.3 62.9 + - - +
815A LYS* 3.6 5.4 + - - +
816A TYR* 3.2 21.3 + - - +
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Residues in contact with TYR 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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802A LEU* 4.0 17.2 - - + +
808A PHE* 3.5 36.3 - + + -
809A THR 3.1 11.5 + - - +
810A GLN* 3.9 3.8 - - - +
812A VAL* 1.3 76.2 - - - +
814A HIS* 1.3 62.4 + - - +
816A TYR* 3.2 3.3 + + - -
817A ARG* 2.8 68.2 + - + +
838A LEU* 4.3 5.8 - - + -
841A PHE* 3.6 29.2 - + - -
842A TRP* 2.9 26.8 + - - -
854A MET* 3.8 21.2 - - + +
857A GLU* 4.6 1.6 + - - -
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Residues in contact with HIS 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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810A GLN 2.8 22.0 + - - +
811A HIS* 3.9 6.3 - - - +
813A TYR* 1.3 80.5 - - - +
815A LYS* 1.3 68.9 + - + +
817A ARG* 4.0 14.0 + - - +
818A ARG* 3.0 51.8 + - + +
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Residues in contact with LYS 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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811A HIS 3.4 14.2 + - - +
812A VAL* 4.0 4.9 - - - +
813A TYR 3.3 0.2 - - - -
814A HIS* 1.3 85.7 - - + +
816A TYR* 1.3 61.6 + - - +
818A ARG* 3.4 5.2 + - - +
819A ARG* 3.1 29.6 + - + +
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Residues in contact with TYR 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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797A HIS* 3.6 22.0 - + - -
798A PRO* 3.9 25.4 - - + -
799A SER* 3.6 16.4 - - - -
802A LEU* 3.7 22.7 - - + -
812A VAL 3.2 18.5 + - - +
813A TYR* 3.7 5.4 - + - +
815A LYS* 1.3 75.5 - - - +
817A ARG* 1.3 68.3 + - - +
819A ARG* 3.2 8.5 + - + +
820A CYS* 3.0 46.7 + - - -
834A GLU* 4.0 7.6 - - - -
837A THR* 2.6 29.2 + - - -
838A LEU* 3.1 32.1 + - + -
841A PHE* 4.4 6.1 - + + -
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Residues in contact with ARG 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 TYR* 2.8 57.8 + - + +
814A HIS* 4.0 14.3 + - - +
816A TYR* 1.3 74.8 - - - +
818A ARG* 1.3 69.3 + - - +
820A CYS* 3.2 1.9 + - - +
821A LEU* 2.9 44.9 + - + +
838A LEU* 4.3 17.0 - - + -
842A TRP* 5.0 0.4 - - + -
857A GLU* 2.8 39.7 + - - -
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Residues in contact with ARG 818 (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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814A HIS* 3.0 44.4 + - + +
815A LYS* 3.7 6.1 - - - +
816A TYR 3.2 0.2 - - - -
817A ARG* 1.3 83.3 - - - +
819A ARG* 1.3 58.0 + - - +
821A LEU* 3.8 4.6 - - - +
822A ASN* 2.9 53.8 + - - +
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Residues in contact with ARG 819 (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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815A LYS* 3.1 23.3 + - + +
816A TYR* 3.6 8.0 - - + +
818A ARG* 1.3 76.8 - - - +
820A CYS* 1.3 63.7 + - - +
822A ASN* 3.4 6.8 + - - +
823A GLU* 3.0 41.5 + - + +
834A GLU* 3.2 36.2 + - + +
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Residues in contact with CYS 820 (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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816A TYR* 3.0 49.5 + - - -
817A ARG 3.6 6.5 - - - +
819A ARG* 1.3 77.0 - - - +
821A LEU* 1.3 62.9 + - - +
823A GLU* 3.2 7.7 + - - +
824A ARG* 3.0 22.2 + - - +
834A GLU* 3.4 35.4 - - - +
835A MET* 4.1 10.3 - - - +
838A LEU* 3.6 22.9 - - + -
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Residues in contact with LEU 821 (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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817A ARG* 2.9 62.5 + - + +
818A ARG* 4.0 4.3 - - - +
820A CYS* 1.3 75.9 - - - +
822A ASN* 1.3 59.3 + - - +
824A ARG* 3.3 9.7 + - - +
825A LYS* 3.0 28.4 + - - +
835A MET* 3.9 16.2 - - + -
838A LEU* 4.3 6.1 - - + -
842A TRP* 4.9 0.4 - - + -
857A GLU* 3.7 8.1 - - - +
861A LEU* 3.8 28.3 - - + -
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Residues in contact with ASN 822 (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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818A ARG* 2.9 41.8 + - - +
819A ARG* 3.7 7.4 - - - +
821A LEU* 1.3 77.7 - - - +
823A GLU* 1.3 57.4 + - - +
825A LYS* 3.4 7.6 + - - +
826A ARG* 3.0 30.7 + - - +
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Residues in contact with GLU 823 (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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819A ARG* 3.0 34.7 + - + +
820A CYS* 3.2 7.4 + - - +
822A ASN* 1.3 73.9 - - + +
824A ARG* 1.3 60.3 + - - +
826A ARG* 3.8 27.7 + - - +
827A LEU* 2.8 46.4 + - + +
832A SER* 2.7 27.7 + - - +
833A GLN 4.6 0.9 + - - -
834A GLU* 3.5 28.7 + - - +
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Residues in contact with ARG 824 (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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820A CYS 3.0 13.1 + - - +
821A LEU* 3.6 12.1 - - - +
823A GLU* 1.3 76.8 - - - +
825A LYS* 1.3 58.6 + - - +
828A GLY* 3.0 37.5 + - - +
829A ILE* 3.4 32.1 + - + +
830A GLY 5.3 0.7 - - - +
832A SER* 4.1 5.5 - - - -
835A MET* 3.6 37.2 - - + +
861A LEU* 3.4 31.8 + - - +
864A GLU* 2.9 30.7 + - - +
865A ASP* 2.9 31.8 + - - -
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Residues in contact with LYS 825 (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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821A LEU 3.0 17.2 + - - +
822A ASN* 3.7 8.3 - - - +
823A GLU 3.2 0.2 - - - -
824A ARG* 1.3 79.4 - - - +
826A ARG* 1.3 61.0 + - - +
828A GLY* 4.3 3.3 + - - -
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Residues in contact with ARG 826 (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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822A ASN 3.0 17.9 + - - +
823A GLU* 3.8 30.4 + - - +
825A LYS* 1.3 80.2 - - - +
827A LEU* 1.3 88.3 + - + +
828A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 827 (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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823A GLU* 2.8 42.4 + - - +
826A ARG* 1.3 103.1 - - + +
828A GLY* 1.3 59.3 + - - +
831A GLN* 3.2 45.1 - - + +
832A SER* 4.2 2.9 - - - -
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Residues in contact with GLY 828 (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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824A ARG* 3.0 25.1 + - - +
825A LYS 4.8 2.5 - - - -
826A ARG 3.4 2.3 - - - -
827A LEU* 1.3 78.1 - - - +
829A ILE* 1.3 68.7 + - - -
830A GLY 3.3 0.7 + - - -
831A GLN* 3.0 18.9 + - - +
832A SER 4.1 4.0 + - - -
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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