Contacts of the helix formed by residues 810 - 824 (chain A) in PDB entry 2YD0
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 810 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779A THR* 5.2 4.4 + - - -
808A THR* 3.2 13.3 + - - +
809A GLN* 1.3 74.9 - - - +
811A LYS* 1.3 63.8 + - - +
812A GLU* 2.8 36.9 + - - +
813A LYS* 2.9 44.5 + - + +
814A LEU* 3.2 16.8 + - - +
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Residues in contact with LYS 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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809A GLN 3.5 7.2 + - - +
810A ASN* 1.3 70.1 + - - +
812A GLU* 1.3 65.5 + - - +
814A LEU* 3.2 6.1 + - + -
815A GLN* 3.1 22.5 + - - +
844A VAL* 3.3 37.7 + - + +
847A PRO* 5.8 5.5 - - - +
848A LEU* 3.8 28.7 - - + +
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Residues in contact with GLU 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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810A ASN* 2.8 18.7 + - - +
811A LYS* 1.3 74.1 - - - +
813A LYS* 1.3 61.1 + - + +
815A GLN* 3.5 7.0 + - + +
816A TRP* 3.1 23.1 + - + +
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Residues in contact with LYS 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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779A THR* 4.3 28.5 - - - +
782A TRP* 3.7 47.0 - - + +
783A ASP* 3.7 20.4 + - - -
808A THR* 3.8 10.8 - - + +
810A ASN* 2.9 39.5 + - + +
812A GLU* 1.3 79.1 - - + +
814A LEU* 1.3 61.2 + - - +
816A TRP* 3.4 7.9 - - + +
817A LEU* 3.1 27.8 + - - +
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Residues in contact with LEU 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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805A LEU 4.3 2.5 - - - +
806A CYS* 3.7 24.0 - - - +
808A THR* 3.5 35.2 - - + +
810A ASN 3.2 16.1 + - - +
811A LYS* 3.2 11.8 + - - +
813A LYS* 1.3 73.5 - - - +
815A GLN* 1.3 65.6 + - - +
817A LEU* 3.4 3.1 + - + -
818A LEU* 3.2 28.0 + - - +
839A ILE* 3.4 27.4 - - + +
842A ASN* 4.0 8.5 - - - +
844A VAL* 4.3 10.3 - - + +
845A GLY* 4.0 21.3 - - - -
848A LEU* 4.1 10.3 - - + -
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Residues in contact with GLN 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 LYS 3.1 13.0 + - - +
812A GLU* 3.7 11.0 - - + +
814A LEU* 1.3 73.4 - - - +
816A TRP* 1.3 55.9 + - - +
818A LEU* 2.9 11.0 + - - +
819A ASP* 2.7 67.6 + - - +
848A LEU* 3.6 29.2 - - + +
851A GLN* 5.0 3.9 + - - -
852A PHE* 3.9 20.1 - - - -
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Residues in contact with TRP 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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782A TRP* 4.1 19.1 - + + -
786A TYR* 3.7 44.9 - + - -
812A GLU* 3.1 12.6 + - + +
813A LYS* 3.4 12.1 - - - +
815A GLN* 1.3 78.0 - - - +
817A LEU* 1.3 80.8 + - + +
819A ASP* 4.5 6.5 - - + -
820A GLU* 2.9 71.3 + - + +
826A LYS* 4.7 10.1 - - + -
827A ILE* 4.4 3.8 - - + -
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Residues in contact with LEU 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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782A TRP* 4.1 12.6 - - + -
802A GLU* 6.5 0.4 - - - -
805A LEU* 3.6 48.9 - - + +
806A CYS* 3.9 18.4 - - - -
813A LYS 3.1 17.5 + - - +
814A LEU* 3.7 7.6 - - + +
815A GLN 3.2 0.2 - - - -
816A TRP* 1.3 92.7 - - + +
818A LEU* 1.3 60.5 + - - +
820A GLU* 4.1 0.3 - - - +
821A SER* 2.8 30.8 + - - -
827A ILE* 3.7 26.4 - - + +
835A ILE* 4.4 10.4 - - + +
839A ILE* 4.3 10.3 - - + -
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Residues in contact with LEU 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 LEU 3.2 14.2 + - - +
815A GLN* 2.9 14.0 + - - +
817A LEU* 1.3 80.6 - - - +
819A ASP* 1.3 63.3 + - - +
821A SER* 3.5 3.1 + - - -
822A PHE* 3.2 25.1 + - - +
832A PHE* 3.6 13.1 - - + -
835A ILE* 4.3 4.7 - - + -
836A LEU* 3.7 36.1 - - + -
839A ILE* 3.6 24.0 - - + -
848A LEU* 3.8 33.0 - - + +
849A ALA* 4.3 3.6 - - - -
852A PHE* 4.0 25.6 - - + -
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Residues in contact with ASP 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 GLN* 2.7 44.1 + - - +
816A TRP* 3.8 6.9 + - + +
818A LEU* 1.3 74.3 - - - +
820A GLU* 1.3 61.9 + - - +
822A PHE* 3.5 5.7 - - - +
823A LYS* 2.9 29.8 + - - +
852A PHE* 3.5 19.6 - - - -
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Residues in contact with GLU 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 TRP* 2.9 65.6 + - + +
817A LEU 4.1 1.8 - - - +
819A ASP* 1.3 74.5 - - + +
821A SER* 1.3 55.6 + - - +
823A LYS* 3.1 21.2 + - - +
824A GLY* 2.7 33.6 + - - -
825A ASP* 4.2 4.3 + - - +
826A LYS* 3.7 28.8 + - + +
827A ILE* 3.8 20.4 + - + +
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Residues in contact with SER 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 LEU 2.8 22.6 + - - -
818A LEU* 3.5 0.3 + - - -
820A GLU* 1.3 76.9 - - - +
822A PHE* 1.3 56.1 + - - +
824A GLY* 3.2 3.6 + - - -
827A ILE* 3.5 21.0 - - - +
828A LYS 4.3 2.2 - - - -
829A THR* 3.0 31.0 + - - +
832A PHE* 3.3 31.4 - - - -
835A ILE* 3.9 29.3 - - - +
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Residues in contact with PHE 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 LEU 3.2 19.4 + - - +
819A ASP* 3.5 6.3 - - - +
820A GLU 3.2 0.6 - - - -
821A SER* 1.3 76.1 + - - +
823A LYS* 1.3 67.5 + - + +
824A GLY 3.3 0.5 + - - -
829A THR* 3.5 14.1 + - + +
832A PHE* 3.6 13.6 - + + -
852A PHE* 3.9 17.0 - + + -
856A ASN* 4.2 21.3 - - + -
859A LYS* 3.7 37.2 - - + -
860A LEU* 3.9 37.5 - - + -
863A LYS* 6.1 1.9 - - + +
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Residues in contact with LYS 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 ASP 2.9 17.3 + - - +
820A GLU* 3.4 26.2 - - - +
822A PHE* 1.3 76.6 - - + +
824A GLY* 1.3 57.8 + - - +
825A ASP* 3.3 32.3 + - + +
829A THR* 4.4 0.7 + - - -
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Residues in contact with GLY 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 GLU 2.7 13.5 + - - -
821A SER 3.2 2.0 + - - -
823A LYS* 1.3 72.8 - - - +
825A ASP* 1.3 59.5 + - - +
827A ILE 3.1 25.4 - - - +
828A LYS* 3.7 15.6 - - - +
829A THR* 3.2 21.3 - - - -
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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