Contacts of the helix formed by residues 794 - 806 (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 SER 794 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLN* 4.9 5.4 - - - +
335A ASP* 4.4 9.6 - - - -
338A LYS* 3.5 29.7 + - - +
339A SER* 4.4 4.0 + - - -
792A SER* 3.1 6.0 + - - -
793A LEU* 1.3 77.9 - - - +
795A SER* 1.3 64.4 + - - +
796A THR* 3.4 9.4 + - - -
797A GLU* 3.1 29.9 + - - -
798A LYS* 3.1 23.7 + - - +
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Residues in contact with SER 795 (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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275A LYS* 5.0 4.9 + - - +
278A GLN* 5.2 2.8 + - - -
329A GLU* 3.9 10.9 + - - +
330A SER* 3.5 42.7 + - - -
333A LEU* 4.8 12.5 + - - +
339A SER* 5.6 1.7 + - - -
793A LEU 3.7 4.9 + - - -
794A SER* 1.3 70.9 + - - +
796A THR* 1.3 65.0 + - - +
798A LYS* 3.4 10.1 + - - +
799A SER* 3.0 24.0 + - - -
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Residues in contact with THR 796 (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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338A LYS 3.7 19.7 - - - +
339A SER* 3.5 11.6 + - - -
340A SER* 3.5 30.4 + - - +
343A SER* 3.6 16.5 + - - -
765A VAL* 4.9 0.2 - - + -
794A SER* 3.2 3.9 + - - -
795A SER* 1.3 80.8 - - - +
797A GLU* 1.3 57.4 + - - +
799A SER* 3.2 7.4 + - - -
800A GLN* 2.8 61.6 + - + +
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Residues in contact with GLU 797 (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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338A LYS* 4.0 23.9 - - + +
754A TRP* 4.6 16.3 - - - -
768A THR* 6.1 0.2 - - + -
772A PHE* 4.6 10.6 - - + -
788A LYS* 5.5 5.3 - - - +
792A SER* 3.3 22.9 + - - +
793A LEU 5.2 0.3 + - - -
794A SER* 3.1 21.4 + - - +
796A THR* 1.3 76.4 - - - +
798A LYS* 1.3 58.0 + - - +
800A GLN* 3.2 15.4 + - - +
801A ILE* 2.9 46.5 + - + +
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Residues in contact with LYS 798 (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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275A LYS* 4.1 21.6 - - - +
329A GLU* 5.1 1.8 + - - -
789A TYR* 3.5 47.0 - - + +
792A SER* 3.6 35.7 + - - +
793A LEU* 4.9 1.3 - - - +
794A SER 3.1 17.6 + - - +
795A SER* 3.7 10.3 - - - +
797A GLU* 1.3 73.2 - - - +
799A SER* 1.3 61.8 + - - +
801A ILE* 3.4 1.2 + - - -
802A GLU* 2.8 40.1 + - - +
828A LYS* 5.5 9.3 - - - +
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Residues in contact with SER 799 (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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330A SER* 6.1 1.2 - - - -
795A SER 3.0 17.6 + - - -
796A THR* 3.5 8.5 - - - -
798A LYS* 1.3 76.5 - - - +
800A GLN* 1.3 59.6 + - - +
802A GLU* 3.3 13.8 + - - +
803A PHE* 3.0 29.5 + - - +
831A GLU* 5.0 2.1 + - - -
834A GLN* 4.2 14.8 + - - +
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Residues in contact with GLN 800 (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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338A LYS 4.7 2.9 - - - +
340A SER* 5.0 2.6 - - - -
765A VAL* 3.6 28.3 + - - +
768A THR* 3.7 22.1 - - + +
769A LEU* 4.2 34.2 - - + +
772A PHE* 4.0 16.1 - - + +
796A THR* 2.8 40.1 + - + +
797A GLU* 3.5 16.6 - - - +
798A LYS 3.2 0.2 - - - -
799A SER* 1.3 78.1 - - - +
801A ILE* 1.3 61.1 + - - +
803A PHE* 3.4 3.3 + - - +
804A ALA* 3.1 23.9 + - - +
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Residues in contact with ILE 801 (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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754A TRP* 6.0 0.4 - - + -
772A PHE* 4.0 20.0 - - + -
785A LEU* 4.0 36.6 - - + +
788A LYS* 4.4 9.6 - - + +
789A TYR* 4.0 34.5 - - + +
792A SER* 5.4 1.6 - - - -
797A GLU* 2.9 33.8 + - + +
798A LYS* 3.8 4.0 - - - +
800A GLN* 1.3 73.2 - - - +
802A GLU* 1.3 60.6 + - - +
804A ALA* 3.1 4.6 + - - +
805A LEU* 2.8 53.7 + - + +
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Residues in contact with GLU 802 (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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789A TYR* 2.4 39.4 + - + +
798A LYS* 2.8 29.3 + - - +
799A SER* 3.5 9.9 - - - +
801A ILE* 1.3 72.4 - - - +
803A PHE* 1.3 64.1 + - - +
805A LEU* 3.3 7.4 + - + +
806A CYS* 3.1 30.4 + - - -
817A LEU* 6.5 0.4 - - - -
827A ILE* 4.9 2.5 - - + -
831A GLU* 2.8 41.5 - - - +
834A GLN* 4.0 11.0 - - - +
835A ILE* 4.3 22.4 - - + +
838A LEU* 4.9 4.5 - - + -
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Residues in contact with PHE 803 (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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733A LEU* 3.7 40.2 - - + -
737A VAL* 5.5 0.4 - - + -
769A LEU* 3.8 23.1 - - + -
773A ALA* 4.7 3.6 - - + -
799A SER 3.0 17.0 + - - +
800A GLN 3.7 4.3 - - - +
801A ILE 3.2 0.2 - - - -
802A GLU* 1.3 78.4 - - - +
804A ALA* 1.3 68.4 + - + +
806A CYS* 3.2 10.0 + - - +
807A ARG* 3.4 48.5 + - + +
838A LEU* 3.9 36.1 - - + -
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Residues in contact with ALA 804 (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 LEU* 5.3 0.7 - - + +
772A PHE* 3.6 40.2 - - + +
773A ALA* 3.7 6.9 - - + +
776A ALA* 3.4 17.4 - - + +
785A LEU* 4.2 5.4 - - + -
800A GLN 3.1 17.7 + - - +
801A ILE 3.6 4.0 - - - +
803A PHE* 1.3 84.1 - - + +
805A LEU* 1.3 62.4 + - - +
807A ARG* 3.1 17.2 + - - +
808A THR 4.0 0.9 + - - -
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Residues in contact with LEU 805 (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* 3.0 70.6 + - + +
785A LEU* 4.0 16.8 - - + -
786A TYR* 4.3 22.0 - - + +
789A TYR* 5.7 1.8 - - + -
801A ILE* 2.8 37.7 + - + +
802A GLU* 4.0 6.3 - - + +
804A ALA* 1.3 77.9 - - - +
806A CYS* 1.3 61.3 + - - +
807A ARG 3.3 0.3 + - - -
808A THR* 3.2 13.7 + - - +
817A LEU* 3.6 29.6 - - + +
827A ILE* 5.9 1.3 - - + -
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Residues in contact with CYS 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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802A GLU* 3.1 20.3 + - - +
803A PHE 3.6 5.8 - - - +
805A LEU* 1.3 78.8 - - - +
807A ARG* 1.3 57.0 + - + +
808A THR 3.3 0.7 - - - -
814A LEU* 3.7 9.1 - - - +
817A LEU* 3.9 18.8 - - - -
835A ILE* 4.0 22.2 - - - -
838A LEU* 3.9 32.4 - - + +
839A ILE* 4.0 18.6 - - + +
842A ASN* 3.1 23.7 + - - +
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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