Contacts of the helix formed by residues 900 - 917 (chain A) in PDB entry 3THY
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 900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899A MET* 1.3 74.5 - - - +
901A GLU* 1.3 56.8 + - - +
902A GLU* 3.7 8.1 + - - +
903A ASN* 2.7 53.6 + - - +
904A ILE* 2.9 14.4 + - - +
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Residues in contact with GLU 901 (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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899A MET 4.0 0.8 + - - -
900A SER* 1.3 71.8 - - - +
902A GLU* 1.3 59.5 + - - +
904A ILE* 4.0 17.8 - - - +
905A THR* 3.0 39.3 + - - +
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Residues in contact with GLU 902 (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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900A SER* 3.0 9.3 + - - +
901A GLU* 1.3 79.8 - - - +
903A ASN* 1.3 66.6 + - - +
905A THR* 3.6 3.3 + - - -
906A ILE* 3.0 38.3 + - + +
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Residues in contact with ASN 903 (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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899A MET* 3.4 26.0 - - + +
900A SER* 2.7 41.1 + - - +
902A GLU* 1.3 74.3 - - - +
904A ILE* 1.3 51.4 + - - +
906A ILE* 3.2 6.1 + - - +
907A LYS* 2.7 47.9 + - - +
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Residues in contact with ILE 904 (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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894A MET* 5.1 5.2 - - - -
896A PHE* 4.1 27.4 - - + +
899A MET* 3.4 34.7 - - + +
900A SER 2.9 36.1 + - - +
901A GLU* 4.0 17.3 - - - +
903A ASN* 1.3 76.3 - - - +
905A THR* 1.3 67.6 + - - +
906A ILE 2.9 1.4 + - - -
907A LYS* 3.8 2.0 - - - +
908A LEU* 2.9 46.5 + - + +
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Residues in contact with THR 905 (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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901A GLU* 3.0 29.5 + - - +
902A GLU* 4.0 6.0 - - - -
904A ILE* 1.3 80.2 - - - +
906A ILE* 1.3 59.4 + - + +
908A LEU* 3.9 7.5 - - - +
909A LYS* 3.3 26.5 + - + +
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Residues in contact with ILE 906 (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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902A GLU* 3.0 29.4 + - + +
903A ASN* 3.2 5.8 + - - +
904A ILE 3.0 0.8 - - - -
905A THR* 1.3 80.3 - - + +
907A LYS* 1.3 69.0 + - - +
908A LEU 3.1 1.8 - - - -
909A LYS* 3.0 8.5 + - + +
910A GLN* 2.9 49.1 + - + +
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Residues in contact with LYS 907 (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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894A MET* 4.2 22.4 - - + -
899A MET* 3.4 30.6 - - + +
903A ASN* 2.7 32.6 + - - +
904A ILE* 3.8 3.4 - - - +
906A ILE* 1.3 76.0 - - - +
908A LEU* 1.3 61.5 + - - +
910A GLN* 3.6 14.4 + - + +
911A LEU* 3.2 34.9 + - + +
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Residues in contact with LEU 908 (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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887A PHE* 5.2 1.7 - - + -
891A VAL* 4.4 20.0 - - + -
894A MET* 3.7 25.8 - - + -
904A ILE* 2.9 38.2 + - + +
905A THR* 3.9 7.6 - - - +
907A LYS* 1.3 74.9 - - - +
909A LYS* 1.3 65.6 + - - +
911A LEU* 3.0 7.0 + - + +
912A LYS* 3.0 47.4 + - - +
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Residues in contact with LYS 909 (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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905A THR* 3.3 18.0 + - + +
906A ILE* 3.0 10.1 + - + +
908A LEU* 1.3 79.2 - - - +
910A GLN* 1.3 58.5 + - + +
912A LYS* 3.8 12.3 - - + +
913A ALA* 2.9 27.4 + - - +
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Residues in contact with GLN 910 (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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906A ILE* 2.9 38.8 + - + +
907A LYS* 3.9 16.0 + - + +
909A LYS* 1.3 76.0 - - + +
911A LEU* 1.3 62.8 + - + +
913A ALA* 3.4 9.1 - - + +
914A GLU* 3.2 28.5 + - - +
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Residues in contact with LEU 911 (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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887A PHE* 3.9 15.7 - - + -
890A LYS* 4.2 31.4 - - + +
891A VAL* 4.0 18.2 - - + +
894A MET* 3.7 29.6 - - + -
907A LYS* 3.2 16.9 + - + +
908A LEU* 3.0 9.5 + - + +
910A GLN* 1.3 75.7 - - - +
912A LYS* 1.3 64.4 + - - +
914A GLU* 3.2 40.4 + - - +
915A VAL* 3.3 11.4 + - - +
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Residues in contact with LYS 912 (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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887A PHE* 4.0 25.1 - - + -
908A LEU* 3.0 41.9 + - - +
909A LYS* 3.8 10.0 - - + +
911A LEU* 1.3 72.7 - - - +
913A ALA* 1.3 66.0 + - - +
915A VAL* 3.1 7.0 + - - +
916A ILE* 2.9 32.7 + - + +
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Residues in contact with ALA 913 (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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909A LYS 2.9 19.8 + - - +
910A GLN* 3.4 12.1 - - + +
912A LYS* 1.3 73.4 - - - +
914A GLU* 1.3 66.2 + - - +
916A ILE* 3.3 7.2 + - - +
917A ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 914 (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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890A LYS* 3.3 26.6 + - - -
910A GLN 3.2 16.9 + - - +
911A LEU* 3.2 26.2 + - - +
913A ALA* 1.3 78.8 - - - +
915A VAL* 1.3 64.3 + - + +
917A ALA* 3.4 11.1 + - - +
918A LYS* 3.6 31.1 + - - +
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Residues in contact with VAL 915 (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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883A ILE* 4.3 22.5 - - + +
884A ILE* 5.7 2.2 - - + -
887A PHE* 3.6 43.7 - - + -
911A LEU 3.3 3.3 + - - +
912A LYS* 3.1 10.4 + - - +
914A GLU* 1.3 77.0 - - + +
916A ILE* 1.3 70.6 + - + +
918A LYS* 2.9 22.8 + - - +
919A ASN 4.1 1.4 + - - -
920A ASN* 5.3 1.2 + - - +
923A VAL* 3.8 28.5 - - + -
924A ASN* 5.4 0.7 - - - +
927A ILE* 4.4 10.1 - - + -
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Residues in contact with ILE 916 (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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912A LYS* 2.9 29.3 + - + +
913A ALA* 3.8 5.8 - - - +
915A VAL* 1.3 72.5 - - + +
917A ALA* 1.3 58.9 + - - +
918A LYS 3.1 4.4 + - - -
919A ASN* 3.3 14.4 + - - +
924A ASN* 4.5 13.8 + - - +
927A ILE* 3.7 35.2 - - + -
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Residues in contact with ALA 917 (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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913A ALA 2.9 19.6 + - - +
914A GLU* 3.8 7.9 - - - +
915A VAL 3.0 0.4 + - - -
916A ILE* 1.3 76.1 - - - +
918A LYS* 1.3 59.8 + - - +
919A ASN* 3.3 3.0 + - - +
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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