Contacts of the helix formed by residues 908 - 919 (chain A) in PDB entry 4BIC
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 908 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777A GLU* 2.9 32.5 + - - -
906A SER 3.8 0.4 + - - -
907A MET* 1.3 76.5 - - - +
909A ALA* 1.3 58.2 + - - +
910A GLU* 3.3 19.4 + - - +
911A ALA 3.1 14.7 + - - -
912A LYS* 2.9 27.3 + - - +
937A PHE* 4.7 0.5 - - - -
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Residues in contact with ALA 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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907A MET 3.8 0.8 + - - -
908A SER* 1.3 72.9 - - - +
910A GLU* 1.4 64.3 + - - +
912A LYS* 3.5 11.6 + - - +
913A ALA* 3.0 30.8 + - - +
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Residues in contact with GLU 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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908A SER* 3.2 16.8 + - - +
909A ALA* 1.4 81.6 + - - +
911A ALA* 1.4 58.5 + - - +
913A ALA* 3.7 5.3 - - - +
914A PHE* 3.1 29.3 + - - +
935A ASP* 4.6 1.9 - - - +
936A GLU* 4.5 22.9 - - + +
937A PHE* 3.7 24.8 - - + +
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Residues in contact with ALA 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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777A GLU* 3.5 22.4 - - - +
907A MET* 3.8 24.2 - - + -
908A SER* 3.1 14.1 + - - +
910A GLU* 1.4 73.2 - - - +
912A LYS* 1.4 55.3 + - - +
914A PHE* 3.2 3.7 + - - +
915A ILE* 2.9 41.8 + - + +
937A PHE* 3.7 23.6 - - + -
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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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903A ILE* 3.6 32.4 - - + +
904A PRO 3.8 7.4 - - - -
905A GLU* 2.4 43.6 + - - +
907A MET* 3.6 18.2 + - + +
908A SER 2.9 16.0 + - - +
909A ALA* 3.8 9.4 - - - +
910A GLU 3.5 0.2 - - - -
911A ALA* 1.4 72.9 - - - +
913A ALA* 1.3 57.1 + - - +
915A ILE* 3.5 0.5 + - - +
916A LEU* 3.0 41.0 + - + +
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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 ALA 3.0 19.6 + - - +
910A GLU* 3.7 6.7 - - - +
912A LYS* 1.3 75.0 - - - +
914A PHE* 1.4 62.0 + - - +
916A LEU* 3.2 18.0 + - - +
917A LYS* 3.2 25.0 + - - +
935A ASP* 6.0 0.9 - - - +
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Residues in contact with PHE 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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784A THR* 3.9 7.2 - - + -
788A LEU* 3.8 25.8 - - + -
867A LEU* 5.2 0.4 - - + -
871A ILE* 3.6 29.6 - - + -
910A GLU 3.1 18.6 + - - +
911A ALA 3.4 4.0 - - - +
913A ALA* 1.4 74.4 - - - +
915A ILE* 1.3 66.7 + - + +
917A LYS* 3.3 22.9 + - - +
918A CYS* 3.7 9.4 + - - -
932A LEU* 3.3 42.0 - - + +
935A ASP* 3.4 28.2 + - + +
937A PHE* 3.8 24.9 - + + -
938A LEU* 3.8 13.9 - - + -
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Residues in contact with ILE 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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868A GLY* 4.4 7.2 - - - +
871A ILE* 3.7 37.2 - - + -
872A ILE* 4.3 11.7 - - + -
903A ILE* 3.8 36.3 - - + -
907A MET* 4.3 18.4 - - + -
911A ALA* 2.9 27.6 + - + +
914A PHE* 1.3 75.4 - - + +
916A LEU* 1.4 57.1 + - - +
918A CYS* 2.9 31.1 + - - +
919A PHE* 3.4 31.1 + - + -
937A PHE* 6.2 1.6 - - + -
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Residues in contact with LEU 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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900A HIS* 3.6 29.2 - - + +
903A ILE* 3.7 14.6 - - + -
912A LYS* 3.0 29.4 + - + +
913A ALA* 3.2 9.3 + - - +
915A ILE* 1.4 74.8 - - - +
917A LYS* 1.3 56.1 + - - +
919A PHE* 2.9 22.7 + - + +
920A GLU* 3.5 8.7 + - - +
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Residues in contact with LYS 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* 3.2 21.6 + - - +
914A PHE* 3.3 8.2 + - - +
916A LEU* 1.3 75.4 - - - +
918A CYS* 1.3 59.7 + - - +
920A GLU* 3.7 10.5 + - - +
926A ARG* 3.6 17.0 - - - +
927A ALA* 3.9 27.8 + - + +
931A ASP* 5.5 7.7 + - + +
932A LEU* 4.1 14.6 - - + -
935A ASP* 3.3 27.4 + - - +
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Residues in contact with CYS 918 (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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864A ILE* 3.5 33.7 - - - +
865A TRP* 3.5 15.9 - - - -
867A LEU* 4.2 11.0 - - - -
868A GLY* 3.7 21.1 - - - -
871A ILE* 4.6 1.6 - - - -
914A PHE* 3.9 20.0 - - - -
915A ILE* 2.9 15.5 + - - +
917A LYS* 1.3 75.9 - - - +
919A PHE* 1.3 56.9 + - + +
920A GLU 3.4 1.3 - - - -
926A ARG* 3.4 19.3 + - - -
932A LEU* 4.2 16.4 - - - -
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Residues in contact with PHE 919 (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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865A TRP* 3.4 46.9 - + - -
868A GLY* 3.3 25.6 - - - -
869A CYS* 3.5 12.3 - - - -
872A ILE* 4.0 9.2 - - + -
898A LYS 5.0 1.6 - - - +
900A HIS* 3.3 52.7 - + + -
901A PRO* 3.7 16.8 - - + -
903A ILE* 5.0 0.4 - - + -
915A ILE* 3.4 36.1 + - + +
916A LEU* 2.9 14.0 + - + +
918A CYS* 1.3 82.2 - - - +
920A GLU* 1.4 63.0 + - - +
921A PRO* 3.1 9.9 - - - +
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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