Contacts of the helix formed by residues 916 - 927 (chain B) in PDB entry 3LZB
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 916 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911B GLN* 3.8 1.2 + - - -
915B CYS* 1.3 74.2 - - - +
917B ILE* 1.3 66.4 + - - +
918B ASP* 3.4 16.2 + - - -
919B VAL* 2.9 20.5 + - - +
920B TYR 2.9 10.7 + - - -
953B ARG 3.7 12.9 + - - +
954B TYR* 2.9 37.4 + - - +
956B VAL* 3.9 22.2 - - + -
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Residues in contact with ILE 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911B GLN* 3.9 12.5 - - - +
916B THR* 1.3 74.0 - - - +
918B ASP* 1.3 63.3 + - - +
920B TYR* 4.3 11.9 - - + -
921B MET* 2.6 42.4 + - + +
895C PRO* 5.3 0.7 - - + -
897C SER* 3.1 45.3 - - - +
898C GLU* 2.9 41.5 - - + +
901C SER* 5.0 6.7 - - - +
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Residues in contact with ASP 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916B THR* 3.4 15.8 + - - -
917B ILE* 1.3 81.7 + - - +
919B VAL* 1.3 57.2 + - - +
921B MET* 3.6 10.7 - - - +
922B ILE* 3.1 30.5 + - - +
947B MET* 3.8 18.8 - - + +
953B ARG* 3.8 18.9 + - - +
954B TYR* 4.1 14.8 - - + -
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Residues in contact with VAL 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LEU* 4.8 3.6 - - + -
880B VAL* 5.5 0.4 - - + -
884B MET* 4.5 14.6 - - + -
915B CYS* 3.8 26.0 - - + -
916B THR* 2.9 13.3 + - - +
918B ASP* 1.3 73.0 - - - +
920B TYR* 1.3 66.0 + - - +
922B ILE* 3.0 18.5 + - - +
923B MET* 3.2 16.3 + - + +
944B PHE* 4.8 9.8 - - + -
947B MET* 3.7 18.4 - - - -
954B TYR* 3.4 37.7 - - + +
955B LEU* 4.0 10.8 - - + -
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Residues in contact with TYR 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B ARG* 4.5 2.8 - - - +
909B LEU 2.4 29.0 + - - -
910B PRO* 4.0 3.5 - - - +
911B GLN* 3.4 68.0 + - + +
912B PRO* 4.2 1.1 - - + -
915B CYS* 4.3 2.4 - - + +
916B THR 2.9 7.1 + - - +
917B ILE* 4.0 5.8 - - + +
919B VAL* 1.3 76.6 - - - +
921B MET* 1.3 57.5 + - - +
923B MET* 3.2 19.3 + - + -
924B ARG* 2.8 52.5 + - + +
927B TRP* 4.0 17.3 - + - -
895C PRO* 4.6 13.9 - - + -
898C GLU* 4.1 10.5 - - - -
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Residues in contact with MET 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B ILE* 2.6 23.7 + - - +
918B ASP* 3.6 11.9 - - - +
919B VAL 3.2 0.2 + - - -
920B TYR* 1.3 71.7 - - - +
922B ILE* 1.3 59.1 + - + +
924B ARG* 3.4 3.0 + - - +
925B LYS* 2.9 28.6 + - - +
898C GLU* 2.9 41.7 + - + +
901C SER* 3.6 32.3 - - - -
902C ILE* 3.7 25.6 - - + +
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Residues in contact with ILE 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876B TYR* 5.7 0.4 - - + -
918B ASP 3.1 11.9 - - - +
919B VAL 3.0 7.1 + - - +
921B MET* 1.3 73.8 - - + +
923B MET* 1.3 69.0 + - + +
925B LYS* 3.0 17.5 + - - +
926B CYS* 3.2 13.7 + - - -
935B PRO* 4.7 2.2 - - + +
940B LEU* 3.6 29.2 - - + -
943B GLU* 3.8 24.0 - - + -
944B PHE* 3.9 24.7 - - + -
947B MET* 3.6 29.4 - - + -
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Residues in contact with MET 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B GLY* 3.9 5.4 - - - +
880B VAL* 4.0 25.1 - - + -
881B TRP* 3.0 59.7 - - + +
884B MET* 4.7 0.7 - - - -
912B PRO* 4.2 12.6 - - + -
915B CYS* 4.6 8.5 - - - -
919B VAL* 3.2 10.3 + - + +
920B TYR* 3.5 26.0 - - + +
922B ILE* 1.3 76.5 - - + +
924B ARG* 1.3 59.0 + - - +
926B CYS* 2.9 34.8 + - - +
927B TRP* 3.4 29.0 + - + -
944B PHE* 5.8 1.1 - - + -
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Residues in contact with ARG 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906B GLY 5.9 0.8 + - - -
908B ARG* 3.5 49.1 - - - +
920B TYR* 2.8 47.1 + - + +
921B MET* 3.5 8.7 - - - +
923B MET* 1.3 76.2 - - - +
925B LYS* 1.3 60.2 + - - +
927B TRP* 3.1 19.6 + - - +
928B MET* 2.8 31.7 + - - +
893C GLY* 5.4 5.7 + - - -
894C ILE* 5.1 14.6 - - - +
895C PRO* 5.3 10.8 - - + +
898C GLU* 4.4 12.5 + - - +
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Residues in contact with LYS 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A LYS* 3.9 17.7 - - - +
921B MET 2.9 13.6 + - - +
922B ILE* 3.0 12.0 + - - +
924B ARG* 1.3 76.2 - - - +
926B CYS* 1.3 59.6 + - - +
928B MET* 3.0 34.8 - - + +
933B SER 3.3 23.1 + - - +
934B ARG* 3.4 3.3 - - - +
935B PRO* 3.0 44.1 - - + +
939B GLU* 3.6 21.6 + - - -
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Residues in contact with CYS 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873B VAL* 3.7 37.2 - - - +
874B TRP* 3.4 13.0 - - - -
876B TYR* 4.2 13.0 - - - -
877B GLY* 4.0 19.7 - - - -
922B ILE* 3.2 17.4 + - - -
923B MET* 2.9 12.7 + - - +
925B LYS* 1.3 77.0 - - - +
927B TRP* 1.3 59.3 + - + +
928B MET 3.5 0.4 - - - -
934B ARG* 3.1 22.5 + - - -
935B PRO* 4.0 15.7 - - - -
940B LEU* 4.2 7.4 - - - -
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Residues in contact with TRP 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874B TRP* 3.1 55.1 + + + -
877B GLY* 3.5 23.9 - - - -
878B VAL* 3.6 12.1 - - + +
891B TYR* 5.7 2.9 - - - -
908B ARG* 3.0 53.1 + - + +
909B LEU* 3.9 46.9 - - + -
920B TYR* 4.0 13.2 - + - -
923B MET* 3.5 39.7 - - + -
924B ARG* 3.1 23.9 + - - +
926B CYS* 1.3 84.9 - - + +
928B MET* 1.3 65.6 + - - +
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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