Contacts of the helix formed by residues 916 - 927 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911A GLN* 3.6 3.5 + - - +
915A CYS* 1.3 80.0 - - - +
917A ILE* 1.3 64.5 + - - +
918A ASP* 3.2 17.4 + - - -
919A VAL* 3.3 9.2 + - - +
920A TYR 3.1 17.2 + - - -
953A ARG 3.6 13.2 - - - +
954A TYR* 2.7 41.6 + - - +
956A VAL* 3.8 22.7 - - + -
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Residues in contact with ILE 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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911A GLN* 3.8 13.2 - - - +
916A THR* 1.3 71.5 - - - +
918A ASP* 1.3 65.8 + - - +
920A TYR* 4.1 20.9 - - + -
921A MET* 2.6 66.5 + - + +
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Residues in contact with ASP 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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916A THR* 3.2 17.4 + - - -
917A ILE* 1.3 81.7 + - - +
919A VAL* 1.3 60.0 + - - +
921A MET* 3.5 7.9 - - - +
922A ILE* 3.1 29.1 + - - +
947A MET* 3.8 14.5 - - + +
953A ARG* 4.0 11.5 + - - -
954A TYR* 3.9 20.9 - - + -
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Residues in contact with VAL 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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791A LEU* 4.9 3.4 - - + -
880A VAL* 5.3 0.2 - - + -
884A MET* 4.5 17.0 - - + -
915A CYS* 3.9 24.0 - - + -
916A THR* 3.3 8.9 + - - +
917A ILE 3.2 0.4 - - - -
918A ASP* 1.3 73.0 - - - +
920A TYR* 1.3 67.7 + - - +
922A ILE* 2.9 17.4 + - - +
923A MET* 3.1 21.0 + - + +
944A PHE* 4.9 9.9 - - + -
947A MET* 3.3 25.6 - - + -
954A TYR* 3.3 31.9 - - + +
955A LEU* 4.4 5.2 - - + -
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Residues in contact with TYR 920 (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 ARG 4.7 0.2 + - - -
909A LEU 2.7 28.2 + - - -
910A PRO* 3.8 3.5 - - - +
911A GLN* 3.5 58.5 + - + +
912A PRO* 4.3 7.2 - - + -
915A CYS* 4.4 2.4 - - + +
916A THR 3.1 13.5 + - - +
917A ILE* 3.7 15.9 - - + +
919A VAL* 1.3 79.5 - - - +
921A MET* 1.3 65.3 + - - +
923A MET* 3.1 15.0 + - + +
924A ARG* 2.8 69.9 + - + +
927A TRP* 4.3 7.2 - + - -
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Residues in contact with MET 921 (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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917A ILE* 2.6 48.9 + - + +
918A ASP* 3.5 11.0 - - - +
920A TYR* 1.3 73.2 - - + +
922A ILE* 1.3 58.4 + - + +
924A ARG* 3.4 16.0 + - + +
925A LYS* 3.0 28.6 + - - +
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Residues in contact with ILE 922 (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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918A ASP 3.1 17.5 - - - +
919A VAL* 2.9 7.4 + - - +
921A MET* 1.3 75.6 - - + +
923A MET* 1.3 69.0 + - - +
925A LYS* 3.0 17.4 + - - +
926A CYS* 3.2 13.5 + - - -
935A PRO* 5.2 1.8 - - + -
940A LEU* 3.7 29.2 - - + -
943A GLU* 3.5 37.5 - - + +
944A PHE* 3.9 22.2 - - + -
947A MET* 3.9 23.8 - - + -
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Residues in contact with MET 923 (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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877A GLY* 3.9 5.8 - - - +
880A VAL* 4.0 24.9 - - + -
881A TRP* 3.0 59.5 - - + +
884A MET* 4.8 0.4 - - - -
912A PRO* 4.3 12.3 - - + -
915A CYS* 4.6 9.0 - - - -
919A VAL* 3.1 11.3 + - + +
920A TYR* 3.4 23.1 - - + +
922A ILE* 1.3 78.1 - - + +
924A ARG* 1.3 59.6 + - - +
926A CYS* 2.9 33.7 + - - +
927A TRP* 3.5 29.6 + - + -
944A PHE* 5.8 1.1 - - + -
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Residues in contact with ARG 924 (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 GLY 4.9 7.5 + - - -
908A ARG* 3.6 29.9 + - - +
909A LEU 4.4 0.2 + - - -
920A TYR* 2.8 67.5 + - + +
921A MET* 3.7 18.3 - - + +
923A MET* 1.3 74.8 - - - +
925A LYS* 1.3 56.4 + - - +
927A TRP* 2.9 46.8 + - - +
928A MET* 3.6 14.5 + - + +
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Residues in contact with LYS 925 (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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921A MET 3.0 14.2 + - - +
922A ILE* 3.0 12.3 + - - +
924A ARG* 1.3 76.2 - - - +
926A CYS* 1.3 59.8 + - - +
928A MET* 2.9 39.1 - - + +
933A SER 3.3 23.5 + - - +
934A ARG* 3.4 3.7 + - - +
935A PRO* 3.0 44.1 - - + +
939A GLU* 3.7 21.8 + - - -
943A GLU* 5.6 1.0 + - - -
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Residues in contact with CYS 926 (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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873A VAL* 3.7 35.4 - - - +
874A TRP* 3.4 12.6 - - - -
876A TYR* 4.2 11.9 - - - -
877A GLY* 4.0 20.0 - - - -
922A ILE* 3.2 17.7 + - - -
923A MET* 2.9 12.9 + - - +
925A LYS* 1.3 76.6 - - - +
927A TRP* 1.3 61.3 + - + +
928A MET 3.5 0.2 - - - -
934A ARG* 3.2 21.5 + - - -
935A PRO* 4.0 15.5 - - - -
940A LEU* 4.3 7.4 - - - -
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Residues in contact with TRP 927 (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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874A TRP* 3.1 54.5 + + + -
877A GLY* 3.5 23.5 - - - -
878A VAL* 3.6 12.3 - - + +
881A TRP* 4.4 0.7 - + - -
891A TYR* 5.5 2.7 - - - -
908A ARG* 3.0 55.4 + - + +
909A LEU* 3.9 44.2 - - + -
920A TYR* 4.3 1.8 - + - -
923A MET* 3.5 34.8 - - + -
924A ARG* 2.9 40.7 + - + +
926A CYS* 1.3 84.6 - - + +
928A MET* 1.3 65.2 + - - +
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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