Contacts of the helix formed by residues 918 - 929 (chain A) in PDB entry 3LMG
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 918 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916A ILE 4.0 0.2 + - - -
917A CYS* 1.3 75.1 - - - +
919A ILE* 1.3 67.4 + - - +
920A ASP* 2.9 14.4 + - - +
921A VAL* 2.9 17.3 + - - +
922A TYR* 3.0 10.1 + - - +
955A ARG 3.7 13.0 + - - +
956A TYR* 2.9 40.2 + - - +
957A LEU* 4.4 3.1 - - - +
958A VAL* 5.2 10.8 - - + -
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Residues in contact with ILE 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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913A GLN* 4.6 17.7 - - - +
917A CYS 4.0 1.0 + - - -
918A THR* 1.3 72.2 - - - +
920A ASP* 1.3 68.8 + - - +
922A TYR* 4.2 7.0 - - + -
923A MET* 2.9 59.3 + - + +
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Residues in contact with ASP 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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918A THR* 2.9 11.1 + - - +
919A ILE* 1.3 90.3 - - - +
921A VAL* 1.3 58.9 + - - +
923A MET* 3.8 4.8 + - - +
924A VAL* 3.3 21.1 + - - +
945A GLU* 5.6 0.5 - - - -
948A ARG* 4.9 8.7 + - - -
949A MET* 3.6 15.9 - - + +
955A ARG* 5.1 5.7 + - - -
956A TYR* 4.2 18.0 - - + -
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Residues in contact with VAL 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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793A LEU* 5.2 2.2 - - + -
882A VAL* 5.4 0.9 - - + -
886A MET* 4.1 26.5 - - + -
917A CYS* 4.2 8.5 - - + -
918A THR* 2.9 7.1 + - - +
920A ASP* 1.3 73.8 - - - +
922A TYR* 1.3 66.1 + - - +
924A VAL* 3.3 16.9 - - - +
925A MET* 3.7 9.5 + - + +
946A PHE* 4.4 15.5 - - + -
949A MET* 3.7 17.3 - - + -
956A TYR* 3.2 45.3 - - + +
957A LEU* 4.1 11.7 - - + -
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Residues in contact with TYR 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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883A TRP* 5.2 0.2 - + - -
909A GLU 5.3 0.7 + - - -
910A ARG* 5.1 4.3 - - - +
911A LEU 2.6 24.2 + - - -
912A ALA 3.5 20.4 - - - -
913A GLN* 3.3 41.4 - - + +
914A PRO* 3.6 9.9 - - + -
917A CYS* 4.6 7.6 - - + +
918A THR 3.0 14.2 + - - +
919A ILE* 3.8 9.4 - - + +
920A ASP 3.3 0.2 - - - -
921A VAL* 1.3 78.2 - - - +
923A MET* 1.3 70.6 + - + +
925A MET* 3.1 34.5 + - + +
926A VAL* 3.1 45.5 + - + +
929A TRP* 4.7 9.2 - + - -
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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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913A GLN* 5.7 0.7 - - - +
919A ILE* 2.9 48.6 + - + +
920A ASP* 4.1 5.8 - - - +
921A VAL 3.4 0.4 - - - -
922A TYR* 1.3 78.1 - - + +
924A VAL* 1.3 65.6 + - - +
926A VAL* 3.1 24.0 + - - +
927A LYS* 3.0 39.6 + - - +
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Residues in contact with VAL 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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878A TYR* 5.5 1.1 - - + -
920A ASP 3.3 18.2 - - - +
921A VAL* 3.3 15.3 - - + +
923A MET* 1.3 79.3 - - - +
925A MET* 1.3 64.2 + - + +
927A LYS* 3.5 16.0 + - - +
928A CYS* 3.6 13.7 + - - -
937A PRO* 4.6 0.5 - - - +
942A LEU* 3.8 21.8 - - + +
945A GLU* 3.6 31.0 - - + +
946A PHE* 3.6 30.7 - - + -
949A MET* 4.1 4.7 - - + -
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Residues in contact with MET 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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879A GLY* 4.2 4.7 - - - +
882A VAL* 3.8 22.0 - - + +
883A TRP* 3.6 38.6 - - + -
886A MET* 4.7 1.6 - - - -
914A PRO* 3.7 21.3 - - + -
917A CYS* 4.6 7.4 - - - -
921A VAL* 3.8 9.6 - - + +
922A TYR* 3.1 50.8 + - + +
924A VAL* 1.3 76.2 - - + +
926A VAL* 1.3 58.8 + - - +
928A CYS* 3.0 32.4 + - - +
929A TRP* 3.2 30.4 - - + -
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Residues in contact with VAL 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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910A ARG* 4.6 26.8 - - - +
922A TYR* 3.1 51.8 + - + +
923A MET* 3.1 24.2 + - - +
925A MET* 1.3 76.4 - - - +
927A LYS* 1.3 62.7 + - + +
929A TRP* 3.2 23.6 + - + +
930A MET* 3.6 18.9 + - - +
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Residues in contact with LYS 927 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923A MET* 3.0 26.3 + - + +
924A VAL* 3.8 9.9 - - - +
925A MET 3.2 0.2 - - - -
926A VAL* 1.3 77.6 - - + +
928A CYS* 1.3 62.1 + - - +
929A TRP 3.2 0.7 + - - -
930A MET* 3.5 17.5 - - + +
935A ILE 5.1 4.5 - - - +
936A ARG* 3.4 14.4 - - - +
937A PRO* 3.3 28.9 - - + +
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Residues in contact with CYS 928 (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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875A VAL* 3.5 37.0 - - - +
876A TRP* 3.4 20.2 - - - +
878A TYR* 4.4 4.7 - - - -
879A GLY* 4.0 19.7 - - - -
924A VAL* 3.6 16.4 + - - -
925A MET* 3.0 13.5 + - - +
927A LYS* 1.3 77.3 - - - +
929A TRP* 1.3 56.8 + - + +
930A MET 3.4 0.9 - - - -
936A ARG* 3.4 16.0 - - - -
937A PRO* 4.0 14.1 - - - -
942A LEU* 4.2 11.2 - - - -
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Residues in contact with TRP 929 (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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876A TRP* 3.1 75.7 + + + -
879A GLY* 3.3 28.1 - - - -
880A VAL* 3.3 13.9 - - - +
883A TRP* 4.2 10.3 - + + -
910A ARG* 4.9 28.5 + - + +
911A LEU* 3.7 45.1 - - + -
922A TYR* 4.7 10.8 - + - -
925A MET* 3.2 41.7 - - + -
926A VAL* 3.2 19.6 + - + +
928A CYS* 1.3 77.1 - - - +
930A MET* 1.3 64.2 + - - +
931A ILE* 3.5 4.3 + - - +
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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