Contacts of the helix formed by residues 918 - 929 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913B GLN* 4.9 0.2 - - - -
916B ILE 3.9 0.4 + - - -
917B CYS* 1.3 75.3 - - - +
919B ILE* 1.3 68.1 + - - +
920B ASP* 2.8 12.4 + - - +
921B VAL* 2.8 18.9 + - - +
922B TYR* 3.4 5.7 + - - +
955B ARG 3.2 24.4 + - - +
956B TYR* 2.8 37.2 + - - +
958B VAL* 4.4 17.9 - - + -
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Residues in contact with ILE 919 (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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913B GLN* 4.2 20.2 + - - +
917B CYS 3.9 0.8 + - - -
918B THR* 1.3 71.7 - - - +
920B ASP* 1.3 72.6 + - - +
922B TYR* 3.5 12.7 + - + +
923B MET* 3.0 48.5 + - + +
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Residues in contact with ASP 920 (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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918B THR* 2.8 16.1 + - - +
919B ILE* 1.3 85.6 - - - +
921B VAL* 1.3 63.8 + - - +
923B MET* 3.5 8.6 + - - +
924B VAL* 3.2 22.8 + - - +
945B GLU* 5.0 4.2 - - - +
948B ARG* 6.3 1.8 - - - +
949B MET* 5.0 4.2 - - - +
956B TYR* 4.4 22.0 - - + -
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Residues in contact with VAL 921 (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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793B LEU* 5.0 0.2 - - + -
886B MET* 4.5 15.5 - - + -
917B CYS* 3.7 23.8 - - + -
918B THR* 2.8 18.8 + - - +
920B ASP* 1.3 70.0 - - - +
922B TYR* 1.3 66.9 + - - +
924B VAL* 2.9 25.6 + - - +
925B MET* 3.5 10.9 + - - +
946B PHE* 4.9 9.9 - - + -
949B MET* 3.3 27.6 - - + -
956B TYR* 3.2 27.4 - - + +
957B LEU* 3.9 11.7 - - + -
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Residues in contact with TYR 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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909B GLU* 5.0 4.2 + - - -
910B ARG* 4.5 8.7 - - - +
911B LEU 2.8 28.9 + - - -
912B ALA* 4.0 2.6 - - - -
913B GLN* 3.4 53.1 + - + +
917B CYS* 4.4 5.7 - - + +
918B THR 3.4 5.4 + - - +
919B ILE* 3.7 18.2 - - + +
921B VAL* 1.3 78.3 - - - +
923B MET* 1.3 61.5 + - - +
925B MET* 3.1 26.4 + - + +
926B VAL* 3.0 52.7 + - + +
929B TRP* 4.5 4.3 - + - -
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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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919B ILE* 3.0 42.8 + - + +
920B ASP* 3.6 10.5 - - - +
921B VAL 3.1 0.2 - - - -
922B TYR* 1.3 77.9 - - - +
924B VAL* 1.3 64.6 + - - +
926B VAL* 3.4 20.4 + - + +
927B LYS* 3.0 38.3 + - + +
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Residues in contact with VAL 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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878B TYR* 5.5 0.9 - - + -
920B ASP 3.2 17.5 - - - +
921B VAL* 3.3 14.8 - - - +
923B MET* 1.3 77.5 - - - +
925B MET* 1.3 63.6 + - + +
927B LYS* 3.5 14.0 - - - +
928B CYS* 3.4 24.2 + - - -
937B PRO* 4.9 0.2 - - - +
942B LEU* 3.7 20.7 - - + +
945B GLU* 3.2 30.7 - - + +
946B PHE* 3.7 33.0 - - + -
949B MET* 4.5 8.7 - - - -
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Residues in contact with MET 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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879B GLY* 3.6 17.3 - - - +
882B VAL* 4.1 21.8 - - + +
883B TRP* 3.1 46.9 - - + -
886B MET* 5.0 2.5 - - - -
914B PRO* 4.0 11.7 - - + -
917B CYS* 5.2 0.2 - - - -
921B VAL* 3.5 18.3 + - - +
922B TYR* 3.1 29.5 + - + +
924B VAL* 1.3 78.0 - - + +
926B VAL* 1.3 60.5 - - - +
928B CYS* 2.9 30.9 + - - +
929B TRP* 3.2 30.5 - - + -
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Residues in contact with VAL 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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910B ARG* 5.0 12.1 - - + -
922B TYR* 3.0 54.4 + - + +
923B MET* 3.4 18.3 + - + +
925B MET* 1.3 74.8 - - - +
927B LYS* 1.3 57.4 + - + +
929B TRP* 3.0 27.4 + - + +
930B MET* 3.3 29.1 + - + +
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Residues in contact with LYS 927 (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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923B MET* 3.0 33.7 + - + +
924B VAL* 3.5 10.5 + - - +
926B VAL* 1.3 76.1 - - + +
928B CYS* 1.3 61.5 + - - +
930B MET* 3.3 26.1 - - + +
935B ILE 6.1 0.2 - - - +
936B ARG* 3.5 6.2 - - - +
937B PRO* 3.3 41.2 - - + +
945B GLU* 4.7 15.5 + - - +
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Residues in contact with CYS 928 (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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875B VAL* 3.5 37.0 - - + +
876B TRP* 3.5 13.5 + - - +
878B TYR* 4.1 5.6 - - - -
879B GLY* 3.9 16.2 - - - -
924B VAL* 3.4 15.5 - - - -
925B MET* 2.9 13.2 + - - +
927B LYS* 1.3 79.1 - - - +
929B TRP* 1.3 65.1 + - + +
930B MET 3.5 1.1 - - - -
936B ARG* 3.2 21.3 + - - -
937B PRO* 4.3 1.1 - - - -
942B LEU* 3.9 23.1 - - - -
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Residues in contact with TRP 929 (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 TRP* 3.0 61.9 + + + -
879B GLY* 3.3 30.0 - - - -
880B VAL* 3.5 16.5 - - + +
883B TRP* 4.3 4.9 - + - -
910B ARG* 2.5 72.9 + - + -
911B LEU* 4.0 27.1 - - + -
922B TYR* 4.5 4.5 - + - -
925B MET* 3.2 50.0 - - + -
926B VAL* 3.0 16.3 + - + +
928B CYS* 1.3 82.1 - - - +
930B MET* 1.3 58.8 + - - +
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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