Contacts of the helix formed by residues 870 - 887 (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 870 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B VAL* 3.6 20.9 - - - +
862B GLU* 4.4 0.5 + - - -
868B LYS* 3.9 28.0 - - + -
869B TYR* 1.3 79.7 - - - +
871B HIS* 1.3 65.8 + - - +
872B GLN* 2.9 23.5 + - - +
873B SER* 2.8 33.9 + - - -
874B ASP* 3.2 6.4 + - - -
933B GLU* 3.4 10.0 + - - +
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Residues in contact with HIS 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B GLU* 3.4 53.6 + - + +
810B GLY* 3.6 33.6 + - - -
811B MET 4.0 6.0 + - - -
812B VAL* 3.8 18.7 - - + +
870B THR* 1.3 74.8 - - - +
872B GLN* 1.3 72.6 + - - +
874B ASP* 3.3 12.4 + - - +
875B VAL* 3.2 28.4 + - - +
939B PHE* 3.6 4.1 - - + -
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Residues in contact with GLN 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B GLU* 5.9 0.6 + - - -
870B THR* 2.9 32.1 + - - +
871B HIS* 1.3 93.6 - - - +
873B SER* 1.3 60.0 + - - +
875B VAL* 3.4 22.9 - - + +
876B TRP 3.6 1.6 + - - -
933B GLU* 3.7 40.4 - - + +
934B ASN* 5.4 5.8 - - - +
936B ARG* 3.1 20.4 + - + +
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Residues in contact with SER 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B VAL* 5.1 0.5 - - - +
860B ALA* 3.8 7.6 + - - +
862B GLU* 3.7 13.9 - - - -
863B SER* 3.6 21.3 + - - -
868B LYS 4.5 1.1 - - - -
869B TYR* 3.6 9.4 - - - +
870B THR* 2.8 38.4 + - - -
872B GLN* 1.3 74.4 - - - +
874B ASP* 1.3 66.0 + - - +
875B VAL 3.2 1.3 - - - -
876B TRP* 3.2 17.3 + - - +
877B SER* 3.3 10.4 + - - -
936B ARG* 3.9 7.9 - - - +
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Residues in contact with ASP 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B MET* 4.9 4.7 - - - +
811B MET 4.4 2.1 - - - +
812B VAL* 3.6 10.4 - - - +
813B HIS* 2.7 37.0 + - - +
814B ARG* 3.0 25.7 + - - -
815B ASN 4.6 0.3 + - - -
816B LEU* 4.0 5.6 - - + +
870B THR 3.2 11.0 + - - +
871B HIS* 3.3 13.0 + - - +
873B SER* 1.3 77.5 + - - +
875B VAL* 1.3 53.2 + - - +
877B SER* 3.0 12.1 + - - -
878B TYR* 2.8 33.3 + - - +
939B PHE* 3.7 17.0 - - + -
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Residues in contact with VAL 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B GLU* 5.6 0.9 - - - +
871B HIS 3.2 15.2 + - - +
872B GLN* 3.4 15.7 - - + +
873B SER 3.2 0.4 - - - -
874B ASP* 1.3 76.9 - - - +
876B TRP* 1.3 62.5 + - - +
878B TYR* 3.2 3.3 + - - +
879B GLY 3.1 18.0 + - - -
928B CYS* 3.5 24.0 - - - +
936B ARG* 4.1 18.2 - - + -
937B PRO* 3.3 30.1 - - + +
938B THR* 4.8 1.8 - - - -
939B PHE* 3.7 29.6 - - + +
942B LEU* 4.1 5.2 - - + -
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Residues in contact with TRP 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B LYS 5.3 1.0 + - - -
858B TRP 3.9 5.5 - - - -
859B MET 3.3 27.3 + - - -
860B ALA* 3.4 15.7 - - + -
861B LEU* 4.1 18.4 - - + -
872B GLN 3.6 2.8 + - - -
873B SER 3.2 12.9 + - - +
874B ASP 3.2 0.4 - - - -
875B VAL* 1.3 78.5 - - - +
877B SER* 1.3 62.1 + - - +
879B GLY 3.1 3.8 + - - -
880B VAL* 3.3 13.7 + - + +
893B TYR* 5.0 6.3 + - - -
905B LEU* 3.8 36.8 - - + -
910B ARG* 4.4 6.1 - - - -
928B CYS 3.5 11.1 + - - +
929B TRP* 3.0 76.7 + + + -
930B MET 4.2 1.8 - - - -
931B ILE* 4.9 3.8 - - + -
936B ARG* 3.4 34.3 - - - +
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Residues in contact with SER 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B ARG 5.7 3.1 + - - -
816B LEU* 3.4 31.2 + - - +
858B TRP* 2.7 27.4 + - - +
859B MET* 4.8 1.0 - - - -
873B SER 3.3 11.1 + - - -
874B ASP* 3.0 14.2 + - - -
876B TRP* 1.3 73.7 - - - +
878B TYR* 1.3 60.3 + - - +
880B VAL* 3.1 7.4 + - - +
881B THR* 2.6 31.9 + - - -
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Residues in contact with TYR 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B GLY* 2.7 24.7 + - - -
799B ILE* 3.7 31.2 - - + -
800B ALA* 3.7 22.0 - - + +
816B LEU* 3.8 7.9 - - + +
874B ASP 2.8 12.2 + - - +
875B VAL 3.3 8.1 - - - +
877B SER* 1.3 74.8 - - - +
879B GLY* 1.3 58.2 + - - +
881B THR* 3.1 9.2 + - - -
882B VAL* 2.9 49.2 + - + +
924B VAL* 5.5 0.4 - - + -
928B CYS* 4.1 8.3 - - - -
939B PHE* 3.7 23.8 - + + -
942B LEU* 3.7 33.5 - - + +
946B PHE* 3.5 23.2 - + - -
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Residues in contact with GLY 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B VAL 3.1 11.3 + - - -
876B TRP 3.1 0.6 + - - -
878B TYR* 1.3 77.7 - - - +
880B VAL* 1.3 55.1 + - - +
882B VAL* 3.6 1.1 + - - -
883B TRP* 3.0 22.5 + - - +
925B MET* 3.6 10.7 - - - +
928B CYS* 3.9 17.5 - - - -
929B TRP* 3.3 31.8 - - - -
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Residues in contact with VAL 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B LYS 3.6 22.7 - - - +
858B TRP* 3.6 27.8 - - + +
876B TRP* 3.6 28.3 - - + +
877B SER 3.1 7.0 + - - +
879B GLY* 1.3 73.6 - - - +
881B THR* 1.3 61.4 + - - +
883B TRP* 3.3 6.0 - - + +
884B GLU* 3.1 31.3 + - - +
892B PRO* 3.8 21.1 - - + -
893B TYR* 5.4 0.4 - - - +
911B LEU* 4.7 11.9 - - + -
929B TRP* 3.7 18.4 - - + +
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Residues in contact with THR 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B ILE* 4.7 7.4 - - + -
816B LEU* 3.7 7.1 + - + +
817B ALA* 3.5 20.7 + - - +
818B ALA* 3.4 30.5 - - - +
821B VAL* 4.3 11.2 - - + -
858B TRP* 4.4 0.3 - - - -
877B SER 2.6 23.5 + - - -
878B TYR* 3.1 12.4 + - - -
880B VAL* 1.3 74.6 - - - +
882B VAL* 1.3 61.3 + - - +
884B GLU* 2.9 18.2 + - - +
885B LEU* 2.6 33.1 - - + +
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Residues in contact with VAL 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B GLY* 5.1 5.8 - - - -
799B ILE* 5.9 2.2 - - + +
878B TYR* 2.9 56.7 + - + +
879B GLY* 3.8 4.5 - - - +
881B THR* 1.3 73.2 - - - +
883B TRP* 1.3 64.2 + - - +
885B LEU* 3.0 22.3 + - + +
886B MET* 3.1 37.3 + - + +
921B VAL* 5.2 1.8 - - + -
925B MET* 4.1 20.9 - - + -
946B PHE* 3.9 17.0 - - + -
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Residues in contact with TRP 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B GLY 3.0 15.4 + - - +
880B VAL* 3.3 16.6 - - + +
881B THR 3.1 0.2 - - - -
882B VAL* 1.3 76.9 - - - +
884B GLU* 1.3 57.0 + - - +
886B MET* 3.4 1.4 + - - +
887B THR* 2.6 54.2 + - + +
890B ALA* 3.3 39.7 - - + -
891B GLU 4.1 3.4 - - - -
892B PRO* 3.6 24.7 - - + -
893B TYR 5.1 0.4 - - - -
911B LEU* 3.6 36.5 - - + +
912B ALA* 2.7 29.4 + - + -
914B PRO* 3.9 7.8 - - + +
925B MET* 3.1 35.2 - - + -
929B TRP* 4.3 3.6 - + + -
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Residues in contact with GLU 884 (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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777B LEU* 3.4 19.3 - - + +
780B VAL* 5.2 1.1 - - - -
817B ALA* 5.4 0.2 - - - +
818B ALA* 3.3 37.5 + - + +
819B ARG* 4.8 0.5 + - - -
858B TRP* 2.6 42.5 + - - -
880B VAL 3.1 14.8 + - - +
881B THR* 2.9 10.1 + - - +
883B TRP* 1.3 81.2 - - + +
885B LEU* 1.3 58.2 - - - +
887B THR* 3.0 11.4 + - - -
889B GLY* 2.5 39.3 + - - +
890B ALA 4.2 12.3 - - - +
892B PRO* 4.5 5.8 - - + +
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Residues in contact with LEU 885 (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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776B LEU* 3.7 38.1 - - + -
780B VAL* 4.7 11.3 - - + +
792B LEU* 3.7 24.2 - - + +
795B TRP* 4.3 17.0 - - + -
796B GLY* 4.7 6.1 - - - +
799B ILE* 4.0 14.6 - - + -
818B ALA* 4.1 8.5 - - + -
881B THR* 2.6 41.7 - - + +
882B VAL* 3.0 15.1 + - + +
884B GLU* 1.3 78.2 - - - +
886B MET* 1.3 66.1 + - + +
888B PHE* 3.2 25.3 + - - -
889B GLY 4.8 0.4 - - - +
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Residues in contact with MET 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B LEU* 4.2 24.9 - - + +
793B LEU* 4.3 11.0 - - + -
796B GLY* 5.8 0.4 - - - -
882B VAL* 3.1 37.1 + - + +
883B TRP* 5.0 0.2 - - - -
885B LEU* 1.3 77.7 - - + +
887B THR* 1.3 57.6 + - - +
888B PHE* 3.1 14.5 + - - -
914B PRO* 3.8 13.9 - - + +
915B GLN 5.3 0.7 + - - -
916B ILE* 3.3 29.2 + - + +
917B CYS* 3.4 28.3 - - - -
921B VAL* 4.5 5.2 - - + -
925B MET* 5.0 1.3 - - - -
946B PHE* 4.1 18.8 - - + -
957B LEU* 3.8 27.8 - - + -
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Residues in contact with THR 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B ARG* 4.4 6.9 + - - -
883B TRP* 2.6 55.1 + - + +
884B GLU* 3.0 16.1 + - - -
886B MET* 1.3 76.4 - - - +
888B PHE* 1.3 71.8 + - - +
890B ALA* 3.4 28.4 + - + +
914B PRO* 3.6 23.6 - - + -
915B GLN 5.9 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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