Contacts of the helix formed by residues 870 - 887 (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 870 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A VAL* 3.5 20.5 - - - +
862A GLU* 4.1 6.1 + - - +
868A LYS* 3.3 33.2 + - + +
869A TYR* 1.3 79.2 - - - +
871A HIS* 1.3 59.7 + - - +
872A GLN* 2.6 28.0 + - - +
873A SER* 2.6 40.9 + - - -
874A ASP* 3.5 4.0 + - - -
933A GLU* 5.3 1.2 - - - +
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Residues in contact with HIS 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A GLU* 2.9 63.4 + - + +
810A GLY* 3.6 29.5 + - - -
811A MET 3.7 12.0 + - - -
812A VAL* 4.2 10.6 - - + +
870A THR* 1.3 76.4 - - - +
872A GLN* 1.3 72.7 + - - +
874A ASP* 3.4 12.0 + - - +
875A VAL* 3.3 23.1 + - - +
939A PHE* 3.8 5.9 - - + -
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Residues in contact with GLN 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A THR* 2.6 32.0 - - - +
871A HIS* 1.3 85.2 + - - +
873A SER* 1.3 62.8 + - - +
875A VAL* 3.1 28.0 - - + +
876A TRP 3.4 2.3 + - - -
933A GLU* 3.8 39.9 - - + +
934A ASN* 5.2 3.8 + - - +
936A ARG* 3.4 15.1 + - + +
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Residues in contact with SER 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A ALA* 4.0 6.7 + - - +
862A GLU* 3.6 10.3 - - - -
863A SER* 3.5 24.5 - - - -
869A TYR* 3.6 8.7 - - - +
870A THR* 2.6 43.0 + - - -
872A GLN* 1.3 74.6 - - - +
874A ASP* 1.3 67.2 + - - +
876A TRP* 3.2 19.6 - - - +
877A SER* 3.3 8.4 + - - -
936A ARG* 3.8 10.3 - - - +
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Residues in contact with ASP 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A MET* 3.7 23.2 - - + +
811A MET 4.8 0.7 - - - +
812A VAL* 3.6 7.2 - - - +
813A HIS* 2.8 32.1 + - - +
814A ARG* 3.1 27.2 + - - -
815A ASN 4.7 0.5 + - - -
816A LEU* 4.2 4.2 - - + +
869A TYR* 5.7 0.3 - - - -
870A THR 3.8 8.0 - - - +
871A HIS* 3.4 11.6 + - - +
872A GLN 3.2 0.2 - - - -
873A SER* 1.3 84.6 + - - +
875A VAL* 1.3 53.7 + - - +
877A SER* 2.8 16.0 + - - -
878A TYR* 2.7 33.6 + - - +
939A PHE* 4.0 2.7 - - + -
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Residues in contact with VAL 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A GLU* 5.8 0.2 - - - +
871A HIS 3.4 15.3 - - - +
872A GLN* 3.1 19.0 + - + +
874A ASP* 1.3 76.8 - - - +
876A TRP* 1.3 59.2 - - - +
878A TYR* 3.2 6.9 - - - +
879A GLY 3.1 16.3 + - - -
928A CYS* 3.5 26.0 - - + +
936A ARG* 4.4 5.8 - - + -
937A PRO* 3.2 37.0 - - + +
938A THR* 4.9 1.1 - - - -
939A PHE* 3.7 30.5 - - + +
942A LEU* 4.2 5.2 - - + -
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Residues in contact with TRP 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LYS 5.2 1.0 + - - -
858A TRP 3.9 6.4 - - - -
859A MET 3.3 27.8 + - - -
860A ALA* 3.4 14.6 - - + -
861A LEU* 4.0 13.2 - - + -
872A GLN 3.4 3.7 + - - +
873A SER 3.2 13.6 + - - +
875A VAL* 1.3 76.8 - - - +
877A SER* 1.3 58.8 + - - +
879A GLY 2.9 14.7 + - - -
880A VAL* 3.2 12.2 + - + +
893A TYR* 4.9 7.3 + - - -
905A LEU* 4.1 40.8 - - + +
910A ARG* 6.4 0.4 - - + -
928A CYS 3.4 14.0 + - - +
929A TRP* 3.1 76.6 + + + +
930A MET 4.3 2.2 - - - -
931A ILE* 4.9 4.9 - - + -
936A ARG* 3.5 26.7 - - - +
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Residues in contact with SER 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A ARG 5.9 1.2 - - - -
815A ASN 5.8 0.2 + - - -
816A LEU* 3.6 33.4 + - - +
858A TRP* 2.9 26.8 + - - +
859A MET* 4.8 1.2 - - - -
873A SER 3.3 12.6 + - - -
874A ASP* 2.8 18.7 + - - -
876A TRP* 1.3 70.1 - - - +
878A TYR* 1.3 54.0 + - - +
880A VAL* 3.4 5.4 + - - +
881A THR* 2.6 38.0 + - - -
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Residues in contact with TYR 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A GLY* 2.7 25.9 + - - -
799A ILE* 3.6 33.0 - - + -
800A ALA* 3.6 23.6 - - + +
816A LEU* 3.7 12.4 - - + +
874A ASP 2.7 14.1 + - - +
875A VAL 3.2 8.5 - - - +
877A SER* 1.3 73.2 - - - +
879A GLY* 1.3 58.4 + - - +
881A THR* 3.3 5.4 + - - -
882A VAL* 2.9 47.3 + - + +
924A VAL* 5.5 0.9 - - + -
928A CYS* 4.4 6.1 - - - -
939A PHE* 3.8 23.6 - + + -
942A LEU* 3.7 30.7 - - + +
946A PHE* 3.6 19.1 - + - -
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Residues in contact with GLY 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A VAL 3.1 6.3 + - - -
876A TRP 2.9 9.9 + - - -
878A TYR* 1.3 76.7 - - - +
880A VAL* 1.3 59.7 + - - +
881A THR 3.2 0.2 + - - -
882A VAL* 3.3 5.6 + - - +
883A TRP* 2.9 28.1 + - - +
925A MET* 4.2 6.1 - - - +
928A CYS* 4.0 17.5 - - - -
929A TRP* 3.3 19.4 - - - -
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Residues in contact with VAL 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LYS 3.8 19.5 - - - +
858A TRP* 3.6 32.8 - - + +
876A TRP* 3.2 20.7 + - + +
877A SER 3.9 2.2 - - - +
879A GLY* 1.3 73.8 - - - +
881A THR* 1.3 55.9 + - - +
883A TRP* 3.2 7.6 - - + +
884A GLU* 2.8 32.3 + - - +
892A PRO* 3.8 22.7 - - + -
893A TYR* 5.1 1.3 - - - +
911A LEU* 4.8 9.9 - - + -
929A TRP* 3.3 26.1 - - + +
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Residues in contact with THR 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A ILE* 4.5 8.3 - - + -
816A LEU* 3.8 6.4 - - + +
817A ALA* 3.5 39.1 + - - +
818A ALA* 4.0 5.8 - - - +
821A VAL* 4.3 12.6 - - + -
877A SER 2.6 21.7 + - - -
878A TYR* 3.3 11.9 - - - -
879A GLY 3.1 0.2 - - - -
880A VAL* 1.3 72.9 - - - +
882A VAL* 1.3 68.3 + - + +
884A GLU* 2.8 25.3 + - - +
885A LEU* 3.1 27.9 + - + +
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Residues in contact with VAL 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A GLY* 5.0 7.0 - - - -
799A ILE* 6.0 1.8 - - + -
878A TYR* 2.9 56.4 + - + +
879A GLY* 3.7 4.5 - - - +
881A THR* 1.3 72.9 - - + +
883A TRP* 1.3 62.5 + - - +
885A LEU* 3.1 15.3 + - + +
886A MET* 2.9 51.0 + - + +
921A VAL* 5.4 0.7 - - + -
925A MET* 3.8 21.1 - - + -
946A PHE* 3.7 17.7 - - + -
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Residues in contact with TRP 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A GLY 2.9 13.3 + - - +
880A VAL* 3.2 18.4 - - + +
882A VAL* 1.3 73.5 - - - +
884A GLU* 1.3 81.8 + - - +
886A MET* 3.1 4.5 + - - +
887A THR* 2.9 46.8 + - + +
890A ALA* 3.6 27.1 - - + -
891A GLU 4.0 6.7 - - - -
892A PRO* 3.6 32.3 - - + -
893A TYR 4.8 2.2 - - - -
911A LEU* 3.5 32.3 - - + +
912A ALA* 3.0 35.6 + - + -
914A PRO* 3.8 16.0 - - + +
922A TYR* 5.2 0.2 - + - -
925A MET* 3.6 13.0 - - + -
929A TRP* 4.2 9.2 - + + -
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Residues in contact with GLU 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A LEU* 3.8 12.5 - - + +
817A ALA* 3.8 0.5 - - - +
818A ALA* 3.0 46.1 + - + +
819A ARG* 4.8 1.2 + - - -
858A TRP* 3.1 34.0 + - - -
880A VAL 2.8 21.6 + - - +
881A THR* 2.8 23.1 + - - +
883A TRP* 1.3 73.6 - - - +
885A LEU* 1.3 56.3 + - + +
887A THR* 2.7 14.0 + - - -
889A GLY* 2.7 35.1 + - - -
890A ALA 4.4 6.9 - - - +
892A PRO* 4.1 18.6 - - + +
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Residues in contact with LEU 885 (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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776A LEU* 3.3 42.6 - - + -
780A VAL* 3.9 26.7 - - + +
792A LEU* 4.3 21.4 - - + +
795A TRP* 5.7 6.5 - - + -
796A GLY* 6.2 2.0 - - - +
799A ILE* 4.4 8.5 - - + -
818A ALA* 4.5 10.3 - - + -
881A THR* 3.1 42.1 + - + +
882A VAL* 3.3 12.3 - - + +
884A GLU* 1.3 77.8 - - - +
886A MET* 1.3 58.8 + - + +
888A PHE* 2.7 33.3 + - - -
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Residues in contact with MET 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A LEU* 3.3 32.8 - - + +
793A LEU* 4.6 1.8 - - + -
796A GLY* 6.2 0.9 - - - -
882A VAL* 2.9 44.3 + - + +
883A TRP* 3.1 5.6 + - - +
885A LEU* 1.3 76.3 - - + +
887A THR* 1.3 57.1 + - - +
888A PHE* 3.2 6.8 + - - -
914A PRO* 3.8 12.4 - - + +
915A GLN* 5.1 1.0 + - - +
916A ILE* 3.3 28.9 + - - +
917A CYS* 3.4 33.4 - - - -
921A VAL* 4.1 11.2 - - + -
925A MET* 4.7 2.9 - - - -
946A PHE* 3.9 20.2 - - + -
957A LEU* 4.0 13.0 - - + -
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Residues in contact with THR 887 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A ARG* 4.1 9.2 + - - -
883A TRP* 2.9 41.1 + - + +
884A GLU* 2.7 22.9 + - - -
885A LEU 3.0 0.2 + - - -
886A MET* 1.3 75.2 - - - +
888A PHE* 1.3 74.4 + - - +
889A GLY 3.3 0.3 + - - -
890A ALA* 3.2 31.2 + - + +
914A PRO* 3.9 23.6 - - + -
915A GLN 5.4 0.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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