Contacts of the helix formed by residues 870 - 884 (chain B) in PDB entry 5MJ6
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
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840B MET* 3.5 31.8 - - + +
843B PHE* 5.4 1.0 - - - -
867B GLY* 3.2 5.7 + - - +
868B ALA 3.2 1.3 - - - -
869B LYS* 1.3 83.8 - - + +
871B ASP* 1.3 62.8 + - - +
872B LYS* 3.7 6.7 + - - +
873B GLY* 3.2 16.6 + - - -
874B TRP* 3.0 23.1 + - - +
905B LYS* 5.2 1.1 - - - -
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Residues in contact with ASP 871 (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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869B LYS 4.4 0.2 + - - -
870B THR* 1.3 72.4 - - - +
872B LYS* 1.3 62.8 + - - +
874B TRP* 3.4 1.6 + - - +
875B SER* 3.0 27.9 + - - -
902B ASP* 5.2 0.3 - - - +
905B LYS* 2.4 39.0 + - - +
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Residues in contact with LYS 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B MET* 3.7 32.8 - - + -
870B THR* 3.3 6.6 + - - +
871B ASP* 1.3 78.8 - - - +
873B GLY* 1.3 58.9 + - - +
875B SER* 3.7 4.4 - - - -
876B PHE* 3.0 27.8 + - - +
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Residues in contact with GLY 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B PHE* 3.6 24.0 - - - -
847B MET* 4.2 2.6 - - - +
867B GLY 3.6 17.9 - - - -
870B THR* 3.2 7.5 + - - -
872B LYS* 1.3 76.3 - - - +
874B TRP* 1.3 59.9 + - - +
876B PHE* 3.3 4.6 + - - +
877B LEU* 2.9 36.3 + - - +
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Residues in contact with TRP 874 (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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867B GLY 4.0 1.0 + - - -
868B ALA* 3.4 26.7 - - + +
870B THR 3.0 17.9 + - - +
871B ASP 3.7 3.8 - - - +
872B LYS 3.3 0.2 - - - -
873B GLY* 1.3 76.1 - - - +
875B SER* 1.3 71.6 + - - +
877B LEU* 3.2 1.6 + - - -
878B LEU* 2.9 42.7 + - + -
897B LEU* 3.1 52.3 + - + +
900B SER* 3.7 15.2 - - - -
905B LYS* 3.5 49.8 - - + +
908B TRP* 4.0 26.7 - + - -
909B LEU* 4.5 12.8 - - + -
1130B BR 4.6 10.1 - - + -
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Residues in contact with SER 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B ASP 3.0 18.1 + - - -
872B LYS* 3.7 5.4 - - - -
874B TRP* 1.3 86.4 - - - +
876B PHE* 1.3 62.9 + - - +
878B LEU* 3.3 5.9 + - - +
879B GLY* 3.0 20.4 + - - -
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Residues in contact with PHE 876 (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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843B PHE* 4.6 3.1 - + - -
846B TRP* 3.5 37.5 - + - -
847B MET* 3.5 46.7 - - + -
850B ASN* 3.7 18.4 - - - -
851B GLY 3.8 14.4 - - - -
872B LYS 3.0 17.6 + - - +
873B GLY 3.5 4.9 - - - +
874B TRP 3.3 0.2 - - - -
875B SER* 1.3 75.9 - - - +
877B LEU* 1.3 61.7 + - - +
879B GLY* 3.2 3.8 + - - -
880B LYS* 3.1 48.3 + - + +
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Residues in contact with LEU 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B PHE* 4.0 9.2 - - + -
846B TRP* 3.8 31.0 - - + -
864B PHE* 3.5 48.5 - - + +
868B ALA* 3.7 21.1 - - + +
873B GLY 2.9 20.7 + - - +
874B TRP 3.7 3.8 - - - +
876B PHE* 1.3 74.2 - - - +
878B LEU* 1.3 57.8 + - - +
880B LYS* 3.2 5.1 + - - +
881B TYR 2.9 24.4 + - - -
893B ILE* 3.5 26.8 - - + +
896B ALA* 4.3 4.0 - - + -
897B LEU* 3.7 9.9 - - + -
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Residues in contact with LEU 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874B TRP* 2.9 42.5 + - + +
875B SER* 3.6 7.6 - - - +
876B PHE 3.3 0.2 - - - -
877B LEU* 1.3 77.7 - - - +
879B GLY* 1.3 61.1 + - - +
881B TYR* 3.2 11.8 + - + +
882B ILE* 3.2 29.1 + - + +
897B LEU* 4.0 13.8 - - + +
908B TRP* 3.9 21.8 - - + -
918B ASN* 5.5 2.9 - - + +
919B PHE* 4.0 27.6 - - + -
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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
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875B SER 3.0 14.2 + - - -
876B PHE* 3.2 4.7 + - - -
878B LEU* 1.3 76.4 - - - +
880B LYS* 1.3 61.5 + - - +
882B ILE* 3.6 13.4 - - - +
883B SER* 3.3 23.3 + - - -
1R NAG 5.4 1.1 - - - -
2R NAG 4.7 14.8 - - - +
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Residues in contact with LYS 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B TRP* 4.1 20.0 - - + -
850B ASN* 3.3 23.6 + - - -
851B GLY* 3.8 7.9 - - - +
876B PHE* 3.1 40.2 + - + +
877B LEU* 3.2 7.8 + - - +
879B GLY* 1.3 76.4 - - - +
881B TYR* 1.3 64.2 + - - +
883B SER* 3.7 5.9 + - - -
884B ILE* 3.1 44.4 + - + +
889B GLU* 5.6 0.7 - - - +
893B ILE* 4.1 14.8 - - + -
1R NAG 3.1 45.7 + - - -
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Residues in contact with TYR 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B LEU 2.9 13.0 + - - +
878B LEU* 3.2 13.2 + - + +
880B LYS* 1.3 78.1 - - - +
882B ILE* 1.3 68.3 + - + +
883B SER 3.4 0.5 + - - -
884B ILE 4.4 0.7 + - - +
887B GLU* 5.6 0.3 + - - -
890B LYS* 3.4 80.9 + - + +
891B ASN* 5.6 1.0 + - - -
893B ILE* 4.1 15.7 - - + -
894B LEU* 3.9 23.1 - - + +
897B LEU* 4.7 2.7 - - + -
918B ASN* 3.6 15.6 + - + -
919B PHE* 3.4 42.0 - + - -
920B ARG* 5.1 2.1 + - - +
923B LYS* 4.1 13.3 - - - +
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Residues in contact with ILE 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B LEU* 3.2 32.5 - - + +
879B GLY* 3.6 14.6 - - - +
881B TYR* 1.3 82.8 - - + +
883B SER* 1.3 60.9 + - - +
884B ILE 4.8 1.6 - - - +
918B ASN* 4.6 18.2 - - + +
2R NAG 5.6 9.2 - - + -
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Residues in contact with SER 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B GLY 3.3 16.7 + - - -
880B LYS* 3.3 7.7 + - - -
881B TYR 3.2 0.6 - - - -
882B ILE* 1.3 81.8 - - - +
884B ILE* 1.3 73.5 + - - +
1R NAG 3.5 30.4 + - - -
2R NAG 5.2 10.5 - - - -
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Residues in contact with ILE 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B LYS* 3.1 35.8 + - + +
881B TYR 4.4 0.7 + - - +
882B ILE 4.8 1.9 - - - +
883B SER* 1.3 88.5 + - - +
885B GLY* 1.3 60.6 + - - +
886B SER* 4.2 6.3 - - - +
887B GLU* 5.2 0.2 - - - +
889B GLU* 3.5 35.0 - - + +
890B LYS* 3.6 39.2 + - + +
893B ILE* 4.0 12.6 - - + -
1R NAG 5.7 1.1 - - - +
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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