Contacts of the helix formed by residues 902 - 916 (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 ASP 902 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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901A GLU* 4.6 20.0 - - - +
936A PRO* 5.5 1.7 - - - +
871B ASP* 5.2 0.5 - - - +
900B SER* 2.8 14.3 + - - +
901B GLU* 1.3 74.9 - - - +
903B VAL* 1.3 63.2 + - - +
904B ARG* 3.4 20.0 + - - +
905B LYS* 3.0 55.5 + - + +
906B LEU* 3.0 16.1 + - - +
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Residues in contact with VAL 903 (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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901A GLU 4.9 1.9 + - - +
903A VAL* 3.5 31.9 - - + -
935A PHE* 3.8 23.8 - - + +
936A PRO* 4.0 28.2 - - + +
901B GLU 3.4 5.6 + - - +
902B ASP* 1.3 74.8 + - - +
904B ARG* 1.3 61.7 + - - +
906B LEU* 3.5 7.8 + - - -
907B TYR* 3.0 23.4 + - - +
936B PRO* 3.8 16.8 - - + +
940B LEU* 3.9 22.7 - - + +
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Residues in contact with ARG 904 (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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776A TYR* 5.6 0.8 + - - -
780A GLU* 3.1 29.1 + - - +
785A MET* 4.8 14.1 - - + +
901A GLU* 2.4 41.8 + - - -
934A HIS* 4.6 6.1 - - - +
935A PHE* 3.7 38.4 - - + +
936A PRO* 3.8 11.2 - - + +
1032A VAL* 6.4 2.0 - - - -
902B ASP* 3.2 15.9 + - - +
903B VAL* 1.3 77.7 - - - +
905B LYS* 1.3 58.4 + - + +
907B TYR* 3.6 3.1 + - - +
908B TRP* 3.1 27.4 + - - +
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Residues in contact with LYS 905 (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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870B THR 5.2 0.2 - - - -
871B ASP* 2.4 41.5 + - - +
874B TRP* 3.5 58.7 - - + +
900B SER* 4.2 7.0 + - - +
902B ASP* 3.0 37.6 + - + +
904B ARG* 1.3 76.3 - - + +
906B LEU* 1.3 66.0 + - - +
908B TRP* 3.2 8.9 + - - +
909B LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 906 (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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897B LEU 4.1 3.8 - - - +
898B ALA* 3.2 39.5 - - - +
900B SER* 3.5 29.2 - - - +
902B ASP 3.0 18.1 + - - +
903B VAL* 3.9 8.5 - - - +
905B LYS* 1.3 75.1 - - - +
907B TYR* 1.3 62.5 + - - +
909B LEU* 3.3 9.1 + - - +
910B MET* 3.2 29.1 + - - +
931B VAL* 4.0 15.3 - - + +
936B PRO* 4.5 4.9 - - + -
937B GLY* 4.1 28.5 - - - +
940B LEU* 4.0 9.0 - - + -
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Residues in contact with TYR 907 (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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782A LEU 3.6 8.0 + - - -
783A GLY* 3.6 34.6 - - - -
785A MET* 4.1 16.4 - - + -
935A PHE* 4.0 21.8 - + + -
903B VAL 3.0 18.8 + - - +
904B ARG 3.8 4.0 - - - +
905B LYS 3.2 0.2 - - - -
906B LEU* 1.3 78.4 - - - +
908B TRP* 1.3 64.1 + - - +
910B MET* 3.3 17.2 + - + +
911B LYS* 3.0 55.0 + - + +
940B LEU* 3.9 14.3 - - + +
943B ASP* 6.1 1.1 - - - -
944B PHE* 4.1 21.9 - + + -
948B ASN* 5.7 1.0 + - - -
1101B BR 4.2 8.7 - - + -
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Residues in contact with TRP 908 (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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1033A ALA* 3.7 24.7 + - + -
1034A PRO 3.2 20.1 + - - -
1035A ALA* 3.8 4.7 - - - -
874B TRP* 4.0 29.4 - + - -
878B LEU* 3.9 23.3 - - + -
904B ARG 3.1 17.5 + - - +
905B LYS* 3.2 5.4 + - - +
907B TYR* 1.3 77.7 - - - +
909B LEU* 1.3 73.0 + - + +
911B LYS* 3.8 1.4 - - - +
912B SER* 2.5 48.7 + - - -
918B ASN* 4.0 22.7 - - - -
919B PHE* 3.7 28.9 - + - -
1101B BR 3.8 22.4 - - + -
1130B BR 4.0 19.6 - - + +
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Residues in contact with LEU 909 (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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874B TRP* 4.5 6.7 - - + -
894B LEU* 4.3 10.1 - - + -
897B LEU* 3.7 17.3 - - + +
898B ALA* 3.6 41.3 - - + +
905B LYS 3.0 17.6 + - - +
906B LEU* 3.4 13.2 - - + +
908B TRP* 1.3 87.9 - - + +
910B MET* 1.3 57.8 + - - +
912B SER* 3.4 2.9 + - - -
913B SER* 3.0 30.5 + - - -
919B PHE* 3.5 37.8 - - + -
927B ILE* 4.0 15.2 - - + +
931B VAL* 5.4 0.4 - - + -
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Residues in contact with MET 910 (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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906B LEU 3.2 14.3 + - - +
907B TYR* 3.9 8.3 - - + +
909B LEU* 1.3 78.4 - - - +
911B LYS* 1.3 64.7 + - - +
913B SER 3.4 0.5 + - - -
914B LEU* 3.0 26.0 + - - +
924B LEU* 3.6 7.7 - - + +
927B ILE* 3.6 23.1 - - + -
928B ILE* 4.1 21.8 - - + -
931B VAL* 4.2 15.0 - - + -
940B LEU* 3.7 37.5 - - + +
941B ALA* 4.3 10.1 - - - -
944B PHE* 3.5 44.6 - - + -
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Residues in contact with LYS 911 (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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782A LEU 4.2 5.3 + - - -
783A GLY 3.8 20.7 + - - +
784A TYR* 4.8 11.3 - - - +
1035A ALA* 3.5 26.9 - - + -
907B TYR* 3.0 52.7 + - + +
910B MET* 1.3 76.4 - - - +
912B SER* 1.3 60.4 + - - +
914B LEU* 3.7 2.7 + - + +
915B ASN* 2.7 45.1 + - - +
944B PHE* 3.8 15.1 - - + -
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Residues in contact with SER 912 (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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1035A ALA* 3.6 20.2 - - - +
908B TRP* 2.5 45.0 + - - -
909B LEU 3.7 3.6 - - - -
911B LYS* 1.3 75.4 - - - +
913B SER* 1.3 64.4 + - - +
915B ASN* 3.1 2.5 + - - +
916B GLY 3.0 19.4 + - - -
917B ASP* 3.2 28.2 + - - -
918B ASN* 4.9 0.6 + - - -
919B PHE* 4.0 12.1 - - - -
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Residues in contact with SER 913 (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 LEU 3.0 17.4 + - - -
910B MET 3.4 0.2 + - - -
912B SER* 1.3 76.2 - - - +
914B LEU* 1.3 53.4 + - - +
916B GLY 3.3 4.2 + - - -
919B PHE* 3.5 14.9 - - - +
920B ARG 2.9 21.1 + - - -
921B THR* 2.7 36.7 + - - -
924B LEU* 3.2 30.4 + - - +
927B ILE* 3.5 20.6 - - - +
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Residues in contact with LEU 914 (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 MET 3.0 16.7 + - - +
911B LYS* 3.9 5.8 - - + +
913B SER* 1.3 78.2 - - - +
915B ASN* 1.3 65.0 + - - +
921B THR* 3.5 9.5 + - + -
924B LEU* 3.5 27.5 - - + +
944B PHE* 3.7 21.5 - - + -
948B ASN* 3.8 26.2 - - + +
951B LYS* 4.3 20.8 - - + +
952B LEU* 3.8 13.0 - - + +
955B LYS* 3.6 32.3 - - + -
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Residues in contact with ASN 915 (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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1035A ALA 3.6 14.8 + - - -
911B LYS* 2.7 39.4 + - - +
912B SER 3.1 3.7 + - - +
914B LEU* 1.3 83.1 - - - +
916B GLY* 1.3 55.0 + - - +
917B ASP* 3.2 29.4 + - - +
951B LYS* 5.9 2.4 - - - -
955B LYS* 5.9 0.9 - - - -
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Residues in contact with GLY 916 (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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912B SER 3.0 3.8 + - - -
913B SER 3.3 7.4 + - - -
914B LEU 3.4 1.4 + - - -
915B ASN* 1.3 76.3 - - - +
917B ASP* 1.3 59.2 + - - +
918B ASN 3.5 3.3 + - - -
919B PHE 3.2 21.3 + - - +
920B ARG* 4.5 4.4 + - - -
921B THR* 3.8 9.6 + - - -
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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