Contacts of the helix formed by residues 893 - 919 (chain U) in PDB entry 6FF7
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 SER 893 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877U LEU* 6.0 0.4 - - - -
878U ARG* 3.4 14.1 - - - +
891U ASP* 3.4 4.5 - - - -
892U PHE* 1.3 81.2 - - - +
894U ARG* 1.3 66.4 + - - +
895U TYR* 3.1 11.0 - - - -
896U GLY 3.1 5.0 + - - -
897U ARG* 2.9 22.5 + - - +
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Residues in contact with ARG 894 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877U LEU* 6.6 0.7 - - - -
878U ARG 3.9 5.9 + - - +
893U SER* 1.3 72.6 - - - +
895U TYR* 1.3 57.4 + - - +
897U ARG* 4.0 5.0 - - - +
898U VAL* 2.9 32.2 + - - +
1024U SER* 3.6 32.6 - - - +
1027U LEU* 6.4 1.1 - - - -
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Residues in contact with TYR 895 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893U SER* 4.0 7.3 - - - -
894U ARG* 1.3 80.4 - - - +
896U GLY* 1.3 61.8 + - - +
898U VAL* 3.9 5.0 - - - +
899U ASN* 3.1 24.3 + - - +
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Residues in contact with GLY 896 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891U ASP* 3.4 37.6 - - - +
893U SER* 3.1 8.6 + - - -
895U TYR* 1.3 79.3 - - - +
897U ARG* 1.3 56.5 + - - +
899U ASN* 3.6 6.0 + - - +
900U TYR* 3.0 26.5 + - - +
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Residues in contact with ARG 897 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873U GLU 5.7 3.1 - - - +
876U LEU 4.4 16.4 - - - +
877U LEU* 5.6 2.9 - - + -
891U ASP 3.8 2.0 + - - +
892U PHE* 4.8 4.9 - - - +
893U SER 2.9 17.2 + - - +
894U ARG* 4.0 4.0 - - - +
896U GLY* 1.3 77.1 - - - +
898U VAL* 1.3 66.6 + - - +
899U ASN 3.2 0.2 - - - -
900U TYR* 3.4 6.4 + - - +
901U VAL* 3.0 23.9 + - - +
1027U LEU* 5.3 12.8 - - + -
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Residues in contact with VAL 898 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894U ARG 2.9 18.7 + - - +
895U TYR* 3.9 5.2 - - - +
897U ARG* 1.3 76.3 - - - +
899U ASN* 1.3 57.9 + - - +
901U VAL* 3.4 6.8 + - - +
902U LEU* 3.0 29.0 + - - +
1020U GLY* 5.1 9.6 - - - +
1023U ARG* 4.7 21.5 - - + -
1024U SER* 5.3 3.1 - - - +
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Residues in contact with ASN 899 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895U TYR 3.1 18.6 + - - +
896U GLY* 3.7 7.2 - - - +
898U VAL* 1.3 75.1 - - - +
900U TYR* 1.3 65.0 + - - +
902U LEU* 3.4 6.3 + - - +
903U ALA* 3.0 25.5 + - - +
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Residues in contact with TYR 900 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873U GLU* 6.0 4.5 - - + +
874U ARG* 6.5 1.3 - - - -
896U GLY 3.0 18.1 + - - +
897U ARG* 3.7 8.3 - - - +
898U VAL 3.3 0.2 - - - -
899U ASN* 1.3 76.4 - - - +
901U VAL* 1.3 53.2 + - - +
903U ALA* 3.2 5.2 + - - +
904U ARG* 2.8 38.2 + - + +
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Residues in contact with VAL 901 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897U ARG 3.0 16.6 + - - +
898U VAL* 3.6 7.0 - - - +
900U TYR* 1.3 75.9 - - - +
902U LEU* 1.3 58.6 + - - +
904U ARG* 3.8 4.8 - - - +
905U ARG* 2.8 33.1 + - - +
1011U PHE* 5.1 12.8 - - + +
1014U SER* 5.6 9.9 - - - -
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Residues in contact with LEU 902 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898U VAL 3.0 16.6 + - - +
899U ASN* 3.7 8.5 - - - +
901U VAL* 1.3 77.9 - - - +
903U ALA* 1.3 60.0 + - - +
905U ARG* 3.6 6.5 + - - +
906U ILE* 3.4 20.1 + - - +
1014U SER* 5.9 6.7 - - - -
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Residues in contact with ALA 903 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899U ASN 3.0 17.7 + - - +
900U TYR* 3.8 4.7 - - - +
902U LEU* 1.3 74.5 - - - +
904U ARG* 1.3 64.4 + - - +
906U ILE* 3.5 7.8 + - - +
907U GLU* 3.4 19.8 + - - +
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Residues in contact with ARG 904 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900U TYR* 2.8 23.3 + - + +
901U VAL* 3.8 5.2 - - - +
903U ALA* 1.3 70.5 - - - +
905U ARG* 1.3 66.0 + - - +
907U GLU* 3.3 6.8 + - - +
908U LEU* 3.0 26.6 + - - +
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Residues in contact with ARG 905 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901U VAL 2.8 18.6 + - - +
902U LEU* 3.7 7.6 - - - +
903U ALA 3.3 0.2 - - - -
904U ARG* 1.3 77.4 - - - +
906U ILE* 1.3 62.6 + - - +
908U LEU* 3.4 5.3 + - - +
909U LEU* 3.0 26.7 + - - +
1008U LEU* 6.4 1.1 - - - +
1011U PHE* 4.4 20.9 - - + +
1014U SER* 6.3 2.7 - - - -
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Residues in contact with ILE 906 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902U LEU 3.4 10.4 + - - +
903U ALA* 3.6 11.2 - - - +
904U ARG 3.2 0.2 - - - -
905U ARG* 1.3 79.6 - - - +
907U GLU* 1.3 62.4 + - - +
909U LEU* 3.5 5.1 + - - +
910U GLU* 3.2 21.5 + - - +
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Residues in contact with GLU 907 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903U ALA 3.4 10.1 + - - +
904U ARG* 3.3 10.0 + - - +
905U ARG 3.3 0.2 - - - -
906U ILE* 1.3 79.9 - - - +
908U LEU* 1.3 61.7 + - - +
910U GLU* 3.3 9.7 + - - +
911U GLU* 3.2 18.5 + - - +
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Residues in contact with LEU 908 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904U ARG 3.0 18.6 + - - +
905U ARG* 4.0 4.9 - - - +
907U GLU* 1.3 73.9 - - - +
909U LEU* 1.3 63.7 + - - +
910U GLU 3.1 1.8 - - - -
911U GLU* 3.0 18.2 + - - +
912U VAL* 3.1 12.6 + - - +
1004U ILE* 4.6 24.4 - - + +
1007U GLN* 5.9 3.6 - - + -
1008U LEU* 5.3 10.1 - - + +
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Residues in contact with LEU 909 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905U ARG 3.0 18.8 + - - +
906U ILE* 3.9 5.8 - - - +
908U LEU* 1.3 76.9 - - - +
910U GLU* 1.3 57.0 + - - +
912U VAL* 3.4 10.1 + - - +
913U LYS* 3.2 23.7 + - - +
926U SER* 6.5 0.2 - - - -
927U TYR* 4.0 30.5 + - + +
928U THR 5.7 3.4 - - - -
1008U LEU* 6.3 0.2 - - - +
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Residues in contact with GLU 910 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906U ILE 3.2 14.0 + - - +
907U GLU* 3.4 12.8 - - - +
908U LEU 3.1 0.4 - - - -
909U LEU* 1.3 75.9 - - - +
911U GLU* 1.3 59.1 + - - +
913U LYS* 3.4 8.9 + - - +
914U ARG* 3.0 25.8 + - - +
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Residues in contact with GLU 911 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907U GLU 3.2 11.0 + - - +
908U LEU* 3.0 13.8 + - - +
910U GLU* 1.3 75.0 - - - +
912U VAL* 1.3 60.0 + - - +
914U ARG* 3.2 8.0 + - - +
915U LEU* 2.8 29.2 + - - +
1004U ILE* 5.5 10.1 - - + -
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Residues in contact with VAL 912 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M VAL* 4.4 5.4 - - + +
908U LEU 3.1 11.2 + - - +
909U LEU* 3.6 13.0 - - - +
910U GLU 3.3 0.2 - - - -
911U GLU* 1.3 76.8 - - - +
913U LYS* 1.3 56.6 + - - +
915U LEU* 3.2 8.0 + - - +
916U GLN* 2.8 30.2 + - - +
927U TYR* 4.6 13.7 - - + -
932U ALA* 4.9 13.7 - - + -
935U PHE* 6.1 2.9 - - + -
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Residues in contact with LYS 913 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909U LEU 3.2 11.7 + - - +
910U GLU* 3.5 12.8 - - - +
912U VAL* 1.3 77.8 - - - +
914U ARG* 1.3 61.5 + - - +
916U GLN* 3.4 8.6 + - - +
917U LYS* 3.1 22.5 + - - +
926U SER* 6.0 3.8 - - - -
927U TYR* 5.5 7.0 - - + +
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Residues in contact with ARG 914 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910U GLU 3.0 14.5 + - - +
911U GLU* 3.2 11.9 + - - +
913U LYS* 1.3 73.6 - - - +
915U LEU* 1.3 60.3 + - - +
917U LYS* 3.5 5.6 + - - +
918U SER* 3.0 28.8 + - - -
973U TYR* 5.5 1.7 - - - -
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Residues in contact with LEU 915 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M VAL* 4.6 6.1 - - + -
911U GLU 2.8 16.1 + - - +
912U VAL* 3.5 8.7 - - - +
914U ARG* 1.3 74.3 - - - +
916U GLN* 1.3 66.0 + - - +
918U SER* 3.2 8.2 + - - -
919U LEU* 3.2 23.2 + - - +
973U TYR* 4.9 11.9 - - + -
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Residues in contact with GLN 916 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M VAL* 3.5 27.7 - - + +
912U VAL 2.8 17.8 + - - +
913U LYS* 3.4 12.8 - - - +
915U LEU* 1.3 72.7 - - - +
917U LYS* 1.3 60.4 + - - +
919U LEU* 3.2 8.7 + - - +
921U VAL* 3.1 34.5 + - + +
923U GLY 6.1 1.1 - - - +
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Residues in contact with LYS 917 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913U LYS 3.1 12.5 + - - +
914U ARG* 3.9 5.8 - - - +
916U GLN* 1.3 74.8 - - - +
918U SER* 1.3 63.0 + - - +
919U LEU 3.0 4.7 - - - -
920U GLY* 3.1 14.0 + - - +
921U VAL 4.5 6.1 - - - +
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Residues in contact with SER 918 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914U ARG 3.0 18.6 + - - -
915U LEU 3.2 5.6 + - - -
917U LYS* 1.3 76.2 - - - +
919U LEU* 1.3 59.1 + - - +
920U GLY 3.4 0.6 + - - -
972U GLU* 3.7 23.1 - - - +
973U TYR* 3.7 34.5 - - - -
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Residues in contact with LEU 919 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M LEU* 4.6 11.8 - - - +
100M GLU 5.2 4.2 - - - +
103M PHE* 4.2 25.9 - - - +
104M VAL* 5.4 0.4 - - - -
915U LEU 3.2 11.6 + - - +
916U GLN 3.6 9.2 - - - +
917U LYS 3.0 0.8 - - - -
918U SER* 1.3 78.8 - - - +
920U GLY* 1.3 60.8 + - - +
921U VAL 3.5 0.3 + - - -
969U PRO 6.0 2.5 - - - +
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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