Contacts of the helix formed by residues 904 - 921 (chain A) in PDB entry 5A7R
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 904 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A TYR* 3.7 1.0 - - - +
880A ARG* 5.0 5.8 + - - -
901A THR* 2.8 30.4 + - - +
902A PHE 3.4 2.3 - - - +
903A GLY* 1.4 75.7 - - - +
905A SER* 1.3 60.2 + - - +
906A GLU* 3.5 9.5 + - - +
907A LEU* 3.0 30.9 + - + +
908A MET 3.2 12.3 + - - -
1976A GOL 2.8 34.5 + - - +
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Residues in contact with SER 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A TYR* 3.6 39.5 - - - -
903A GLY 3.4 5.6 + - - -
904A ASP* 1.3 70.9 + - - +
906A GLU* 1.3 66.6 + - - +
908A MET* 3.4 11.5 + - - +
909A ARG 3.1 17.7 + - - -
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Residues in contact with GLU 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ARG* 4.1 8.2 + - - +
904A ASP* 3.3 7.5 + - - +
905A SER* 1.3 80.6 + - - +
907A LEU* 1.3 59.0 + - - +
909A ARG 3.3 1.8 + - - +
910A ASP* 2.9 43.3 + - - +
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Residues in contact with LEU 907 (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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869A ASN* 3.4 26.2 - - - +
879A ALA* 3.8 19.5 - - + -
880A ARG* 3.7 47.9 - - + +
901A THR* 4.1 13.9 - - + -
904A ASP* 3.0 25.9 + - - +
906A GLU* 1.3 75.0 - - - +
908A MET* 1.3 59.0 + - - +
910A ASP* 3.1 1.5 + - - +
911A ILE* 2.9 54.4 + - + +
1976A GOL 4.0 14.6 - - - +
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Residues in contact with MET 908 (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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451A LYS* 3.3 24.9 - - + +
452A LYS 3.5 26.9 - - - +
453A TRP* 3.8 4.7 - - - -
454A LEU* 4.0 19.5 - - + -
720A VAL* 3.7 31.3 - - + +
721A THR* 3.8 3.6 - - - +
722A TYR* 3.6 19.3 - - + +
901A THR* 3.8 18.7 - - + +
904A ASP 3.2 11.8 + - - +
905A SER* 3.4 21.8 - - - +
907A LEU* 1.3 79.1 - - - +
909A ARG 1.3 59.6 + - - +
911A ILE* 4.0 0.3 - - - -
912A TYR* 3.0 25.1 + - - +
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Residues in contact with ARG 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 4.3 5.5 - - - +
905A SER 3.1 12.3 + - - -
906A GLU 3.3 2.1 + - - -
908A MET* 1.3 81.3 + - - +
910A ASP* 1.4 58.4 - - - +
912A TYR* 3.5 5.2 - - - -
913A SER* 2.9 35.2 - - - -
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Residues in contact with ASP 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ARG* 3.0 39.1 + - + +
906A GLU* 2.9 30.6 + - - +
907A LEU 3.1 4.0 + - - +
909A ARG 1.4 76.1 - - - +
911A ILE* 1.3 62.0 + - - +
913A SER* 3.4 5.8 + - - -
914A MET* 3.1 18.7 + - - +
953A TYR* 3.5 23.9 - - + -
957A TYR* 4.4 0.9 + - - -
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Residues in contact with ILE 911 (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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718A LEU* 3.8 22.0 - - + -
720A VAL* 4.5 7.0 - - + -
883A ALA* 3.6 27.4 - - + -
887A ILE* 4.1 17.9 - - + +
899A TYR* 3.7 31.4 - - + -
901A THR* 4.5 2.9 - - + -
907A LEU* 2.9 42.6 + - + +
908A MET 4.1 2.2 - - - +
910A ASP* 1.3 72.7 - - - +
912A TYR* 1.3 67.0 + - - +
914A MET* 3.4 1.6 + - - +
915A HIS* 3.0 22.0 + - - +
953A TYR* 4.1 15.0 - - + +
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Residues in contact with TYR 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 3.7 30.5 - - + -
455A GLY* 3.7 36.3 - - - -
718A LEU* 4.3 7.6 - - + -
720A VAL* 3.9 12.9 - - + +
908A MET 3.0 18.8 + - - +
909A ARG 3.7 2.5 - - - -
911A ILE* 1.3 78.0 - - - +
913A SER* 1.3 66.6 + - - +
915A HIS* 3.3 2.4 + - + +
916A ILE* 3.0 66.0 + - + +
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Residues in contact with SER 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A ARG 2.9 24.9 - - - -
910A ASP* 3.9 5.4 - - - -
911A ILE 3.3 0.2 - - - -
912A TYR* 1.3 85.1 - - - +
914A MET* 1.3 61.8 + - - +
916A ILE* 3.5 7.2 - - - +
917A PHE* 3.1 24.9 + - - +
957A TYR* 3.3 15.9 + - - -
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Residues in contact with MET 914 (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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884A LEU* 4.7 9.6 - - + -
910A ASP 3.1 17.0 + - - +
911A ILE 3.9 2.9 - - - +
913A SER* 1.3 74.0 - - - +
915A HIS* 1.3 66.6 + - - +
917A PHE* 3.3 4.4 + - - +
918A LEU* 3.0 56.3 + - + +
953A TYR* 3.6 58.3 - - + +
956A ILE* 3.8 24.5 - - + -
957A TYR* 3.2 34.2 + - + +
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Residues in contact with HIS 915 (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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715A LEU* 4.4 9.5 - - + +
716A THR 2.9 29.0 + - - -
717A ARG* 4.3 2.2 + - - -
718A LEU* 3.7 40.8 - - + +
884A LEU* 6.4 0.7 - - - -
887A ILE* 4.1 34.8 - - + +
911A ILE 3.0 18.8 + - - +
912A TYR* 3.8 5.2 - - + +
914A MET* 1.3 79.5 - - - +
916A ILE* 1.3 61.2 + - - +
918A LEU* 3.5 7.3 + - - +
919A THR* 3.0 50.8 + - + -
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Residues in contact with ILE 916 (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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912A TYR* 3.0 56.7 + - + +
913A SER* 3.5 11.2 - - - +
915A HIS* 1.3 79.1 + - - +
917A PHE* 1.3 63.2 + - - +
919A THR* 4.4 5.4 - - + -
920A GLU* 2.9 62.5 + - + +
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Residues in contact with PHE 917 (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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913A SER 3.1 19.7 + - - +
914A MET* 3.3 6.3 + - - +
916A ILE* 1.3 79.5 - - + +
918A LEU* 1.3 76.8 + - + +
920A GLU* 3.6 3.7 + - - +
921A ARG* 3.2 47.2 + - - +
923A LEU* 5.9 0.2 - - + -
956A ILE* 4.4 2.0 - - + -
957A TYR* 3.7 41.5 - + + -
960A VAL* 3.6 44.2 - - + -
961A GLU* 4.0 28.5 - - + -
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Residues in contact with LEU 918 (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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715A LEU* 3.9 20.9 - - + -
884A LEU* 4.0 22.7 - - + -
914A MET* 3.0 49.9 + - + +
915A HIS* 3.9 1.6 - - - +
917A PHE* 1.3 86.6 - - + +
919A THR* 1.3 61.0 + - - +
921A ARG* 3.4 2.3 + - - -
922A LYS 3.2 3.8 + - - -
923A LEU* 3.1 58.8 + - + +
928A VAL* 4.1 18.8 - - + -
931A LEU* 5.0 1.6 - - + -
956A ILE* 4.3 12.3 - - + -
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Residues in contact with THR 919 (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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715A LEU* 4.1 19.1 - - + +
716A THR 4.8 0.4 + - - +
915A HIS* 3.0 44.2 + - + -
916A ILE* 3.9 7.9 - - + -
918A LEU* 1.3 75.9 - - - +
920A GLU* 1.3 63.8 + - + +
922A LYS* 3.0 22.4 + - - +
923A LEU 5.2 1.3 - - - +
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Residues in contact with GLU 920 (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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916A ILE* 2.9 46.1 + - + +
917A PHE* 4.2 4.3 - - - +
919A THR* 1.3 81.2 - - + +
921A ARG* 1.3 62.1 + - + +
922A LYS* 3.5 9.9 + - - +
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Residues in contact with ARG 921 (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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917A PHE* 3.2 38.1 + - + +
918A LEU 3.4 0.2 + - - -
919A THR 3.2 0.4 - - - -
920A GLU* 1.3 78.1 - - + +
922A LYS* 1.3 71.3 + - - +
923A LEU* 3.2 23.1 + - + +
960A VAL* 3.7 35.9 + - - +
961A GLU* 4.0 22.5 + - - +
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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
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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