Contacts of the helix formed by residues 910 - 923 (chain A) in PDB entry 5V4R
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 LEU 910 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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905A TYR* 3.7 28.0 - - + -
908A GLY 5.8 0.2 - - - -
909A GLN* 1.3 82.1 + - - +
911A TYR* 1.3 67.0 + - - +
912A GLY 3.3 2.9 - - - -
913A LEU* 3.8 17.9 - - + -
914A GLU* 2.9 30.5 + - + +
940A LYS* 4.1 10.1 - - + +
941A PHE* 4.3 7.9 - - + -
833B GLN* 3.9 9.6 - - - +
836B ASN* 3.6 30.3 - - + +
872B TYR* 3.5 49.8 - - + +
875B GLU* 5.3 0.6 + - - -
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Residues in contact with TYR 911 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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871A ARG* 4.4 11.2 - - - +
875A GLU* 3.7 36.1 - - + -
878A PHE* 4.0 13.5 - + + -
879A ARG* 2.6 30.6 + - - +
904A ASP* 3.7 4.5 + - - +
909A GLN* 4.4 1.5 - - + +
910A LEU* 1.3 78.1 - - - +
912A GLY* 1.3 64.3 + - - +
914A GLU* 3.5 10.5 + - - +
915A LYS* 3.1 46.2 + - + +
1001A MGT 2.7 23.9 + - - -
875B GLU* 3.8 34.8 + - - +
879B ARG* 5.1 4.5 - - - -
911B TYR* 3.7 22.7 - + - -
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Residues in contact with GLY 912 (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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878A PHE* 3.7 31.8 - - - -
901A THR* 3.9 9.6 + - - +
904A ASP* 2.8 24.6 + - - -
911A TYR* 1.3 76.6 - - - +
913A LEU* 1.3 54.6 + - - -
915A LYS* 3.1 4.5 + - - +
916A PHE* 2.9 28.4 + - - +
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Residues in contact with LEU 913 (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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901A THR* 3.7 13.4 + - + +
904A ASP* 4.4 1.8 + - - +
905A TYR* 3.6 35.9 - - + -
909A GLN 5.4 0.2 + - - -
910A LEU* 3.2 18.7 + - + +
912A GLY* 1.3 74.4 - - - +
914A GLU* 1.3 58.8 + - - +
916A PHE* 3.3 1.9 + - - +
917A TRP* 2.9 29.8 + - - +
934A LEU* 3.9 21.5 - - + -
937A TYR* 3.8 24.7 - - + +
938A LEU* 3.4 25.1 - - + -
940A LYS* 5.0 0.9 - - + -
941A PHE* 3.8 30.3 - - + -
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Residues in contact with GLU 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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910A LEU 2.9 22.0 + - - +
911A TYR* 3.8 10.3 - - + +
913A LEU* 1.3 75.2 - - - +
915A LYS* 1.3 63.5 + - + +
917A TRP* 3.4 3.9 + - - +
918A ALA* 2.8 30.6 + - - +
941A PHE* 3.7 26.0 - - + -
840B ARG* 6.1 0.3 - - - -
872B TYR* 3.2 36.1 + - + -
875B GLU* 4.9 1.0 - - - +
879B ARG* 3.6 20.5 + - - -
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Residues in contact with LYS 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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878A PHE* 4.0 25.4 - - + +
879A ARG* 3.5 16.8 - - - +
882A SER* 2.8 39.6 + - - +
883A TYR* 4.7 4.7 - - + -
897A PHE* 3.8 4.9 - - + -
911A TYR* 3.1 42.5 + - + +
912A GLY 3.1 8.7 + - - +
914A GLU* 1.3 80.7 - - - +
916A PHE* 1.3 59.0 + - - +
918A ALA* 3.4 6.1 + - + +
919A PHE* 2.9 12.8 + - - +
1001A MGT 2.7 43.9 + - - -
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Residues in contact with PHE 916 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A PHE* 3.7 34.8 - + - -
897A PHE* 3.4 32.6 - + + -
898A GLN* 3.6 21.8 - - + -
901A THR* 3.8 19.7 - - + +
912A GLY 2.9 12.9 + - - +
913A LEU* 3.7 7.0 - - - +
915A LYS* 1.3 75.2 - - - +
917A TRP* 1.3 64.6 + - - +
919A PHE* 3.1 5.5 + + - +
920A LEU* 3.0 35.8 + - + +
930A ILE* 4.4 7.2 - - + -
934A LEU* 3.6 25.4 - - + -
938A LEU* 3.8 27.6 - - + -
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Residues in contact with TRP 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 LEU 2.9 17.2 + - - +
914A GLU* 3.6 5.2 - - - +
916A PHE* 1.3 74.8 - - - +
918A ALA* 1.3 63.0 + - - +
920A LEU* 3.2 22.8 + - + +
921A LYS* 2.9 66.2 + - + +
938A LEU* 4.0 37.2 - - + +
941A PHE* 3.7 29.0 - + + +
942A ARG* 4.3 28.0 - - + -
945A GLU* 3.3 21.6 + - - -
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Residues in contact with ALA 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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882A SER* 4.0 7.6 - - - +
914A GLU 2.8 21.4 + - - +
915A LYS* 3.6 11.4 - - + +
917A TRP* 1.3 73.3 - - - +
919A PHE* 1.3 65.3 + - - +
921A LYS* 3.1 9.0 + - - +
922A TYR* 3.0 40.5 + - + -
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Residues in contact with PHE 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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881A TYR 4.6 0.9 - - - -
882A SER* 3.4 27.5 + - - +
885A LEU* 3.5 33.2 - - + -
886A GLU* 4.0 2.7 - - + -
889A PHE* 4.1 22.4 - + - -
894A PHE* 3.6 26.7 - + - -
897A PHE* 3.8 16.6 - + + -
915A LYS 2.9 14.0 + - - +
916A PHE* 3.1 10.5 + + - +
918A ALA* 1.3 77.7 - - - +
920A LEU* 1.3 67.5 + - + +
922A TYR* 5.0 2.5 - - - -
923A SER* 2.9 63.2 + - - +
925A ALA* 4.7 0.2 - - + -
928A LEU* 4.0 17.3 - - + -
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Residues in contact with LEU 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 PHE* 3.0 26.5 + - + +
917A TRP* 3.2 24.2 + - + +
919A PHE* 1.3 85.6 - - + +
921A LYS* 1.3 63.1 + - + +
923A SER* 4.2 10.2 - - - +
928A LEU* 3.8 28.7 - - + -
930A ILE* 4.0 17.5 - - + -
938A LEU* 3.8 29.6 - - + -
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Residues in contact with LYS 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 TRP* 2.9 52.0 + - + +
918A ALA* 3.1 11.2 + - - +
920A LEU* 1.3 80.4 - - + +
922A TYR* 1.3 67.4 + - + +
923A SER 4.6 2.1 - - - +
945A GLU* 2.9 28.6 + - - -
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Residues in contact with TYR 922 (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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886A GLU* 3.7 40.0 - - + +
918A ALA* 3.0 35.4 + - + +
919A PHE* 4.3 2.5 - - - +
921A LYS* 1.3 86.8 - - + +
923A SER* 1.3 64.8 + - - +
924A LYS* 3.7 8.1 + - - +
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Residues in contact with SER 923 (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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885A LEU 4.7 3.1 + - - -
886A GLU* 4.5 13.7 + - - +
889A PHE* 5.9 0.2 - - - +
919A PHE* 2.9 47.3 + - - -
920A LEU* 4.2 9.7 - - - +
921A LYS 4.6 1.9 - - - +
922A TYR* 1.3 80.5 - - - +
924A LYS* 1.3 59.8 + - - +
925A ALA* 2.9 32.0 + - - +
926A LYS* 4.8 2.6 + - - -
928A LEU* 6.0 0.7 - - - -
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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