Contacts of the helix formed by residues 910 - 920 (chain A) in PDB entry 5LUQ
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 PHE 910 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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884A VAL* 6.2 3.1 - - - +
892A LEU* 3.5 23.6 - - + -
893A SER* 5.9 1.1 - - - -
906A PHE* 3.0 33.4 - - + +
907A LEU* 4.5 11.7 - - + +
908A ASP 3.5 0.8 - - - -
909A VAL* 1.3 88.3 - - - +
911A LEU* 1.3 71.6 + - + +
912A PRO* 3.0 6.4 - - - +
913A ARG* 2.8 20.4 + - + +
914A VAL* 2.9 17.6 + - + +
934A LEU* 5.3 3.0 - - + +
937A MSE 4.2 16.8 - - + -
938A VAL* 6.2 0.7 - - + -
941A MSE 3.4 35.0 - - + -
958A MSE 5.7 0.9 - - - -
962A TYR* 4.1 28.3 - + + -
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Residues in contact with LEU 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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881A LYS 3.5 22.7 - - - +
882A SER* 3.9 6.3 - - - -
883A TYR* 3.4 51.6 - - + +
884A VAL* 5.0 5.8 - - + +
907A LEU 5.5 0.6 + - - -
910A PHE* 1.3 76.9 - - + +
912A PRO* 1.3 69.9 - - + +
914A VAL* 3.2 19.4 - - + +
915A THR* 3.0 26.7 + - - +
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Residues in contact with PRO 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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908A ASP 3.4 20.4 - - - +
910A PHE 3.3 9.9 - - - +
911A LEU* 1.3 94.3 - - + +
913A ARG* 1.3 93.9 + - - +
915A THR* 2.5 27.3 + - + +
916A GLU* 3.0 9.1 + - - +
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Residues in contact with ARG 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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909A VAL* 3.0 43.5 - - - +
910A PHE* 2.8 13.8 + - + +
912A PRO* 1.3 99.6 - - - +
914A VAL* 1.3 55.5 + - - +
916A GLU* 2.3 73.6 + - - +
917A LEU* 3.0 12.0 + - - +
930A ALA 4.9 0.9 - - - -
933A LEU* 4.5 12.3 - - - +
934A LEU* 3.3 25.3 - - + +
937A MSE 3.8 29.2 - - + -
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Residues in contact with VAL 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A TYR* 6.2 1.6 - - + -
910A PHE* 2.9 21.2 + - + +
911A LEU* 3.2 27.1 - - + +
913A ARG* 1.3 74.7 - - - +
915A THR* 1.3 67.6 + - + +
916A GLU 3.1 1.2 + - - -
917A LEU* 3.2 14.2 + - + +
918A ALA* 3.2 18.0 + - + +
934A LEU* 4.4 2.6 - - + +
961A LEU 6.1 0.2 - - - +
962A TYR* 5.7 4.7 - - + -
965A THR* 4.4 30.1 - - + +
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Residues in contact with THR 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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911A LEU 3.0 12.1 + - - +
912A PRO* 2.5 25.6 + - + +
914A VAL* 1.3 79.0 - - + +
916A GLU* 1.3 57.9 + - - +
918A ALA* 3.6 9.6 - - + +
919A LEU* 2.9 34.4 + - - +
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Residues in contact with GLU 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 PRO 3.0 8.5 + - - +
913A ARG* 2.3 73.4 + - - +
915A THR* 1.3 69.2 - - - +
917A LEU* 1.3 66.6 + - + +
918A ALA 3.0 1.1 - - - -
919A LEU* 3.0 33.2 + - + +
920A THR 4.3 1.6 + - - -
926A THR* 5.6 1.2 - - - -
927A LYS* 5.8 3.8 - - - -
930A ALA* 3.4 43.0 - - + +
933A LEU* 5.5 1.0 - - - +
934A LEU* 4.7 0.5 - - - +
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Residues in contact with LEU 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 ARG 3.0 11.4 + - - +
914A VAL* 3.2 8.3 + - - +
916A GLU* 1.3 77.6 - - + +
918A ALA* 1.3 61.6 + - - +
920A THR* 4.6 5.5 + - - +
931A CYS* 4.7 19.7 - - + -
934A LEU* 4.2 16.2 - - + -
965A THR* 3.9 19.3 - - - +
968A VAL* 5.7 1.1 - - + -
969A LEU* 3.4 53.2 - - + -
972A LEU* 3.0 41.4 - - + +
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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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914A VAL* 3.2 13.4 + - + +
915A THR* 3.4 11.2 + - - +
916A GLU 3.0 1.0 - - - -
917A LEU* 1.3 79.3 - - - +
919A LEU* 1.3 65.6 + - - +
920A THR* 3.5 9.2 + - - +
972A LEU* 5.2 3.1 - - - -
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Residues in contact with LEU 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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915A THR* 2.9 26.9 + - - +
916A GLU* 3.0 30.2 + - + +
918A ALA* 1.3 77.0 - - - +
920A THR* 1.3 67.0 + - - +
921A ALA* 2.8 27.0 + - + +
926A THR* 3.6 35.4 - - + +
930A ALA* 5.5 0.2 - - + -
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Residues in contact with THR 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 GLU 4.3 2.2 + - - -
917A LEU 4.6 7.6 + - - +
918A ALA 3.5 11.6 + - - +
919A LEU* 1.3 84.3 + - - +
921A ALA* 1.3 64.3 + - - +
923A ASP* 4.6 13.4 + - - +
926A THR* 5.1 2.1 + - - -
972A LEU* 5.2 7.4 - - + +
976A VAL* 5.0 17.3 - - + -
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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