Contacts of the helix formed by residues 917 - 925 (chain A) in PDB entry 3E0D
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 917 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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915A PHE* 3.6 1.4 - - - +
916A LYS* 1.3 80.1 + - - +
918A LEU* 1.3 59.4 + - - +
920A ASP* 3.2 13.5 + - - +
921A PHE* 3.0 26.5 + - - +
947A PHE* 3.6 20.5 - - - -
984A GLU* 2.6 36.8 + - - -
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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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917A SER* 1.3 72.6 - - - +
919A GLY* 1.3 65.8 + - - +
921A PHE* 3.2 10.3 + - + +
922A LEU* 3.0 39.7 + - + +
935A LEU* 5.8 0.9 - - + -
939A VAL* 5.5 1.1 - - + -
944A LEU* 4.6 26.2 - - + -
947A PHE* 3.9 13.9 - - + +
953A LEU* 3.7 48.9 - - + +
956A SER* 4.1 1.6 - - - -
957A LEU* 4.3 19.7 - - + -
960A LEU* 3.7 23.8 - - + -
984A GLU* 4.5 0.4 + - - +
987A LEU* 4.1 11.0 - - + -
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Residues in contact with GLY 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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918A LEU* 1.3 78.3 - - - +
920A ASP* 1.3 61.8 + - - +
922A LEU* 2.9 15.4 + - - -
923A LYS* 3.0 15.6 + - - +
960A LEU* 4.7 8.3 - - - +
963A TRP* 3.6 26.9 - - - -
984A GLU* 3.0 22.9 + - - -
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Residues in contact with ASP 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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914A PRO 4.3 0.3 - - - +
915A PHE* 3.8 5.3 - - - -
916A LYS* 2.8 35.9 + - + +
917A SER* 3.2 26.7 + - - +
919A GLY* 1.3 73.7 - - - +
921A PHE* 1.3 59.3 + - - +
923A LYS* 3.7 23.2 - - - +
924A ARG* 3.1 48.9 + - - +
963A TRP* 5.0 0.2 - - - -
984A GLU* 4.1 1.6 + - - +
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Residues in contact with PHE 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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873A VAL* 3.8 22.2 - - + -
905A ILE* 4.1 8.3 - - + -
915A PHE* 3.4 39.2 - + + -
917A SER 3.0 14.3 + - - +
918A LEU* 3.3 14.4 - - + +
919A GLY 3.1 0.2 - - - -
920A ASP* 1.3 76.6 - - - +
922A LEU* 1.3 63.9 + - + +
924A ARG* 3.4 1.7 + - - +
925A LEU* 3.0 59.0 + - + +
930A VAL* 4.7 3.1 - - + -
935A LEU* 3.7 30.1 - - + -
938A LEU* 4.0 22.7 - - + -
944A LEU* 4.3 17.7 - - + -
947A PHE* 4.8 2.9 - - + -
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Residues in contact with LEU 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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918A LEU* 3.0 35.9 + - + +
919A GLY* 2.9 6.5 + - - +
921A PHE* 1.3 79.6 - - + +
923A LYS* 1.3 57.7 + - - +
925A LEU 2.9 22.6 - - - +
926A PRO* 4.1 0.5 - - - +
927A GLU 5.1 0.2 + - - -
935A LEU* 3.6 44.2 - - + -
957A LEU* 4.5 11.2 - - + +
960A LEU* 3.6 36.6 - - + +
961A LEU* 4.1 12.9 - - + +
964A ALA* 3.9 15.7 - - + +
968A ARG* 3.0 12.8 + - - -
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Residues in contact with LYS 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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919A GLY 3.0 12.1 + - - +
920A ASP* 3.7 31.0 - - - +
922A LEU* 1.3 75.6 - - - +
924A ARG* 1.3 69.2 + - + +
963A TRP* 4.0 22.2 - - + -
964A ALA* 4.1 8.5 - - + +
967A THR* 5.4 9.6 - - + -
968A ARG* 2.8 33.7 + - + +
981A GLU* 2.9 34.6 + - - +
983A GLU* 5.0 10.5 + - - +
984A GLU* 5.9 1.4 - - - +
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Residues in contact with ARG 924 (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 GLU* 3.2 60.8 + - + +
912A GLY* 3.3 16.7 - - - -
913A GLY* 3.0 27.0 + - - -
914A PRO 3.4 4.6 + - - -
915A PHE* 3.2 46.6 - - + +
920A ASP* 3.1 38.5 + - - +
921A PHE 3.9 2.7 - - - +
923A LYS* 1.3 84.1 - - + +
925A LEU* 1.3 61.3 + - - +
926A PRO* 3.4 9.2 - - - +
968A ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 925 (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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904A ALA* 4.1 10.8 - - + +
905A ILE* 3.8 25.1 - - + +
908A GLU* 3.9 25.8 - - + +
915A PHE* 4.0 14.4 - - + -
921A PHE* 3.0 52.4 + - + +
922A LEU* 2.9 21.2 - - - +
924A ARG* 1.3 80.0 - - - +
926A PRO* 1.3 70.8 - - + +
929A VAL* 4.7 5.4 - - + -
930A VAL* 4.0 23.0 - - + +
935A LEU* 6.0 0.3 - - - +
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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