Contacts of the helix formed by residues 920 - 927 (chain A) in PDB entry 3HIL
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 TYR 920 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912A LEU* 4.2 0.7 - - - -
917A MET* 2.9 38.8 + - + +
919A ARG* 1.3 100.9 - - + +
921A ILE* 1.3 62.5 + - - +
922A LEU 3.3 2.2 - - - -
923A HIS* 3.1 35.8 + + - +
924A PHE* 3.2 22.5 + - + -
947A GLY 4.7 1.8 - - - -
948A ILE* 3.7 51.1 - - + +
949A THR 5.2 0.2 + - - -
950A LEU* 4.0 13.7 + - - +
953A HIS* 2.6 40.8 + - + +
957A ILE* 4.4 2.7 - - + -
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Residues in contact with ILE 921 (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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908A VAL* 3.9 15.5 - - + -
909A SER* 3.9 23.3 - - - -
912A LEU* 3.6 24.1 - - + +
918A LYS* 3.1 33.6 + - + +
919A ARG 3.4 1.9 - - - -
920A TYR* 1.3 75.9 - - - +
922A LEU* 1.3 68.0 + - + +
924A PHE* 3.3 5.4 + - - +
925A HIS* 3.1 55.8 + - + +
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Residues in contact with LEU 922 (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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919A ARG 5.1 1.0 + - - +
920A TYR 3.3 0.8 - - - -
921A ILE* 1.3 83.2 - - + +
923A HIS* 1.3 63.0 + - + +
925A HIS* 4.4 13.9 - - + +
926A SER* 2.8 44.2 + - - +
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Residues in contact with HIS 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 ARG 4.0 9.1 + - - -
920A TYR* 3.1 42.4 + + - +
922A LEU* 1.3 81.6 + - + +
924A PHE* 1.3 61.9 + - - +
926A SER* 3.8 6.3 + - - -
927A ALA* 3.3 24.6 + - - +
946A MET* 3.7 28.7 - - + +
947A GLY* 3.9 18.6 + - - -
948A ILE* 3.9 16.2 - - + -
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Residues in contact with PHE 924 (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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908A VAL* 4.2 11.0 - - + -
911A TRP* 3.6 33.0 - + - -
912A LEU* 3.8 23.1 - - + -
920A TYR* 3.2 18.6 + - + -
921A ILE* 3.3 7.4 + - + +
923A HIS* 1.3 78.0 - - - +
925A HIS* 1.3 60.2 + - + +
927A ALA 3.4 1.9 + - - -
928A GLY 3.3 4.0 + - - -
929A LEU* 2.9 56.2 + - + +
935A VAL* 4.1 8.5 - - + -
938A LEU* 3.7 27.4 - - + -
943A LEU* 4.4 2.5 - - + -
946A MET* 4.6 6.1 - - - -
948A ILE* 3.5 27.1 - - + -
957A ILE* 4.3 10.5 - - + -
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Residues in contact with HIS 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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908A VAL* 5.0 5.3 - - - +
909A SER* 5.6 3.5 + - - -
921A ILE* 3.1 54.8 + - + +
922A LEU* 4.0 13.1 + - + +
924A PHE* 1.3 76.8 - - + +
926A SER* 1.3 58.4 + - - +
928A GLY* 2.9 20.4 + - - -
929A LEU 4.3 4.3 - - - +
930A ASP* 3.9 31.8 + - + +
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Residues in contact with SER 926 (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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922A LEU* 2.8 32.9 + - - +
923A HIS* 3.8 6.6 + - - -
925A HIS* 1.3 76.8 - - - +
927A ALA* 1.3 57.6 + - - +
928A GLY 3.3 1.7 + - - -
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Residues in contact with ALA 927 (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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923A HIS 3.3 18.6 + - - +
924A PHE 3.9 3.1 - - - +
925A HIS 3.1 1.2 - - - -
926A SER* 1.3 75.8 - - - +
928A GLY* 1.3 61.8 + - - +
929A LEU* 3.4 15.8 - - + +
946A MET* 3.9 26.0 - - + -
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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