Contacts of the helix formed by residues 920 - 929 (chain A) in PDB entry 4AY6
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 HIS 920 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A PRO* 3.8 8.7 - - + +
694A PHE* 3.3 23.0 - + + -
917A CYS* 4.5 0.6 - - - -
918A ASN* 3.1 29.7 + - + -
919A GLY* 1.3 75.8 - - - -
921A THR* 1.3 65.6 + - - +
922A THR 3.2 0.4 - - - +
923A GLY 3.4 5.2 + - - -
924A MET 3.6 1.4 + - - -
942A ALA* 3.0 44.7 + - + -
945A VAL* 3.9 21.8 - - + +
949A GLN* 3.1 21.8 + - - -
1200A 12V 2.9 60.8 + - + +
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Residues in contact with THR 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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559A PRO* 3.8 10.1 - - + +
562A HIS* 5.3 0.4 - - + -
563A LEU* 4.0 24.3 - - + +
694A PHE* 3.9 7.5 - - - -
698A HIS* 5.3 0.4 - - - +
898A LYS* 3.5 28.7 - - - +
920A HIS* 1.3 78.0 - - - +
922A THR* 1.3 63.8 + - - +
924A MET* 3.1 7.1 + - - +
925A ASP* 3.0 22.4 + - - +
1200A 12V 2.9 51.7 + - - +
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Residues in contact with THR 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A PHE* 4.2 28.2 + - + +
838A ASN* 3.4 36.6 + - - +
901A HIS* 4.7 9.9 - - + +
911A CYS* 6.0 3.6 - - - -
919A GLY* 4.2 2.2 - - - -
920A HIS 3.2 0.6 - - - -
921A THR* 1.3 75.0 - - - +
923A GLY* 1.3 65.8 + - - +
925A ASP* 2.9 11.5 + - + +
926A VAL* 2.9 29.2 + - + +
1200A 12V 3.2 28.0 + - - -
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Residues in contact with GLY 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* 3.6 13.7 - - - -
920A HIS 3.4 5.9 + - - -
921A THR 3.3 1.4 - - - -
922A THR* 1.3 78.2 - - - +
924A MET* 1.3 62.2 + - - +
926A VAL* 3.4 4.9 + - - +
927A LEU* 3.1 28.6 + - - +
933A MET* 4.3 14.6 - - - -
949A GLN* 3.5 20.9 - - - -
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Residues in contact with MET 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LEU* 4.6 1.1 - - + -
694A PHE* 3.8 17.0 - - + -
695A ILE* 3.8 8.5 - - - +
696A GLY 3.7 22.0 - - - +
698A HIS* 3.2 25.6 - - + -
920A HIS 3.7 13.7 - - - +
921A THR* 3.1 6.9 + - - +
923A GLY* 1.3 75.0 - - - +
925A ASP* 1.3 58.1 + - - +
927A LEU* 3.4 1.7 + - - -
928A TRP* 2.9 27.0 + - - +
949A GLN* 3.3 29.8 - - - +
996A LEU* 3.9 28.5 - - + +
997A PHE* 3.2 33.6 - - + -
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Residues in contact with ASP 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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698A HIS* 2.7 35.1 + - - -
898A LYS* 3.7 12.8 + - - -
901A HIS* 3.2 19.9 + - + +
902A VAL* 3.8 25.4 - - + +
921A THR* 3.0 15.9 + - - +
922A THR* 2.9 12.0 + - + +
924A MET* 1.3 80.1 - - - +
926A VAL* 1.3 61.9 + - - +
928A TRP* 3.3 13.0 + - - +
929A ALA* 3.5 9.0 + - - +
1200A 12V 2.6 31.5 + - - -
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Residues in contact with VAL 926 (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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835A CYS* 4.2 9.0 - - - -
837A PHE* 5.0 12.6 - - + -
902A VAL 5.9 0.2 - - - -
905A GLY* 5.0 6.5 - - - +
911A CYS* 3.7 31.2 - - + -
922A THR* 2.9 17.6 + - + +
923A GLY* 3.4 14.1 - - - +
925A ASP* 1.3 74.3 - - - +
927A LEU* 1.3 73.5 + - + +
929A ALA* 3.3 9.3 + - - +
931A THR* 3.3 54.0 + - + +
933A MET* 4.3 7.9 - - + -
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Residues in contact with LEU 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 GLY 3.1 16.9 + - - +
924A MET* 3.8 3.6 - - - +
926A VAL* 1.3 77.4 - - - +
928A TRP* 1.3 58.5 + - - +
930A GLY* 2.9 19.6 + - - -
931A THR 3.5 19.3 - - - +
932A PRO* 4.6 2.5 - - + -
933A MET* 3.7 38.4 - - + +
949A GLN* 4.2 15.0 - - + +
950A LEU* 4.4 7.9 - - + -
953A LEU* 4.3 23.8 - - + -
987A VAL* 3.9 7.9 - - + +
991A ARG* 3.8 10.6 - - + +
996A LEU* 4.2 20.4 - - + -
997A PHE* 4.2 12.6 - - + -
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Residues in contact with TRP 928 (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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698A HIS* 3.6 31.4 - - + -
699A ALA* 3.6 19.7 - - + -
702A PHE* 3.2 35.3 + - + +
705A LEU* 3.6 26.0 - - + +
706A LYS* 4.0 18.4 - - + -
902A VAL* 4.1 6.1 - - + -
924A MET 2.9 17.4 + - - +
925A ASP 3.5 6.5 - - - +
926A VAL 3.2 0.2 - - - -
927A LEU* 1.3 76.2 - - - +
929A ALA* 1.3 57.6 + - - +
930A GLY 3.1 0.6 + - - -
991A ARG* 2.7 46.0 + - + +
992A ILE* 3.9 31.4 - - + -
997A PHE* 3.6 47.3 - + + -
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Residues in contact with ALA 929 (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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705A LEU* 5.6 4.7 - - + -
708A LYS* 4.6 2.6 + - - -
902A VAL* 3.8 16.6 - - + +
905A GLY* 3.8 9.4 - - - +
906A GLN* 3.7 43.0 - - + +
925A ASP 3.5 4.6 + - - +
926A VAL* 3.3 11.1 + - - +
927A LEU 3.1 0.6 - - - -
928A TRP* 1.3 80.1 - - - +
930A GLY* 1.3 60.3 + - - +
931A THR* 3.4 2.5 + - - +
984A ARG* 4.8 1.6 + - - -
988A TRP* 3.7 17.1 - - - -
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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