Contacts of the helix formed by residues 921 - 929 (chain A) in PDB entry 1Y6A
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 ASN 921 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A AAZ 3.0 29.0 + - - +
919A PHE 4.4 0.5 - - - +
920A GLY* 1.3 73.6 - - - -
922A LEU* 1.3 58.7 + - - +
923A SER* 3.2 14.7 + - - -
924A THR* 2.9 38.9 + - - -
925A TYR* 3.1 27.9 + - - +
927A ARG* 5.0 0.2 + - - -
1030A ARG* 3.4 33.3 - - - +
1032A ILE 3.3 6.7 - - - +
1033A LEU* 3.7 5.4 - - + -
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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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920A GLY 3.8 0.8 + - - -
921A ASN* 1.3 70.8 - - - +
923A SER* 1.3 59.8 + - - +
925A TYR* 4.3 10.3 - - + -
926A LEU* 2.8 52.2 + - + +
1006A TYR* 4.0 33.0 - - + -
1010A VAL* 5.3 1.1 - - + -
1029A ALA* 3.4 16.5 + - + +
1032A ILE* 2.8 39.4 + - + +
1033A LEU* 4.6 1.1 - - - +
1034A LEU* 4.9 7.9 - - + -
1040A VAL* 4.3 12.1 - - + -
1092A LEU* 5.1 1.1 - - + -
1096A ILE* 4.0 30.5 - - + -
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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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921A ASN* 3.2 10.4 + - - -
922A LEU* 1.3 79.0 - - - +
924A THR* 1.3 61.7 + - - +
926A LEU* 3.5 0.8 + - - -
927A ARG* 3.1 41.7 + - - -
1029A ALA* 3.6 13.9 + - - +
1030A ARG* 4.0 19.5 - - - -
1095A GLU* 4.2 9.1 + - - -
1100A GLY* 3.7 23.1 + - - -
1101A ALA 5.1 0.5 + - - -
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Residues in contact with THR 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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921A ASN* 2.9 31.6 + - - -
923A SER* 1.3 75.7 - - - +
925A TYR* 1.3 63.8 + - - +
927A ARG* 3.5 30.0 + - - +
928A SER* 3.2 20.7 + - - -
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Residues in contact with TYR 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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919A PHE* 4.3 33.6 + + + +
921A ASN 3.1 18.2 + - - +
922A LEU* 3.7 8.5 - - + +
924A THR* 1.3 75.9 - - - +
926A LEU* 1.3 77.6 + - + +
928A SER* 2.5 30.2 + - - -
929A LYS* 3.3 43.3 + - + +
998A LEU* 4.0 15.4 - - + +
1006A TYR* 4.2 12.9 + - - -
1034A LEU* 3.4 33.8 - - + +
1038A ASN* 5.2 1.9 + - - -
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Residues in contact with LEU 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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922A LEU* 2.8 41.5 + - + +
923A SER* 4.1 1.6 - - - +
925A TYR* 1.3 78.8 - - + +
927A ARG* 1.3 64.4 + - - +
929A LYS* 3.0 15.7 + - - +
930A ARG 3.5 6.9 + - - -
998A LEU* 3.5 27.8 - - + -
1003A LEU* 3.9 13.5 - - + -
1006A TYR* 4.1 14.1 - - + -
1029A ALA* 5.8 2.0 - - + -
1095A GLU 4.4 3.6 - - - +
1096A ILE* 3.7 40.4 - - + +
1099A LEU* 3.6 28.1 - - + +
1100A GLY* 3.9 2.9 - - - +
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Residues in contact with ARG 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 SER* 3.1 29.4 + - - +
924A THR* 3.5 44.4 + - - +
925A TYR 3.2 0.2 - - - -
926A LEU* 1.3 77.2 - - - +
928A SER* 1.3 59.3 + - - +
930A ARG* 3.0 37.6 + - - +
1099A LEU 3.5 11.2 + - - +
1100A GLY 3.1 28.5 + - - +
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Residues in contact with SER 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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924A THR* 3.2 9.4 + - - -
925A TYR* 2.5 30.4 + - - -
927A ARG* 1.3 76.7 - - - +
929A LYS* 1.3 67.4 + - - +
930A ARG 3.5 0.6 + - - -
931A ASN 5.0 1.6 + - - -
932A GLU* 4.0 13.7 - - - +
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Residues in contact with LYS 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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925A TYR* 3.5 44.2 + - + +
926A LEU 3.0 7.6 + - - +
928A SER* 1.3 85.2 - - - +
930A ARG* 1.3 59.0 + - - +
931A ASN 3.1 3.1 - - - -
932A GLU* 2.4 67.3 + - - +
933A PHE* 3.3 6.2 + - - +
996A ASP* 2.7 33.0 + - - +
998A LEU* 3.5 37.5 - - + -
1099A LEU* 4.8 1.6 - - - -
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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