Contacts of the helix formed by residues 1064 - 1070 (chain A) in PDB entry 3U9Y
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 ASN1064 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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975A THR* 2.9 24.5 + - - +
977A ARG* 2.9 33.5 + - - +
1030A PHE* 4.2 1.1 - - - -
1062A ALA* 3.5 8.4 - - - +
1063A GLU* 1.3 75.9 - - - +
1065A SER* 1.3 64.6 + - - +
1066A SER* 4.1 4.7 - - - +
1067A LYS* 3.1 28.2 + - + +
1068A SER* 3.4 8.7 + - - -
1134A LEU 4.7 1.0 + - - -
1136A LEU* 2.9 52.6 + - - +
1137A ALA 4.6 1.0 + - - -
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Residues in contact with SER1065 (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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972A MET* 2.8 38.0 + - - -
975A THR* 3.2 23.2 + - - -
976A VAL 3.9 0.2 + - - -
992A TYR* 2.5 25.0 + - - -
1030A PHE* 3.8 23.3 - - - -
1063A GLU 3.5 2.0 + - - -
1064A ASN* 1.3 72.1 - - - +
1066A SER* 1.3 50.6 + - - +
1068A SER* 3.1 6.2 + - - -
1069A ASN* 2.8 32.7 + - - +
1096A LEU* 3.7 4.4 - - - +
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Residues in contact with SER1066 (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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975A THR 4.0 1.8 + - - -
976A VAL* 3.8 2.1 - - - -
977A ARG* 3.0 31.5 + - - +
979A HIS* 2.6 32.6 + - - -
989A PHE* 3.8 20.5 - - - -
992A TYR* 3.5 8.5 - - - -
1064A ASN* 4.1 0.5 - - - +
1065A SER* 1.3 81.3 + - - +
1067A LYS* 1.3 59.3 + - - +
1069A ASN* 3.5 9.6 + - - +
1070A GLN* 3.3 24.3 + - - +
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Residues in contact with LYS1067 (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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977A ARG* 3.7 10.5 - - - +
979A HIS* 3.5 11.8 - - + -
1062A ALA* 3.7 17.7 - - + -
1064A ASN* 3.1 20.1 + - + +
1066A SER* 1.3 77.9 + - - +
1068A SER* 1.3 65.9 + - - +
1070A GLN* 2.8 44.0 + - - +
1071A TYR* 3.5 29.0 + - + +
1138A GLU* 3.3 29.2 + - + +
1163A SO4 2.8 30.6 + - - -
1165A 09L 3.8 4.0 - - + -
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Residues in contact with SER1068 (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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1030A PHE* 3.1 33.0 + - - +
1032A GLY* 3.7 8.0 - - - -
1062A ALA* 3.5 7.3 - - - +
1064A ASN 3.4 1.8 + - - -
1065A SER 3.1 8.8 + - - -
1067A LYS* 1.3 76.2 - - - +
1069A ASN* 1.3 66.0 + - - +
1071A TYR* 2.9 17.2 + - - +
1072A VAL 3.6 5.5 + - - -
1096A LEU* 3.6 20.6 - - - -
1165A 09L 2.8 27.8 + - - -
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Residues in contact with ASN1069 (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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985A ALA 5.1 0.2 - - - +
986A GLY* 2.8 35.2 + - - -
989A PHE* 3.4 23.7 - - + -
992A TYR* 4.5 4.0 - - - +
1065A SER 2.8 17.2 + - - +
1066A SER* 3.5 15.8 + - - +
1067A LYS 3.2 0.4 - - - -
1068A SER* 1.3 72.2 - - - +
1070A GLN* 1.3 61.6 + - - +
1071A TYR 3.2 1.0 + - - -
1072A VAL* 3.4 15.3 + - - +
1073A TYR* 5.0 0.9 + - - -
1094A ARG* 3.1 24.0 + - - +
1096A LEU* 4.1 1.7 - - + +
1155A TYR* 2.7 33.5 + - - +
1157A ILE* 4.1 2.9 - - - +
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Residues in contact with GLN1070 (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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979A HIS* 3.5 31.8 + - + +
981A ASP* 3.2 27.1 + - - -
985A ALA* 4.0 12.9 - - + +
986A GLY* 4.1 16.3 - - - +
1066A SER 3.3 14.4 - - - +
1067A LYS* 2.8 43.8 + - - +
1068A SER 3.0 0.4 + - - -
1069A ASN* 1.3 77.9 - - - +
1071A TYR* 1.3 64.7 + - + +
1072A VAL 3.5 0.4 - - - -
1074A GLY 3.4 0.2 - - - +
1076A GLY* 3.9 2.1 + - - -
1077A GLY* 3.0 31.8 + - - -
1163A SO4 3.8 5.3 + - - -
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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