Contacts of the helix formed by residues 90 - 98 (chain B) in PDB entry 2Q53
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 4.0 3.6 - - + -
35B ASN* 5.4 1.3 - - - +
37B SER* 3.8 14.1 + - - -
86B MSE 3.5 32.4 - - + +
87B ASN* 3.0 39.0 + - - +
88B LYS 2.9 0.8 - - - -
89B SER* 1.3 95.6 + - - +
91B LEU* 1.3 64.9 + - - +
92B ASN 3.2 3.1 - - - -
93B SER* 3.0 11.8 + - - +
94B LEU* 2.9 22.7 + - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 5.8 0.9 - - - +
17B PHE* 3.8 27.9 - - + -
88B LYS* 3.3 32.2 + - + +
90B ASN* 1.3 77.0 - - - +
92B ASN* 1.3 59.2 + - - +
94B LEU* 4.6 2.5 - - - -
95B ASP* 2.8 39.5 + - - +
123B ARG* 3.5 47.6 - - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.3 16.3 + - - +
89B SER* 4.6 9.4 + - - +
90B ASN 3.0 1.6 + - - -
91B LEU* 1.3 78.6 - - - +
93B SER* 1.3 53.5 + - - +
95B ASP* 3.4 4.3 - - - +
96B GLU* 2.7 37.3 + - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 3.1 22.7 + - - +
35B ASN* 4.5 2.2 + - - -
89B SER 5.2 0.8 + - - -
90B ASN* 3.0 11.9 + - - +
92B ASN* 1.3 74.2 - - - +
94B LEU* 1.3 57.4 + - - +
96B GLU* 3.1 6.8 + - - +
97B GLN* 2.6 62.6 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.5 33.0 - - + -
19B TYR* 3.8 29.8 - - + -
25B ASN* 5.0 4.7 - - - +
35B ASN* 3.8 29.3 + - - +
86B MSE 3.8 15.3 - - + -
90B ASN 2.9 20.4 + - - +
91B LEU* 4.0 3.1 - - - +
93B SER* 1.3 71.9 - - - +
95B ASP* 1.3 64.7 + - - +
97B GLN* 3.5 11.0 - - - +
98B GLU* 3.1 31.6 + - - +
123B ARG* 5.2 0.2 - - - -
125B TYR* 3.4 22.0 - - + +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 4.1 3.3 - - - +
111A LYS* 4.4 16.5 + - - +
91B LEU* 2.8 30.9 + - - +
92B ASN* 3.4 5.4 - - - +
94B LEU* 1.3 72.8 - - - +
96B GLU* 1.3 64.9 + - - +
98B GLU 2.9 12.3 + - - -
99B GLY 3.4 2.3 + - - -
100B VAL* 3.4 31.0 + - + +
107B VAL* 3.9 10.5 - - - +
123B ARG* 2.6 36.5 + - - -
125B TYR* 3.1 15.2 + - - -
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 4.5 14.6 + - - +
92B ASN 2.7 21.0 + - - +
93B SER* 3.6 7.0 - - - +
95B ASP* 1.3 73.4 - - - +
97B GLN* 1.3 67.0 + - - +
99B GLY* 3.1 14.1 + - - +
100B VAL 5.0 2.0 - - - +
101B LYS* 5.4 19.4 - - + +
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 5.4 2.4 + - - -
34B ARG* 3.3 46.0 + - + +
35B ASN* 2.9 40.1 + - - -
93B SER* 2.6 50.6 + - - +
94B LEU* 3.5 11.1 - - + +
96B GLU* 1.3 78.0 - - - +
98B GLU* 1.3 65.4 + - - +
99B GLY 3.0 5.2 + - - -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 4.5 5.6 + - - -
25B ASN* 4.4 15.4 + - - -
94B LEU* 3.1 17.6 + - + +
95B ASP 2.9 9.8 + - - +
97B GLN* 1.3 81.1 - - - +
99B GLY* 1.3 63.4 + - - +
100B VAL* 3.2 1.3 - - + -
104B MSE 4.4 0.8 - - - +
105B TYR* 3.1 49.2 + - + +
125B TYR* 3.5 53.8 - - + +
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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