Contacts of the helix formed by residues 90 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.0 2.7 - - + -
35A ASN* 4.8 9.4 + - - +
37A SER* 3.8 19.0 + - - -
86A MSE 3.7 27.9 - - + +
87A ASN* 2.5 46.7 + - - +
89A SER* 1.3 84.2 + - - +
91A LEU* 1.3 56.1 + - - +
92A ASN 3.4 1.6 - - - -
93A SER* 2.9 13.4 + - - -
94A LEU* 2.7 33.8 + - - +
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Residues in contact with LEU 91 (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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17A PHE* 3.5 47.3 - - + -
88A LYS* 3.1 26.6 + - + +
89A SER 3.3 0.4 - - - -
90A ASN* 1.3 77.9 - - - +
92A ASN* 1.3 69.6 + - - +
94A LEU* 3.1 2.4 + - - +
95A ASP* 3.0 27.4 + - - +
123A ARG* 4.4 28.7 + - - +
109B GLU* 5.8 1.8 - - - +
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Residues in contact with ASN 92 (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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89A SER 4.8 3.9 + - - +
90A ASN 3.4 0.4 - - - -
91A LEU* 1.3 83.3 - - - +
93A SER* 1.3 64.5 + - - +
95A ASP* 3.3 10.1 + - - +
96A GLU* 2.9 27.6 + - - +
111B LYS* 4.5 18.9 + - - -
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Residues in contact with SER 93 (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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34A ARG* 3.8 11.7 + - - +
35A ASN* 4.5 0.9 + - - -
89A SER 4.9 3.2 + - - -
90A ASN* 2.9 21.7 + - - -
92A ASN* 1.3 78.7 - - - +
94A LEU* 1.3 57.5 + - - +
96A GLU* 3.5 4.5 + - - +
97A GLN* 2.8 52.8 + - - +
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Residues in contact with LEU 94 (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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17A PHE* 3.7 31.2 - - + -
19A TYR* 3.8 32.1 - - + -
25A ASN* 4.7 3.8 - - - +
35A ASN* 4.3 4.9 + - - +
86A MSE 3.7 25.6 - - + -
90A ASN 2.7 19.6 + - - +
91A LEU 3.6 4.3 - - - +
93A SER* 1.3 69.6 - - - +
95A ASP* 1.3 60.8 + - - +
97A GLN* 3.0 22.7 + - + +
98A GLU* 2.8 42.0 + - + +
123A ARG* 4.9 1.8 - - - +
125A TYR* 3.3 20.0 - - + +
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Residues in contact with ASP 95 (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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91A LEU* 3.0 16.1 + - - +
92A ASN* 3.6 12.9 - - - +
94A LEU* 1.3 75.7 - - - +
96A GLU* 1.3 62.1 + - - +
98A GLU 2.9 11.6 + - - -
99A GLY 3.2 8.1 + - - -
100A VAL* 3.3 27.0 + - + +
101A LYS* 6.4 0.2 - - - -
107A VAL* 3.9 9.0 - - - +
123A ARG* 2.8 33.8 + - - -
125A TYR* 2.6 30.8 + - - -
109B GLU* 3.7 7.4 - - - +
111B LYS* 4.7 9.4 - - - -
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Residues in contact with GLU 96 (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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34A ARG* 4.9 12.5 + - - -
92A ASN 2.9 18.1 + - - +
93A SER* 4.0 4.3 - - - +
95A ASP* 1.3 76.0 - - - +
97A GLN* 1.3 63.4 + - - +
99A GLY* 3.3 12.3 + - - +
100A VAL 4.9 2.5 - - - +
101A LYS* 4.8 30.5 - - + +
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Residues in contact with GLN 97 (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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25A ASN* 5.5 1.2 + - - -
34A ARG* 3.4 52.3 + - + +
35A ASN* 2.9 42.1 + - - -
93A SER* 2.8 43.0 + - - +
94A LEU* 3.0 16.9 + - + +
96A GLU* 1.3 80.5 - - - +
98A GLU* 1.3 59.5 + - + +
99A GLY 3.3 2.4 + - - -
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Residues in contact with GLU 98 (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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19A TYR* 3.7 5.9 + - - -
25A ASN* 3.7 21.5 + - - -
94A LEU* 2.8 23.0 + - + +
95A ASP 2.9 2.2 + - - +
97A GLN* 1.3 80.8 - - - +
99A GLY* 1.3 63.8 + - - +
100A VAL 3.3 1.7 + - - -
105A TYR* 3.0 43.7 - - + +
125A TYR* 3.4 55.3 - - + +
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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