Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 2QMQ
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 PHE 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PRO 3.5 14.7 + - - +
82A LEU 3.1 16.5 + - - +
84A ARG* 1.3 76.2 - - - +
86A GLY* 1.3 70.4 + - - +
87A ASP* 3.9 31.6 - - + -
88A MET* 3.0 4.9 + - + +
89A GLN* 2.9 20.1 + - - +
300A PRO* 3.8 24.7 - - + -
301A GLY* 3.5 29.4 - - - -
304A THR* 3.5 17.5 - - - -
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Residues in contact with GLY 86 (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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84A ARG 3.3 6.1 + - - -
85A PHE* 1.3 77.3 - - - +
87A ASP* 1.3 63.8 + - - +
89A GLN* 3.3 19.8 + - - +
90A GLU* 3.3 17.4 + - - +
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Residues in contact with ASP 87 (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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85A PHE* 3.3 25.7 - - + -
86A GLY* 1.3 76.1 - - - +
88A MET* 1.3 60.5 + - - +
90A GLU* 3.5 13.4 - - - +
91A ILE* 3.4 25.6 + - - +
304A THR* 3.5 10.5 - - + -
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Residues in contact with MET 88 (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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82A LEU* 3.1 52.7 - - + +
83A PHE* 3.9 11.4 - - + +
85A PHE* 3.0 5.8 + - + +
87A ASP* 1.3 74.9 - - - +
89A GLN* 1.3 67.2 + - - +
90A GLU 3.1 0.2 - - - -
91A ILE* 2.8 5.9 + - - -
92A ILE* 2.8 53.8 + - + +
304A THR* 3.4 28.4 + - - +
307A PHE* 3.5 46.0 - - + -
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Residues in contact with GLN 89 (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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83A PHE 3.6 15.7 - - - +
84A ARG* 2.7 55.2 + - - +
85A PHE 2.9 13.0 + - - +
86A GLY* 3.3 15.4 + - - +
88A MET* 1.3 76.1 - - - +
90A GLU* 1.3 56.7 + - + +
92A ILE* 4.2 4.7 - - - -
93A GLN* 2.9 36.7 + - - +
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Residues in contact with GLU 90 (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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86A GLY 3.4 15.6 - - - +
87A ASP* 3.5 16.8 - - - +
88A MET 3.1 0.2 - - - -
89A GLN* 1.3 77.4 - - - +
91A ILE* 1.3 67.1 + - + +
93A GLN* 3.0 35.9 + - - +
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Residues in contact with ILE 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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87A ASP 3.4 15.0 + - - +
88A MET* 2.8 16.0 + - - +
90A GLU* 1.3 82.7 - - + +
92A ILE* 1.3 66.3 + - + +
94A ASN* 5.1 0.9 + - - +
95A PHE* 3.9 15.2 - - - -
304A THR* 3.8 14.1 - - + -
307A PHE 4.4 0.2 - - - -
308A LYS* 4.0 47.3 - - + +
311A LEU* 3.9 24.2 - - + -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A BEZ 4.5 0.7 - - - +
65A ILE* 3.8 25.8 - - + -
83A PHE* 3.0 55.9 - - + +
88A MET* 2.8 44.2 + - + +
89A GLN* 4.2 4.3 - - - +
91A ILE* 1.3 87.5 - - + +
93A GLN* 1.3 66.9 + - - +
94A ASN 3.2 3.1 - - - -
95A PHE* 3.0 20.9 + - - +
97A ARG* 3.4 26.1 + - - +
307A PHE* 5.3 0.4 - - + -
311A LEU* 4.4 4.3 - - + -
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Residues in contact with GLN 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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56A GLY* 5.1 4.2 - - - -
59A LYS* 4.7 2.6 + - - -
89A GLN 2.9 15.9 + - - +
90A GLU* 3.0 39.7 + - - +
91A ILE 3.5 0.6 - - - -
92A ILE* 1.3 78.6 - - - +
94A ASN* 1.3 82.1 + - - +
95A PHE 4.0 0.7 - - - +
97A ARG* 3.6 16.5 + - - +
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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