Contacts of the helix formed by residues 80 - 93 (chain A) in PDB entry 3QTA
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 GLU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A MSE 4.0 17.9 - - - +
56A GLY* 4.1 17.5 - - - -
57A GLY 4.6 4.7 + - - -
58A GLY 5.3 2.7 + - - +
59A THR 4.3 7.6 - - - +
60A ILE* 4.8 7.9 - - + +
61A TYR 5.6 0.2 - - - -
79A PHE* 1.3 81.1 - - - +
81A THR* 1.3 65.1 + - - +
82A GLU* 3.4 5.4 - - + +
83A THR* 3.2 8.0 + - - +
84A ALA* 3.0 24.1 + - - +
177A SER 5.0 0.6 + - - -
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Residues in contact with THR 81 (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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59A THR* 4.0 28.4 + - + +
80A GLU* 1.3 72.2 - - - +
82A GLU* 1.3 68.2 + - - +
84A ALA* 3.1 8.3 + - + +
85A ALA* 2.9 25.3 + - - +
100A PHE* 4.8 8.6 - - + -
140A GLN* 6.2 2.2 - - - +
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Residues in contact with GLU 82 (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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80A GLU* 3.4 4.2 - - + +
81A THR* 1.3 79.9 + - - +
83A THR* 1.3 63.4 + - - +
85A ALA* 3.3 6.8 + - - +
86A GLU* 3.1 33.1 + - + +
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Residues in contact with THR 83 (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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79A PHE* 3.6 20.9 - - + -
80A GLU* 3.2 10.5 + - - +
82A GLU* 1.3 76.0 - - - +
84A ALA* 1.3 65.7 + - - +
86A GLU* 3.1 8.2 + - - +
87A ILE* 2.9 35.9 + - + +
175A ALA 4.5 1.7 + - - -
176A PHE* 3.8 12.9 - - + +
177A SER* 2.9 49.3 + - - +
178A LEU* 4.4 0.9 - - + -
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Residues in contact with ALA 84 (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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61A TYR* 5.1 3.6 - - + -
79A PHE* 3.6 27.1 - - + -
80A GLU 3.0 12.2 + - - +
81A THR* 3.1 13.4 + - + +
83A THR* 1.3 76.1 - - - +
85A ALA* 1.3 57.5 + - - +
88A ALA* 3.0 27.9 + - - +
100A PHE* 3.9 13.7 - - + -
108A LEU* 3.2 22.2 - - + +
140A GLN* 5.8 3.4 - - - +
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Residues in contact with ALA 85 (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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81A THR 2.9 11.9 + - - +
82A GLU* 3.5 10.5 - - - +
84A ALA* 1.3 74.1 - - - +
86A GLU* 1.3 66.2 + - + +
88A ALA* 3.9 0.3 - - - +
89A GLU* 3.0 33.0 + - - +
96A VAL* 3.8 22.9 - - + -
100A PHE* 3.7 13.8 - - + -
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Residues in contact with GLU 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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82A GLU* 3.1 25.9 + - + +
83A THR 3.1 7.9 + - - +
85A ALA* 1.3 76.5 - - + +
87A ILE* 1.3 62.4 + - - +
89A GLU* 4.0 8.4 - - - +
90A LEU* 3.0 26.7 + - - +
173A ASP 5.2 1.2 - - - +
174A VAL* 3.7 32.0 - - + +
175A ALA 3.9 23.2 + - - +
176A PHE* 3.9 10.9 - - + -
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Residues in contact with ILE 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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79A PHE* 3.7 35.0 - - + -
83A THR* 2.9 27.4 + - + +
84A ALA 3.7 3.6 - - - +
86A GLU* 1.3 76.5 - - - +
88A ALA* 1.3 59.4 + - - +
90A LEU* 3.3 0.5 + - - +
91A MSE 2.9 36.8 + - + +
107A ALA 4.1 6.5 - - - +
108A LEU* 3.9 11.9 - - + -
111A MSE 3.5 39.5 - - + -
176A PHE* 3.7 33.2 - - + -
178A LEU* 4.8 4.5 - - + -
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Residues in contact with ALA 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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84A ALA 3.0 18.1 + - - +
85A ALA 3.9 0.2 - - - +
87A ILE* 1.3 78.8 - - - +
89A GLU* 1.3 61.1 + - - +
92A THR* 2.8 32.5 + - - +
96A VAL* 3.7 22.0 - - + -
100A PHE* 3.9 5.8 - - + -
104A HIS* 3.8 27.4 - - + +
107A ALA* 4.5 9.4 - - - -
108A LEU* 4.3 2.2 - - + -
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Residues in contact with GLU 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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85A ALA* 3.0 23.7 + - - +
86A GLU* 4.1 9.0 - - - +
88A ALA* 1.3 74.9 - - - +
90A LEU* 1.3 63.5 + - - +
93A GLY* 3.0 27.2 + - - -
94A SER 3.3 20.4 + - - +
95A SER* 3.4 12.9 + - - -
96A VAL* 2.9 38.7 + - + +
97A GLU 4.3 0.5 + - - -
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Residues in contact with LEU 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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34A VAL* 3.8 32.5 - - + -
86A GLU 3.0 18.2 + - - +
87A ILE 3.7 1.3 - - - +
89A GLU* 1.3 78.5 - - - +
91A MSE 1.3 72.2 + - + +
92A THR 3.5 0.3 + - - -
93A GLY* 4.1 4.3 + - - -
169A ILE* 4.8 14.8 - - + -
172A SER* 5.8 0.2 - - - +
174A VAL* 4.7 20.6 - - + -
176A PHE* 3.4 29.6 - - + -
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Residues in contact with MSE 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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32A ALA* 3.4 31.6 - - + +
34A VAL* 4.0 20.9 - - - -
87A ILE* 2.9 23.1 + - + +
90A LEU* 1.3 83.5 - - + +
92A THR* 1.3 62.5 + - - +
93A GLY 3.9 0.2 - - - -
107A ALA* 3.9 20.1 - - + +
110A GLU* 6.3 1.8 - - + -
111A MSE 3.5 35.0 - - + -
114A ILE* 4.9 6.7 - - + -
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Residues in contact with THR 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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88A ALA 2.8 22.7 + - - +
91A MSE 1.3 84.4 - - - +
93A GLY* 1.3 64.3 + - - +
94A SER* 2.7 32.9 + - - -
103A LEU* 3.8 49.4 - - + +
104A HIS* 3.4 8.2 - - + -
107A ALA* 3.8 9.6 - - + -
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Residues in contact with GLY 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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89A GLU 3.0 11.3 + - - -
90A LEU 4.1 4.7 + - - -
91A MSE 3.9 0.4 - - - -
92A THR* 1.3 77.2 - - - +
94A SER* 1.3 58.5 + - - +
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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