Contacts of the helix formed by residues 85 - 98 (chain B) in PDB entry 3QN3
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B ASP* 3.3 32.2 + - - +
83B ALA 3.5 2.0 - - - -
84B PHE* 1.3 75.0 - - - +
86B GLN* 1.3 61.3 + - - +
87B THR* 3.6 8.8 + - - -
88B GLN* 2.9 49.1 + - + +
89B LEU* 3.1 21.5 + - - +
131C ARG* 4.7 2.9 - - - +
405C GLU* 4.9 13.8 + - - +
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Residues in contact with GLN 86 (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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83B ALA 5.0 2.3 - - - +
84B PHE 3.4 7.6 + - - +
85B ASN* 1.3 74.7 - - - +
87B THR* 1.3 58.4 + - - +
89B LEU* 3.5 10.8 + - - +
90B ASP* 2.9 55.6 + - - +
114B SER* 3.2 29.0 + - - -
117B THR* 4.4 6.8 - - - +
118B ALA* 3.6 29.3 + - - +
132B TYR* 4.5 9.2 + - + +
133B LEU* 5.5 1.1 - - + -
339B ILE* 4.2 15.3 - - + +
340B THR* 3.8 4.7 - - - +
343B MET* 5.1 2.7 - - + -
131C ARG* 5.0 1.6 - - - +
136C ALA* 4.5 22.2 - - + -
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Residues in contact with THR 87 (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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85B ASN* 3.2 6.2 + - - -
86B GLN* 1.3 77.0 - - - +
88B GLN* 1.3 60.0 + - - +
90B ASP* 3.4 1.2 + - - +
91B ASP* 2.9 47.0 + - - +
340B THR* 3.6 24.2 + - + +
343B MET* 5.6 2.3 - - - +
136C ALA 5.1 6.2 + - - -
139C SER* 5.7 1.4 + - - -
405C GLU 6.0 2.2 - - - -
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.1 21.2 - - + +
82B ASP* 4.0 22.7 + - - +
85B ASN* 2.9 41.4 + - - +
87B THR* 1.3 75.0 - - - +
89B LEU* 1.3 61.4 + - - +
91B ASP* 4.1 5.0 - - - +
92B THR* 2.6 42.3 + - - +
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Residues in contact with LEU 89 (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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4B ILE* 4.3 7.9 - - + -
78B ILE* 3.6 43.3 - - + -
81B LEU* 4.5 9.0 - - + -
82B ASP 5.6 2.7 - - - +
85B ASN 3.1 14.6 + - - +
86B GLN* 3.8 22.4 - - - +
88B GLN* 1.3 75.6 + - - +
90B ASP* 1.3 69.1 + - - +
92B THR* 3.3 6.5 + - - -
93B LEU* 3.0 31.9 + - + +
113B VAL* 4.2 7.6 - - + +
114B SER* 4.3 2.2 - - - -
117B THR* 3.4 41.5 - - + +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 2.9 28.2 + - - +
87B THR 4.0 0.4 - - - +
89B LEU* 1.3 78.0 - - - +
91B ASP* 1.3 56.8 + - - +
93B LEU* 3.3 12.5 + - - +
94B ARG* 3.0 26.0 + - - +
102B TYR* 4.2 3.5 + - - -
114B SER* 2.5 29.2 + - - -
338B THR* 3.5 16.8 - - - +
340B THR* 2.4 52.2 + - + +
341B GLN* 4.9 1.9 + - + -
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Residues in contact with ASP 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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87B THR* 2.9 39.5 + - - +
88B GLN* 4.1 5.1 - - - +
90B ASP* 1.3 69.5 - - - +
92B THR* 1.3 61.5 + - - +
94B ARG* 2.6 36.2 + - - +
95B GLU* 3.0 34.1 + - + +
340B THR* 4.9 7.6 - - - +
341B GLN* 5.9 2.3 - - - +
344B ARG* 6.2 0.2 - - - -
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.7 32.5 - - + +
78B ILE* 4.4 6.5 - - + -
81B LEU* 4.0 25.1 - - + +
88B GLN* 2.6 29.1 + - - +
89B LEU 3.4 5.2 - - - -
91B ASP* 1.3 74.6 - - - +
93B LEU* 1.3 65.2 + - - +
95B GLU* 3.3 4.9 + - - +
96B LEU* 2.9 24.7 + - + +
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Residues in contact with LEU 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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74B ILE* 3.7 42.4 - - + -
78B ILE* 4.4 11.2 - - + -
89B LEU* 3.0 26.9 + - + +
90B ASP* 3.3 27.8 + - - +
92B THR* 1.3 77.3 - - - +
94B ARG* 1.3 60.9 + - - +
96B LEU* 3.4 6.2 + - + -
97B ASP* 3.0 24.9 + - - +
102B TYR* 4.1 2.5 - - - -
105B LEU* 3.7 5.6 - - + +
110B THR* 3.8 35.0 - - + +
113B VAL* 4.5 4.3 - - + -
114B SER* 4.4 5.4 - - - +
338B THR* 4.1 9.2 - - + -
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Residues in contact with ARG 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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90B ASP 3.0 11.7 + - - +
91B ASP* 2.6 40.5 + - - +
92B THR 3.3 0.2 - - - -
93B LEU* 1.3 75.6 - - - +
95B GLU* 1.3 87.6 + - - +
97B ASP* 3.4 3.8 + - - +
98B GLY* 3.0 24.4 + - - -
99B THR 4.5 11.9 - - - +
100B ASN* 6.4 0.7 - - - +
102B TYR* 3.3 26.4 + - + +
341B GLN* 4.0 22.8 + - - +
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Residues in contact with GLU 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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91B ASP* 3.0 22.9 + - + +
92B THR* 3.9 5.4 - - + +
94B ARG* 1.3 95.9 + - - +
96B LEU* 1.3 64.3 + - - +
98B GLY* 3.4 13.7 + - - +
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Residues in contact with LEU 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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73B THR* 3.8 31.9 - - + +
74B ILE* 3.9 15.3 - - + -
77B GLU* 3.8 46.7 - - + +
78B ILE* 5.9 0.4 - - + -
92B THR* 2.9 18.6 + - + +
93B LEU* 3.7 7.2 - - + +
95B GLU* 1.3 73.0 - - - +
97B ASP* 1.3 69.0 + - - +
98B GLY* 3.4 0.7 + - - -
104B ASN* 5.5 0.3 - - - +
105B LEU* 3.9 19.0 - - + +
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Residues in contact with ASP 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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93B LEU 3.0 13.7 + - - +
94B ARG 3.6 3.6 - - - +
96B LEU* 1.3 79.5 - - - +
98B GLY* 1.3 57.0 + - - +
99B THR* 2.5 40.7 + - - +
102B TYR* 3.2 37.3 + - + -
104B ASN* 3.0 42.1 + - - +
105B LEU* 2.9 41.8 + - + +
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Residues in contact with GLY 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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94B ARG 3.0 13.2 + - - -
95B GLU* 3.6 12.6 - - - -
96B LEU 3.3 1.6 - - - -
97B ASP* 1.3 76.0 - - - +
99B THR* 1.3 61.8 + - - +
104B ASN* 5.1 0.4 - - - -
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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