Contacts of the helix formed by residues 83 - 97 (chain B) in PDB entry 2QNC
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 ASP 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B GLY 4.1 1.0 + - - -
82B VAL* 1.3 74.5 - - - +
84B TYR* 1.3 62.0 + - - +
85B LEU* 3.3 15.7 + - - +
86B GLU* 2.8 49.0 + - + +
87B TRP* 2.7 36.0 + - - +
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Residues in contact with TYR 84 (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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68A MET* 5.2 1.1 - - + -
91A LEU* 4.7 1.6 - - - +
95A LEU* 4.0 18.4 - - + +
54B ARG* 6.0 1.3 - - - -
65B GLU* 3.0 26.8 + - - -
68B MET* 3.5 13.0 - - + +
69B LYS* 3.4 48.0 + - + -
72B PHE* 3.6 48.5 - + + -
83B ASP* 1.3 78.3 + - - +
85B LEU* 1.3 74.3 + - + +
87B TRP* 3.5 6.6 - + - +
88B LEU* 2.8 45.8 + - + +
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Residues in contact with LEU 85 (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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92A LEU* 4.0 12.3 - - + +
95A LEU* 3.4 41.5 - - + +
96A LYS* 3.8 35.7 - - + +
49B LYS* 4.7 15.5 - - - +
83B ASP* 3.3 14.0 + - - +
84B TYR* 1.3 85.8 - - + +
86B GLU* 1.3 67.0 + - + +
88B LEU* 3.5 4.3 - - + +
89B GLU* 3.0 23.3 + - - +
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Residues in contact with GLU 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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82B VAL* 5.9 0.7 - - + -
83B ASP* 2.8 48.3 + - + +
85B LEU* 1.3 72.5 - - + +
87B TRP* 1.3 66.8 + - - +
89B GLU* 3.1 11.3 + - - +
90B ASN* 3.1 30.7 + - - +
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Residues in contact with TRP 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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25A ILE* 3.0 33.1 - - + +
26A CYS* 3.9 15.7 - - + +
61A CYS* 3.5 9.3 - - - -
64A ALA* 3.5 26.7 - - + -
65A GLU 4.3 4.0 - - - -
68A MET* 3.6 48.7 - - + -
72B PHE* 3.7 22.0 - + + -
77B LEU* 3.3 22.7 - - + +
82B VAL* 3.8 12.5 - - + +
83B ASP 2.7 19.9 + - - +
84B TYR* 3.5 5.6 - + - +
86B GLU* 1.3 72.2 - - - +
88B LEU* 1.3 83.9 + - + +
90B ASN* 3.0 10.7 + - - +
91B LEU* 2.8 40.2 + - + +
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Residues in contact with LEU 88 (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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68A MET* 5.4 5.4 - - - -
88A LEU* 4.1 23.3 - - + -
91A LEU* 3.8 25.6 - - + -
92A LEU* 3.8 23.1 - - + +
95A LEU* 3.9 16.4 - - + -
68B MET* 5.9 2.5 - - + -
84B TYR* 2.8 35.5 + - + +
85B LEU* 3.5 5.4 - - + +
87B TRP* 1.3 88.9 - - + +
89B GLU* 1.3 62.6 + - - +
91B LEU* 3.1 30.1 - - + +
92B LEU* 3.1 9.4 + - - +
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Residues in contact with GLU 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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92A LEU* 3.3 27.5 - - + +
96A LYS* 3.3 36.0 + - - +
85B LEU 3.0 14.6 + - - +
86B GLU* 3.5 10.9 - - - +
87B TRP 3.1 0.2 - - - -
88B LEU* 1.3 71.0 - - - +
90B ASN* 1.3 69.0 + - - +
91B LEU 2.8 6.0 + - - -
92B LEU* 3.0 6.4 + - - +
93B THR* 3.0 25.7 + - - +
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Residues in contact with ASN 90 (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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24A LEU 4.2 7.6 - - - +
25A ILE* 3.4 27.7 + - - +
26A CYS 5.4 0.4 + - - -
27A GLN* 3.5 30.9 + - - -
86B GLU* 3.1 22.6 + - - +
87B TRP* 3.0 5.1 + - - +
89B GLU* 1.3 80.9 - - - +
91B LEU* 1.3 61.9 + - - +
93B THR* 3.3 12.4 + - - -
94B TYR* 3.1 22.0 + - - +
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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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25A ILE* 3.5 34.5 - - + +
65A GLU* 4.2 17.7 - - + -
68A MET* 4.3 15.0 - - + -
84A TYR* 4.8 0.2 - - - +
88A LEU* 4.5 12.1 - - + -
87B TRP* 2.8 37.9 + - + +
88B LEU* 3.1 24.2 - - + +
89B GLU 2.8 0.8 - - - -
90B ASN* 1.3 74.1 - - - +
92B LEU* 1.3 59.5 + - - +
93B THR 3.0 1.1 - - - -
94B TYR* 2.7 26.0 + - - +
95B LEU* 2.8 33.2 + - + +
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Residues in contact with LEU 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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85A LEU* 3.8 30.1 - - + +
88A LEU* 4.0 21.3 - - + +
89A GLU* 3.2 40.6 - - + +
92A LEU* 4.1 20.4 - - + -
88B LEU 3.1 6.8 + - - +
89B GLU 3.0 8.4 + - - +
91B LEU* 1.3 79.2 - - - +
93B THR* 1.3 57.5 + - - +
95B LEU* 4.4 2.0 - - - -
96B LYS* 2.9 53.7 + - + +
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Residues in contact with THR 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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89B GLU* 3.0 19.4 + - - +
90B ASN* 3.3 18.6 + - - +
91B LEU 3.0 0.8 - - - -
92B LEU* 1.3 78.7 - - - +
94B TYR* 1.3 58.7 + - - +
96B LYS* 3.7 4.3 - - - +
97B SER* 2.9 30.5 + - - -
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Residues in contact with TYR 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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24A LEU* 3.9 30.3 - - + +
25A ILE* 3.5 22.2 - - + -
40A ASP* 3.1 36.0 + - - +
54A ARG* 3.0 50.9 + - + +
55A GLY* 3.6 2.5 + - - -
57A LEU* 3.5 27.0 - - + +
65A GLU* 5.6 2.0 - - + -
90B ASN 3.1 9.3 + - - +
91B LEU* 2.7 12.8 + - + +
93B THR* 1.3 78.0 - - - +
95B LEU* 1.3 72.8 + - + +
97B SER* 2.6 30.2 + - - +
99B TYR* 4.7 3.8 - - - -
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Residues in contact with LEU 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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49A LYS* 4.7 2.8 + - - -
54A ARG* 3.0 33.9 - - - +
65A GLU* 4.3 13.0 - - + +
84A TYR* 3.9 30.5 - - + +
85A LEU* 3.7 31.3 - - + +
88A LEU* 4.2 12.1 - - + -
91B LEU* 2.8 31.2 + - + +
92B LEU* 4.0 2.9 - - - +
94B TYR* 1.3 87.5 - - + +
96B LYS* 1.3 61.4 + - - +
97B SER 3.5 0.3 + - - +
99B TYR* 3.7 20.7 + - + +
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Residues in contact with LYS 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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85A LEU* 4.0 23.1 - - + -
86A GLU* 6.2 0.2 - - - +
89A GLU* 2.7 43.9 + - - +
92B LEU* 2.9 43.5 + - + +
93B THR* 3.8 4.9 - - - +
95B LEU* 1.3 73.4 - - - +
97B SER* 1.3 68.5 + - - +
98B ASP* 3.7 0.7 + - - +
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Residues in contact with SER 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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49A LYS* 5.6 1.2 - - - -
54A ARG 5.3 2.9 + - - -
93B THR* 2.9 14.3 + - - -
94B TYR* 2.6 26.6 + - - -
95B LEU 3.7 0.3 - - - +
96B LYS* 1.3 81.0 - - - +
98B ASP* 1.3 58.4 + - - +
99B TYR* 3.2 29.3 + - - +
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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