Contacts of the helix formed by residues 77 - 91 (chain C) in PDB entry 2QB0
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 SER 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C LEU* 3.4 46.4 - - - +
48C ARG 4.1 3.3 + - - -
50C ILE* 4.0 12.7 - - - +
74C SER* 3.1 12.5 + - - -
76C HIS* 1.3 83.5 + - - +
78C GLY* 1.3 66.2 + - - +
79C ASP* 3.4 7.6 - - - -
80C GLU* 3.1 7.9 + - - +
81C LEU* 2.9 24.8 + - - +
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 3.3 35.6 - - - +
71C ARG* 4.1 0.9 - - - -
74C SER* 2.7 31.9 + - - -
75C PRO 4.8 0.2 - - - -
76C HIS 3.9 0.2 - - - -
77C SER* 1.3 71.1 - - - +
79C ASP* 1.3 56.8 + - - +
81C LEU* 3.3 5.8 + - - +
82C TYR 2.9 24.1 + - - -
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.8 20.4 - - - +
71C ARG* 3.3 37.4 + - - +
76C HIS 4.8 3.3 - - - +
77C SER* 3.9 9.5 + - - -
78C GLY* 1.3 71.3 + - - +
80C GLU* 1.3 78.5 + - - +
82C TYR* 3.4 3.8 + - - +
83C GLU* 3.0 30.2 + - - +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 3.4 42.2 - - - -
47C LEU* 3.9 30.1 - - + -
77C SER* 3.1 10.1 + - - +
79C ASP* 1.3 85.5 + - - +
81C LEU* 1.3 60.2 + - + +
83C GLU* 3.3 6.9 + - - +
84C LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TRP* 3.5 24.8 - - + -
38C LEU* 4.5 10.8 - - + +
41C ALA* 3.9 28.5 - - + -
47C LEU* 3.9 18.2 - - + -
50C ILE* 4.5 11.4 - - + -
55C PHE* 4.4 20.9 - - + -
70C PHE* 3.8 11.9 - - + -
74C SER* 4.2 17.3 - - - +
77C SER* 2.9 18.4 + - - +
78C GLY* 3.5 8.1 - - - +
80C GLU* 1.3 80.2 - - + +
82C TYR* 1.3 62.7 + - - +
84C LEU* 3.3 10.7 + - + +
85C LEU* 3.1 17.8 + - - +
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU 3.8 14.1 - - - -
66C THR* 4.5 2.4 - - - +
67C LYS* 3.7 44.4 + - + -
70C PHE* 3.6 38.8 - + + -
78C GLY 2.9 16.3 + - - +
79C ASP 3.6 4.3 - - - +
80C GLU 3.3 0.2 - - - -
81C LEU* 1.3 76.6 - - - +
83C GLU* 1.3 76.6 + - - +
85C LEU* 3.2 8.5 + - + +
86C GLN* 3.0 64.7 + - + +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 2.7 32.0 + - - +
79C ASP 3.0 21.0 + - - +
80C GLU* 3.8 7.9 - - - +
82C TYR* 1.3 84.6 - - - +
84C LEU* 1.3 65.3 + - - +
86C GLN* 3.2 13.2 + - - +
87C HIS* 3.0 41.4 + - + -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.6 23.8 - - + -
37C TRP* 3.7 23.8 - - + +
40C TRP* 4.8 7.6 - - + +
41C ALA* 3.7 19.3 - - + -
45C PHE* 3.6 37.5 - - + -
80C GLU* 2.9 18.1 + - - +
81C LEU* 3.3 13.9 - - + +
83C GLU* 1.3 75.9 - - - +
85C LEU* 1.3 58.1 + - - +
87C HIS* 3.2 7.0 + - - +
88C ILE* 3.0 38.1 + - + +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PRO* 4.1 29.4 - - + -
29C TRP* 4.3 11.9 - - + -
37C TRP* 4.2 9.6 - - + -
62C LEU* 3.4 43.5 - - + +
63C LEU* 4.3 11.9 - - + -
70C PHE* 4.0 16.2 - - + -
81C LEU 3.1 12.9 + - - +
82C TYR* 3.3 9.6 - - + +
84C LEU* 1.3 78.3 - - - +
86C GLN* 1.3 67.2 + - - +
88C ILE* 3.2 5.4 + - + +
89C LEU* 2.9 37.7 + - + +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.0 60.2 + - + +
83C GLU* 3.2 18.8 + - - +
85C LEU* 1.3 84.9 - - - +
87C HIS* 1.3 59.3 + - + +
89C LEU* 3.6 22.4 + - - +
90C LYS* 2.9 29.5 + - - +
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 3.8 18.9 - - + +
83C GLU* 3.0 36.7 + - + +
84C LEU* 3.5 9.0 - - - +
86C GLN* 1.3 77.2 - - + +
88C ILE* 1.3 63.9 + - - +
90C LYS* 3.5 8.1 - - + +
91C GLN* 3.1 30.6 + - + +
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 4.0 14.6 - - + -
18C LEU* 3.9 30.7 - - + -
22C LEU 5.5 0.9 - - - +
24C LEU 5.5 0.9 - - - +
26C PRO* 3.9 27.0 - - + +
29C TRP* 4.2 11.4 - - + -
37C TRP* 3.5 29.4 - - + +
40C TRP* 5.3 1.6 - - + +
84C LEU* 3.0 27.5 + - + +
85C LEU* 3.6 8.1 - - - +
87C HIS* 1.3 78.4 - - - +
89C LEU* 1.3 61.5 + - - +
91C GLN* 3.4 24.7 + - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PRO* 3.8 30.3 - - + -
63C LEU* 3.8 32.3 - - + -
85C LEU* 2.9 22.6 + - + +
86C GLN* 3.8 29.2 - - - +
88C ILE* 1.3 76.6 - - - +
90C LYS* 1.3 61.2 + - - +
91C GLN* 3.5 5.0 + - - +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C GLN 2.9 19.7 + - - +
87C HIS* 3.5 11.7 - - + +
88C ILE 3.3 0.4 - - - -
89C LEU* 1.3 78.1 - - - +
91C GLN* 1.3 63.6 + - + +
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.4 21.4 + - - +
16C ILE* 3.3 50.5 + - - +
17C ARG* 4.6 8.9 + - - -
18C LEU* 5.3 2.4 - - - +
87C HIS* 3.1 18.8 + - + +
88C ILE* 3.5 17.5 - - - +
89C LEU 3.3 4.8 - - - +
90C LYS* 1.3 81.7 - - + +
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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
------------------------------------------------------------
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