Contacts of the helix formed by residues 68 - 84 (chain C) in PDB entry 3CQ6
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 ALA 68 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU* 2.9 13.1 + - - -
66C ARG 3.4 2.4 - - - +
67C ASP* 1.3 77.4 - - - +
69C VAL* 1.3 63.7 + - - +
70C GLU 3.4 2.9 - - - -
71C LEU* 3.3 12.1 + - + -
72C ARG* 3.0 27.6 + - + +
93C TRP* 6.2 0.7 - - + -
94C ALA* 5.3 2.5 - - + +
258C HIS* 5.9 2.7 - - + -
259C LEU* 4.4 16.8 - - + -
264C GLN* 3.4 35.2 - - + +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 2.7 29.5 + - - +
67C ASP* 3.0 15.5 + - + +
68C ALA* 1.3 72.1 - - - +
70C GLU* 1.3 59.0 + - - +
72C ARG* 3.2 14.5 + - - +
73C ASP* 2.9 32.5 + - - +
89C ARG* 2.8 44.3 - - - +
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 4.5 1.4 + - - -
68C ALA 3.4 0.8 - - - -
69C VAL* 1.3 78.8 - - + +
71C LEU* 1.3 64.4 + - - +
73C ASP* 3.3 14.1 + - + +
74C GLU* 3.1 28.8 + - + +
264C GLN* 6.1 1.3 - - - +
268C ILE* 3.9 31.1 - - + +
272C ARG* 5.6 1.0 + - - -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA* 3.3 13.4 + - + +
70C GLU* 1.3 77.8 - - - +
72C ARG* 1.3 58.2 + - - +
74C GLU* 3.2 2.8 + - - -
75C LEU* 2.9 45.5 + - + +
94C ALA* 3.8 24.7 - - + -
237C LEU* 3.8 20.0 - - + -
259C LEU* 3.9 10.8 - - + -
264C GLN* 4.3 19.7 - - + +
267C ALA* 3.5 24.9 - - + -
268C ILE* 3.8 22.6 - - + +
271C LEU* 3.9 17.5 - - + -
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 2.9 43.7 + - - +
68C ALA* 3.0 18.4 + - + +
69C VAL* 3.6 13.5 - - - +
71C LEU* 1.3 72.7 - - - +
73C ASP* 1.3 65.7 + - - +
75C LEU* 3.8 8.0 - - + +
76C ALA* 3.0 25.3 + - - +
89C ARG* 3.0 42.0 + - + +
90C ASP* 4.2 9.5 + - - +
92C LEU* 2.9 30.8 + - + +
93C TRP* 4.2 20.5 - - - -
94C ALA* 4.5 14.8 - - + +
247C ILE* 3.9 17.0 - - - +
251C MET* 5.5 2.2 - - - -
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 2.9 20.5 + - - +
70C GLU* 3.4 14.0 - - + +
72C ARG* 1.3 74.9 - - - +
74C GLU* 1.3 65.1 + - - +
76C ALA* 3.4 6.1 + - - +
77C ALA* 3.0 26.2 + - - +
89C ARG* 3.0 44.4 + - - +
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Residues in contact with GLU 74 (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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70C GLU* 3.1 20.6 + - + +
71C LEU* 3.2 7.8 + - - +
73C ASP* 1.3 80.7 - - - +
75C LEU* 1.3 60.3 + - - +
77C ALA* 3.4 11.7 + - - +
78C TYR* 3.0 26.9 + - - +
268C ILE* 4.5 21.1 - - + +
271C LEU* 3.8 26.4 - - + +
272C ARG* 5.8 4.3 + - - +
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 2.9 30.2 + - + +
72C ARG* 3.8 7.2 - - + +
73C ASP 3.4 0.2 - - - -
74C GLU* 1.3 74.8 - - - +
76C ALA* 1.3 59.8 + - - +
78C TYR* 3.4 5.1 + - + +
79C ILE* 2.9 32.4 + - - +
92C LEU* 3.2 19.1 - - + -
94C ALA* 4.0 19.7 - - + +
226C MET* 4.5 9.4 - - - -
237C LEU* 4.5 2.0 - - + -
239C TYR* 3.8 51.8 - - + -
271C LEU* 3.7 27.4 - - + -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ARG 3.0 14.4 + - - +
73C ASP* 3.7 4.5 - - - +
75C LEU* 1.3 74.4 - - - +
77C ALA* 1.3 59.3 + - - +
80C THR* 2.8 34.7 + - - -
87C VAL* 3.5 12.8 - - - +
88C THR* 3.4 25.4 - - - -
89C ARG 3.7 0.9 - - - +
92C LEU* 3.3 28.4 - - + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASP 3.0 16.5 + - - +
74C GLU* 3.7 15.9 - - - +
75C LEU 3.3 0.2 - - - -
76C ALA* 1.3 77.8 - - - +
78C TYR* 1.3 62.3 + - - +
80C THR* 3.5 6.4 + - - -
81C LYS* 3.1 23.7 + - - +
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Residues in contact with TYR 78 (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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74C GLU 3.0 14.8 + - - +
75C LEU* 3.6 8.1 - - - +
76C ALA 3.3 0.2 - - - -
77C ALA* 1.3 76.8 - - - +
79C ILE* 1.3 57.5 + - + +
81C LYS* 3.3 5.7 + - + +
82C GLN* 2.7 69.0 + - + +
202C GLU* 2.6 39.5 + - - +
224C ARG* 4.0 4.7 - - - -
230C PHE* 3.6 24.9 - + - -
239C TYR* 3.5 27.1 - + - -
271C LEU* 4.3 13.5 - - + +
274C SER* 4.7 8.5 - - - -
278C LEU* 3.6 25.1 - - + +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU 2.9 20.4 + - - +
76C ALA* 4.0 3.1 - - - +
78C TYR* 1.3 80.5 - - + +
80C THR* 1.3 57.6 + - - +
82C GLN* 4.3 1.3 - - - -
83C THR* 2.8 57.2 + - + +
85C VAL 4.4 2.2 - - - +
87C VAL* 3.6 22.4 - - + -
92C LEU* 4.5 1.6 - - + -
210C THR* 4.5 9.4 - - + -
224C ARG* 4.0 24.0 - - + +
239C TYR* 3.7 30.7 - - + +
241C VAL* 3.9 26.9 - - + -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ALA 2.8 21.8 + - - -
77C ALA* 3.6 7.4 - - - -
79C ILE* 1.3 76.3 - - - +
81C LYS* 1.3 57.7 + - - +
84C GLY* 3.0 29.9 + - - -
85C VAL 3.3 14.6 - - - +
86C ALA* 4.2 11.9 - - + -
87C VAL* 3.3 25.8 + - - +
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Residues in contact with LYS 81 (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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77C ALA 3.1 17.6 + - - +
78C TYR* 3.8 5.4 - - + +
80C THR* 1.3 78.8 - - - +
82C GLN* 1.3 64.5 + - - +
84C GLY* 3.9 3.6 + - - -
275C ALA* 5.8 5.9 - - - +
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Residues in contact with GLN 82 (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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78C TYR* 2.7 58.7 + - + +
79C ILE* 4.0 1.8 - - - +
81C LYS* 1.3 76.7 - - - +
83C THR* 1.3 60.2 + - + +
202C GLU* 4.0 11.7 + - - +
224C ARG* 4.1 3.8 - - - +
278C LEU* 4.7 4.9 - - - +
404C PO4 2.7 46.5 + - - +
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Residues in contact with THR 83 (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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79C ILE* 2.8 42.4 + - + +
82C GLN* 1.3 75.2 - - + +
84C GLY* 1.3 58.8 + - - +
85C VAL* 3.2 16.1 + - - +
208C SER* 3.6 15.3 + - - +
210C THR* 3.2 27.2 + - - +
211C THR* 4.3 9.0 - - - +
224C ARG* 4.1 7.6 - - - +
404C PO4 2.7 26.2 - - - +
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Residues in contact with GLY 84 (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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80C THR* 3.0 18.0 + - - -
81C LYS 3.9 2.6 + - - -
82C GLN 3.5 2.2 + - - -
83C THR* 1.3 78.2 - - - +
85C VAL* 1.3 60.3 + - - +
86C ALA 3.7 2.4 + - - -
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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