Contacts of the helix formed by residues 65 - 80 (chain C) in PDB entry 3COG
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 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C SER 4.6 3.3 - - - +
44C SER 5.2 0.4 - - - +
47C PHE* 4.3 4.9 - - + -
58C PHE* 3.5 10.0 - - - -
61C SER* 2.9 40.6 + - - +
64C GLY* 1.3 73.7 - - - +
66C PRO* 1.3 77.7 - - + +
67C THR 3.6 3.6 + - - -
68C ARG* 3.0 48.0 + - - +
69C ASN* 2.9 27.4 + - - +
247C PRO 5.1 2.4 + - - -
249C PRO* 3.7 23.5 - - + +
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Residues in contact with PRO 66 (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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34A SER* 3.9 19.1 - - - -
32C TRP* 4.2 24.5 - - + -
40C PRO 5.7 1.1 - - - +
42C SER* 3.9 27.1 - - - +
47C PHE* 4.1 9.2 - - + -
58C PHE* 3.6 29.3 - - + -
65C ASN* 1.3 89.1 - - + +
67C THR* 1.3 58.1 + - - +
69C ASN* 3.4 2.2 + - + +
70C CYS* 3.0 35.9 + - - -
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Residues in contact with THR 67 (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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39C PRO* 5.6 5.4 - - + +
40C PRO 2.8 27.1 + - - +
41C ILE* 4.6 0.9 - - - -
42C SER* 3.1 17.1 + - - -
65C ASN* 3.4 1.4 + - - -
66C PRO* 1.3 74.2 - - - +
68C ARG* 1.3 66.0 + - - +
70C CYS* 3.4 8.5 + - + +
71C LEU* 3.2 20.3 + - - +
249C PRO* 3.2 37.5 - - - +
252C CYS* 4.0 1.1 - - + +
253C TYR* 3.7 26.2 - - + +
256C ASN* 5.0 1.3 - - + +
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Residues in contact with ARG 68 (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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61C SER 3.6 10.1 + - - -
62C ARG* 3.0 21.8 + - - +
63C SER 3.0 29.3 + - - -
64C GLY* 3.5 9.2 - - - -
65C ASN* 3.0 25.8 + - - +
67C THR* 1.3 73.6 - - - +
69C ASN* 1.3 65.4 + - - +
71C LEU* 3.1 3.1 + - - +
72C GLU* 2.9 52.6 + - - +
86C ALA* 4.0 5.6 - - + -
237C ARG* 4.8 2.0 - - - +
240C GLN* 3.2 25.1 + - - +
241C ASN* 6.3 0.2 - - - +
246C VAL* 3.6 20.4 - - - +
247C PRO* 3.9 22.3 + - - +
252C CYS* 3.7 25.4 - - - +
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Residues in contact with ASN 69 (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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58C PHE* 3.5 22.6 - - + -
64C GLY* 3.9 8.0 - - - -
65C ASN 2.9 32.5 + - - +
66C PRO* 3.9 5.6 - - + +
68C ARG* 1.3 82.8 + - - +
70C CYS* 1.3 61.3 + - - +
72C GLU* 3.4 16.9 + - - +
73C LYS* 3.1 29.3 + - + +
237C ARG* 5.4 0.7 + - - -
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Residues in contact with CYS 70 (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 GLY* 3.2 33.5 - - - +
27C GLN* 4.3 1.8 - - - +
31C GLN* 3.8 7.9 - - - -
32C TRP* 3.7 29.6 - - - -
39C PRO* 4.3 10.5 - - + -
66C PRO 3.0 25.9 + - - +
67C THR* 3.6 7.0 - - + +
69C ASN* 1.3 75.2 - - - +
71C LEU* 1.3 64.7 + - - +
73C LYS* 3.5 6.1 + - - +
74C ALA* 3.2 21.3 + - - +
256C ASN* 3.8 9.8 - - - +
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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
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67C THR 3.2 9.6 + - - +
68C ARG 3.1 7.3 + - - +
70C CYS* 1.3 77.6 - - - +
72C GLU* 1.3 59.1 + - - +
74C ALA* 3.2 2.5 + - - +
75C VAL* 2.9 42.7 + - + +
86C ALA* 4.5 4.9 - - + -
222C MET* 3.6 31.2 - - - -
224C LEU* 4.3 8.3 - - + -
252C CYS* 3.7 32.5 - - + +
255C CYS* 4.1 6.3 - - + -
256C ASN* 3.4 28.9 + - - +
259C LEU* 3.6 27.4 - - + -
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Residues in contact with GLU 72 (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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68C ARG* 2.9 31.9 + - - +
69C ASN* 3.7 16.7 - - - +
71C LEU* 1.3 78.6 - - - +
73C LYS* 1.3 61.0 + - - +
75C VAL* 4.7 0.4 - - - -
76C ALA* 3.0 21.0 + - - +
84C CYS* 3.2 37.4 + - - +
85C LEU 4.2 0.2 - - - -
86C ALA* 2.9 34.8 + - + +
224C LEU* 5.6 0.4 - - + -
237C ARG* 2.6 27.5 + - - -
240C GLN* 3.0 16.8 + - - -
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Residues in contact with LYS 73 (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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25C VAL* 3.4 14.9 - - + +
26C GLY* 4.0 22.5 - - - +
31C GLN* 4.5 15.8 + - - +
69C ASN* 3.1 17.6 + - - +
70C CYS* 3.6 10.1 - - - +
71C LEU 3.3 0.2 - - - -
72C GLU* 1.3 75.7 - - - +
74C ALA* 1.3 64.2 + - - +
76C ALA* 3.6 6.2 - - - +
77C ALA* 3.0 18.2 + - - +
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Residues in contact with ALA 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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21C GLN 5.0 4.8 - - - +
22C ALA* 5.1 4.7 - - - +
25C VAL* 3.4 30.5 - - + +
70C CYS 3.2 7.2 + - - +
71C LEU* 3.2 8.0 + - - +
73C LYS* 1.3 77.8 - - - +
75C VAL* 1.3 65.6 + - - +
77C ALA* 3.1 5.4 + - - +
78C LEU* 3.0 28.5 + - + +
256C ASN* 4.2 18.4 - - - +
259C LEU* 4.6 7.4 - - + -
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Residues in contact with VAL 75 (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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71C LEU* 2.9 30.2 + - + +
72C GLU 4.1 0.2 - - - +
74C ALA* 1.3 71.8 - - - +
76C ALA* 1.3 64.2 + - - +
78C LEU* 3.0 10.6 + - + +
79C ASP* 3.0 28.4 + - - +
84C CYS* 3.4 26.2 - - - -
208C TYR* 4.9 0.7 - - + -
214C MET* 4.2 11.7 - - + -
224C LEU* 3.8 34.5 - - + -
226C SER* 3.8 7.4 - - - +
259C LEU* 3.7 21.5 - - + -
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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
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72C GLU 3.0 20.3 + - - +
73C LYS* 3.6 7.0 - - - +
75C VAL* 1.3 76.5 - - - +
77C ALA* 1.3 64.3 + - - +
79C ASP* 3.1 2.9 + - - -
80C GLY 3.1 3.5 + - - -
81C ALA* 2.8 47.2 + - - +
82C LYS 4.2 3.4 - - - +
83C TYR* 3.7 26.9 - - - +
84C CYS* 3.7 5.3 - - - +
226C SER* 4.2 1.1 - - - -
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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
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21C GLN* 3.8 22.2 - - + +
25C VAL* 3.7 30.5 - - + -
73C LYS 3.0 14.5 + - - +
74C ALA 3.1 8.9 + - - +
76C ALA* 1.3 74.0 - - - +
78C LEU* 1.3 63.4 + - + +
80C GLY* 3.0 14.7 + - - +
81C ALA 4.2 3.1 + - - +
197C ARG* 3.7 7.3 + - - -
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Residues in contact with LEU 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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18C PHE* 3.5 52.5 - - + +
21C GLN* 4.3 5.8 - - + +
22C ALA* 3.8 27.4 - - + +
74C ALA* 3.0 17.4 + - + +
75C VAL* 3.0 11.0 + - - +
77C ALA* 1.3 75.1 - - - +
79C ASP* 1.3 56.9 - - - +
193C PRO* 3.3 24.4 - - + +
197C ARG* 2.9 27.4 + - - +
214C MET* 5.3 0.9 - - + -
259C LEU* 4.0 32.8 - - + -
262C LEU* 4.3 4.7 - - + -
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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
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75C VAL* 3.0 13.9 + - - +
76C ALA 3.7 7.0 - - - +
78C LEU* 1.3 75.6 - - - +
80C GLY* 1.3 59.7 + - - +
81C ALA* 3.9 3.6 - - + -
188C ASN* 4.7 0.7 + - - -
193C PRO* 3.7 6.5 - - - +
196C GLN 5.0 0.2 - - - +
197C ARG* 3.8 18.7 - - - +
198C PRO* 4.7 4.2 - - - +
199C LEU* 4.1 17.7 + - + +
200C ALA* 5.2 0.9 + - - +
206C SER* 3.1 12.9 + - - -
208C TYR* 2.6 43.3 + - - -
226C SER* 2.7 37.1 + - - +
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Residues in contact with GLY 80 (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* 3.0 16.0 + - - -
78C LEU 3.3 1.4 + - - -
79C ASP* 1.3 77.5 - - - +
81C ALA* 1.3 59.0 + - - +
197C ARG* 4.0 12.7 - - - +
199C LEU* 4.8 2.5 - - - +
228C ASN* 3.8 12.0 + - - +
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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