Contacts of the helix formed by residues 63 - 78 (chain C) in PDB entry 3E6G
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 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C TYR* 3.0 27.1 + - - +
42C THR 4.6 7.3 + - - -
45C TYR* 4.3 5.7 + - - -
61C THR* 3.9 3.9 + - - -
62C HIS* 1.3 76.1 + - - +
64C PRO* 1.3 70.5 - - - +
65C THR* 3.5 9.2 + - - -
66C ARG* 2.9 62.0 + - + +
67C PHE* 3.0 22.9 + - - -
246C GLN 5.7 0.7 - - - -
248C PRO* 3.4 22.8 - - - +
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Residues in contact with PRO 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 4.4 12.3 - - + -
37C PRO* 6.1 0.7 - - - -
40C TYR* 3.4 39.7 - - + -
45C TYR* 3.3 16.4 - - + +
62C HIS* 3.6 23.8 - - + -
63C ASN* 1.3 82.4 - - - +
65C THR* 1.3 57.5 + - - +
67C PHE* 2.9 13.4 + - + +
68C ALA* 2.8 31.2 + - - +
71C ARG* 5.0 1.0 + - - -
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Residues in contact with THR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PRO* 5.4 5.2 - - + +
38C PRO 2.7 27.9 + - - +
39C ILE* 3.3 2.4 - - + -
40C TYR* 3.1 17.1 + - - -
63C ASN* 3.2 9.4 + - - -
64C PRO* 1.3 76.2 - - - +
66C ARG* 1.3 63.6 + - - +
68C ALA* 3.2 7.6 + - - +
69C TYR* 3.2 19.9 + - - +
248C PRO* 3.4 27.1 - - - +
251C SER* 4.2 0.6 - - - -
252C PHE* 3.8 28.5 - - + +
255C LEU* 4.4 5.3 - - + +
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 3.6 28.7 + - - +
63C ASN* 2.9 44.3 + - + +
65C THR* 1.3 77.0 - - - +
67C PHE* 1.3 75.4 + - - +
69C TYR* 3.3 3.2 + - + +
70C GLU* 2.9 50.7 + - - +
84C ALA* 3.7 14.6 - - + -
239C GLN* 4.0 13.1 + - - +
245C VAL* 3.0 34.7 - - - +
246C GLN 3.3 19.3 + - - +
251C SER* 3.6 22.3 - - - +
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR 4.3 3.1 - - - -
62C HIS* 3.4 39.7 - + - -
63C ASN 3.0 26.9 + - - -
64C PRO* 2.9 13.3 + - + +
66C ARG* 1.3 99.4 - - - +
68C ALA* 1.3 54.3 + - - +
70C GLU* 3.4 19.8 - - - +
71C ARG* 2.8 59.4 + - + +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 3.0 29.7 - - - +
37C PRO* 4.2 13.5 - - + -
64C PRO 2.8 11.8 + - - +
65C THR* 3.3 11.4 - - - +
66C ARG 3.1 0.2 - - - -
67C PHE* 1.3 75.8 - - - +
69C TYR* 1.4 66.8 + - - +
71C ARG* 3.5 18.0 + - - +
72C CYS* 3.3 10.0 + - - +
255C LEU* 3.7 17.5 - - + -
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Residues in contact with TYR 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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65C THR 3.2 12.1 + - - +
66C ARG 3.6 6.3 - - - +
68C ALA* 1.4 71.6 - - - +
70C GLU* 1.3 63.3 + - - +
72C CYS* 3.0 6.1 + - - +
73C VAL* 3.0 39.1 + - + +
84C ALA* 3.9 20.6 - - + -
208C ALA* 3.0 31.4 - - - +
212C LEU* 3.9 5.0 - - + +
221C GLY 5.2 0.2 - - - -
222C ILE* 3.4 25.5 - - + +
246C GLN* 4.1 13.2 - - - -
251C SER* 4.1 27.6 - - - +
254C ALA* 3.3 28.2 - - + +
255C LEU* 3.7 22.0 - - + +
258C LEU* 4.1 11.9 - - + -
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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
----------------------------------------------------------
66C ARG* 2.9 37.7 + - - +
67C PHE* 3.4 29.9 - - - +
68C ALA 3.3 0.2 - - - -
69C TYR* 1.3 75.9 - - - +
71C ARG* 1.3 59.9 + - + +
72C CYS 3.1 0.3 + - - -
73C VAL* 3.2 2.0 + - - -
74C ALA* 2.9 25.9 + - - +
82C ALA* 3.3 40.5 - - + +
83C PHE* 3.7 2.2 - - - +
84C ALA* 2.7 35.5 + - + +
222C ILE* 5.9 1.6 - - + -
239C GLN* 3.3 8.1 + - - +
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY 4.4 2.7 - - - +
25C GLY* 3.2 38.2 + - - -
26C GLN* 5.4 1.2 - - - +
64C PRO 5.0 0.8 + - - -
67C PHE* 2.8 55.0 + - + +
68C ALA* 4.0 17.7 - - - +
69C TYR 3.4 0.2 - - - -
70C GLU* 1.3 75.0 - - + +
72C CYS* 1.3 60.8 + - - +
74C ALA* 3.7 7.4 + - - +
75C ALA* 3.2 21.8 + - - +
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Residues in contact with CYS 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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20C LEU 3.8 17.0 - - - -
21C ALA* 4.3 15.3 - - - -
24C GLY 3.5 24.0 + - - +
26C GLN* 3.7 5.8 - - - +
68C ALA 3.3 10.8 + - - +
69C TYR 3.0 9.5 + - - +
71C ARG* 1.3 75.4 - - - +
73C VAL* 1.3 65.3 + - - +
75C ALA* 3.0 4.2 + - - +
76C LEU* 3.0 24.4 + - - +
255C LEU* 4.0 9.9 - - + -
258C LEU* 3.5 24.7 - - + -
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR* 3.0 44.9 + - + +
70C GLU* 3.9 4.0 - - - +
72C CYS* 1.3 75.5 - - - +
74C ALA* 1.3 62.2 + - - +
75C ALA 3.1 0.3 + - - -
76C LEU* 3.3 6.2 + - + +
77C GLU* 3.0 27.9 + - + +
82C ALA* 4.2 5.2 - - + -
191C PRO* 5.9 2.5 - - + -
206C HIS* 5.0 1.1 - - + -
212C LEU* 4.2 16.6 - - + -
222C ILE* 3.4 35.2 - - + -
224C VAL* 3.9 8.5 - - + -
258C LEU* 3.7 14.4 - - + -
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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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70C GLU 2.9 12.6 + - - +
71C ARG* 3.9 8.1 - - - +
72C CYS 3.3 0.2 - - - -
73C VAL* 1.3 75.7 - - - +
75C ALA* 1.3 56.5 + - - +
77C GLU 3.6 0.2 + - - -
78C GLY 3.0 6.2 + - - -
79C GLY 2.7 40.5 + - - +
80C THR 4.1 4.7 - - - +
81C ARG* 3.9 12.1 - - - +
82C ALA* 3.6 25.0 - - - +
224C VAL* 3.7 12.6 - - + -
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Residues in contact with ALA 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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17C LEU* 5.1 0.7 - - - +
20C LEU* 4.5 23.3 - - + +
24C GLY* 4.3 20.9 - - - -
25C GLY 4.7 1.8 - - - +
71C ARG 3.2 13.9 + - - +
72C CYS 3.0 10.5 + - - +
74C ALA* 1.3 79.1 - - - +
76C LEU* 1.3 62.1 + - - +
78C GLY* 3.2 12.8 + - - -
79C GLY 5.0 1.1 - - - -
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Residues in contact with LEU 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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17C LEU* 3.7 50.9 - - + +
20C LEU* 4.2 5.6 - - + -
21C ALA* 3.7 24.2 - - + +
72C CYS* 3.0 20.0 + - - +
73C VAL* 4.1 4.9 - - + +
75C ALA* 1.3 76.5 - - - +
77C GLU* 1.3 61.8 + - - +
191C PRO* 3.7 22.5 - - + +
192C MET* 4.8 8.3 - - - -
195C ARG* 3.4 18.2 - - - -
258C LEU* 4.0 29.6 - - + -
261C LEU* 4.2 17.5 - - + -
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Residues in contact with GLU 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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73C VAL* 3.0 18.6 + - + +
76C LEU* 1.3 79.0 - - - +
78C GLY* 1.3 57.4 + - - +
79C GLY 3.1 2.4 + - - +
186C ASN* 2.6 33.8 + - - -
191C PRO* 3.5 13.4 - - + +
195C ARG* 3.9 30.1 - - - +
196C PRO* 3.9 3.3 - - - +
197C LEU* 3.5 14.2 - - + +
198C SER* 5.6 0.3 + - - -
204C VAL* 3.7 11.6 - - + +
206C HIS* 2.9 18.1 + - - +
224C VAL* 3.5 39.3 - - + -
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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
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74C ALA 3.0 4.9 + - - -
75C ALA* 3.2 11.2 + - - -
76C LEU 3.2 1.0 - - - -
77C GLU* 1.3 78.4 - - - +
79C GLY* 1.3 65.0 + - - +
80C THR* 5.1 1.9 - - - +
195C ARG* 5.1 4.5 - - - -
197C LEU* 3.9 5.1 - - - +
226C GLY* 5.3 1.6 - - - -
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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