Contacts of the helix formed by residues 61 - 75 (chain C) in PDB entry 3QI6
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 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR 5.0 6.0 - - - +
39C SER 4.8 2.5 - - - +
42C PHE* 4.0 11.9 - - + -
54C TYR* 3.4 8.8 - - - -
57C ALA* 3.0 32.7 + - + +
60C GLY* 1.3 73.7 - - - +
62C PRO* 1.3 76.6 - - + +
63C THR* 3.6 9.9 + - - -
64C ARG* 3.1 48.1 + - - +
65C THR* 2.9 21.8 + - - -
243C PRO 4.9 7.5 + - - +
244C GLY 5.9 0.2 - - - -
245C PRO* 4.7 11.5 - - - +
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Residues in contact with PRO 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.7 30.5 - - + -
37C TYR* 3.3 39.0 - - + -
42C PHE* 3.8 17.3 - - + -
54C TYR* 3.5 23.8 - - + +
61C ASN* 1.3 86.1 - - + +
63C THR* 1.3 63.0 + - - +
65C THR* 3.4 1.9 + - - -
66C ALA* 3.1 21.5 + - - +
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Residues in contact with THR 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ALA* 5.2 1.6 - - + -
35C PRO 2.5 31.4 + - - +
36C ILE* 4.7 0.4 - - - -
37C TYR* 2.9 20.1 + - - +
61C ASN* 3.4 4.0 + - - -
62C PRO* 1.3 77.0 - - - +
64C ARG* 1.3 62.9 + - - +
66C ALA* 3.3 5.2 + - - -
67C LEU* 3.0 18.7 + - - +
245C PRO* 3.3 37.5 - - + +
248C ALA* 3.7 13.0 - - + -
249C TYR* 4.0 4.7 - - + +
252C MET* 3.4 19.3 - - + +
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Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 3.6 12.5 + - - -
58C ARG 3.0 22.6 + - - -
59C THR 3.0 28.7 + - - -
60C GLY* 3.7 5.8 - - - -
61C ASN* 3.1 31.6 + - - +
63C THR* 1.3 78.9 - - - +
65C THR* 1.3 56.6 + - - +
67C LEU* 3.3 6.1 + - + +
68C GLU* 2.9 57.4 + - + +
81C ARG* 5.1 1.2 - - - +
82C ALA* 3.9 11.2 - - + -
236C GLN* 3.4 22.9 + - - +
242C VAL* 3.3 20.2 - - - +
243C PRO* 3.6 30.9 + - + +
248C ALA* 4.6 5.1 - - + +
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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
----------------------------------------------------------
54C TYR* 3.0 33.2 + - - +
60C GLY* 5.2 1.7 - - - -
61C ASN 2.9 16.3 + - - -
62C PRO 3.7 2.9 - - - -
64C ARG* 1.3 72.9 - - - +
66C ALA* 1.3 59.7 + - - +
68C GLU* 3.3 12.2 + - - +
69C ALA* 2.9 33.4 + - + +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY 3.5 22.5 - - - +
23C TYR* 4.1 9.4 - - + -
34C ALA* 3.8 18.6 - - + -
62C PRO 3.1 12.0 + - - +
63C THR 3.5 8.3 - - - +
65C THR* 1.3 77.6 - - - +
67C LEU* 1.3 62.7 + - - +
69C ALA* 3.3 1.4 + - - -
70C ALA* 3.0 22.5 + - - +
252C MET* 3.6 18.5 - - - +
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Residues in contact with LEU 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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63C THR 3.0 13.4 + - - +
64C ARG* 3.3 6.9 + - + +
66C ALA* 1.3 74.7 - - - +
68C GLU* 1.3 53.6 + - - +
70C ALA* 3.1 3.7 + - + +
71C LEU* 2.8 56.5 + - + +
82C ALA* 3.6 24.5 - - + -
243C PRO* 4.8 5.2 - - + -
248C ALA* 3.7 26.9 - - + -
251C THR* 3.6 31.2 - - + -
252C MET* 3.7 31.4 - - + +
255C LEU* 5.6 1.6 - - + -
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Residues in contact with GLU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ARG* 2.9 34.9 + - - +
65C THR* 3.7 11.8 + - - +
67C LEU* 1.3 74.7 - - - +
69C ALA* 1.3 57.5 + - - +
71C LEU* 3.9 6.4 - - - +
72C ALA* 3.0 30.7 + - - +
80C GLY* 3.4 30.4 - - - +
81C ARG* 3.7 12.8 + - - -
82C ALA* 2.9 26.8 + - + +
236C GLN* 2.9 29.6 + - - -
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER 5.1 1.2 - - - +
22C GLY* 3.6 23.0 - - - +
65C THR* 2.9 20.1 + - + +
66C ALA 3.5 4.7 - - - +
68C GLU* 1.3 75.2 - - - +
70C ALA* 1.3 57.9 + - - +
72C ALA* 3.8 5.4 - - - +
73C ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG 5.6 1.6 - - - +
18C ALA* 5.0 9.6 - - - +
21C SER* 5.5 0.2 - - - -
22C GLY* 3.8 14.9 - - - +
66C ALA 3.0 13.1 + - - +
67C LEU* 3.1 8.3 + - - +
69C ALA* 1.3 73.7 - - - +
71C LEU* 1.3 65.7 + - - +
73C ALA* 3.1 7.3 + - - +
74C VAL* 3.0 27.0 + - - +
252C MET* 4.8 9.2 - - + -
255C LEU* 3.9 19.5 - - + -
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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
----------------------------------------------------------
67C LEU* 2.8 51.9 + - + +
68C GLU* 3.9 6.3 - - - +
70C ALA* 1.3 74.2 - - - +
72C ALA* 1.3 62.2 + - - +
74C VAL* 3.3 19.4 - - + +
75C GLU* 3.5 8.0 + - - +
80C GLY* 5.4 0.9 - - - -
81C ARG 4.7 3.4 - - - +
82C ALA* 4.1 13.5 - - + -
204C HIS* 5.9 1.8 - - + -
206C THR* 3.9 24.7 - - + -
210C ILE* 4.2 22.0 - - + -
219C GLY 4.8 0.2 - - - +
220C ALA* 3.5 24.7 - - + -
222C VAL* 3.8 19.3 - - + +
255C LEU* 4.5 6.1 - - + -
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLU 3.0 18.9 + - - +
69C ALA* 3.8 6.3 - - - +
71C LEU* 1.3 76.5 - - - +
73C ALA* 1.3 63.0 + - - +
75C GLU 3.2 2.6 + - - -
76C ASP 3.1 3.8 + - - -
77C ALA* 2.8 47.4 + - - +
78C ALA 4.6 2.5 - - - +
79C PHE* 3.9 22.2 - - - +
80C GLY 3.9 0.7 - - - +
222C VAL* 4.1 11.1 - - - +
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Residues in contact with ALA 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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17C ARG* 3.1 27.3 + - + +
21C SER* 3.5 32.5 - - - +
69C ALA 3.0 18.6 + - - +
70C ALA* 3.1 7.1 + - - +
72C ALA* 1.3 76.4 - - - +
74C VAL* 1.3 56.6 + - + +
76C ASP* 3.0 18.9 + - - +
77C ALA 4.4 1.1 + - - -
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Residues in contact with VAL 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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14C LEU* 3.6 29.5 - - + +
17C ARG* 4.5 1.9 + - - +
18C ALA* 3.8 35.0 - - + +
70C ALA 3.0 11.5 + - - +
71C LEU* 3.3 22.2 - - + +
73C ALA* 1.3 75.1 - - + +
75C GLU* 1.3 57.2 + - - +
76C ASP 3.4 0.9 - - - -
189C PRO* 3.6 28.3 - - + +
193C GLN* 2.9 23.9 + - - +
255C LEU* 4.1 20.0 - - + -
258C LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 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 3.5 11.3 + - - +
72C ALA 3.2 4.6 + - - +
74C VAL* 1.3 76.1 - - - +
76C ASP* 1.3 69.2 + - - +
77C ALA* 3.1 1.5 + - + -
184C ASN* 2.9 18.0 + - - -
189C PRO* 3.4 14.2 - - + +
192C GLN 3.8 0.5 - - - +
193C GLN* 3.4 20.8 - - - +
194C PRO* 3.6 18.2 - - - +
195C LEU* 3.7 18.1 + - + +
202C VAL* 3.7 11.2 - - - +
204C HIS* 2.6 33.5 + - + +
222C VAL* 3.7 29.8 - - + -
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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