Contacts of the helix formed by residues 4 - 29 (chain C) in PDB entry 3QIR
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 CYS 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO 3.6 8.7 - - - -
111B GLU* 3.4 30.7 - - - -
113B SER 3.4 7.0 - - - -
114B PHE* 3.6 23.0 - - + -
3C ASP* 1.3 72.0 - - - +
5C VAL* 1.4 67.6 + - - +
6C LEU* 3.7 8.7 - - - -
7C ASP* 3.0 40.4 + - - +
8C VAL* 3.1 14.7 + - - +
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Residues in contact with VAL 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.7 36.6 - - + -
33B VAL* 3.8 23.8 - - + -
87B LEU* 4.2 5.2 - - + -
110B PRO* 3.4 27.4 - - + +
113B SER* 2.8 28.8 + - - +
114B PHE 4.1 0.9 - - - +
115B MET* 4.3 13.5 - - + -
3C ASP 3.6 0.8 + - - -
4C CYS* 1.4 69.7 - - - +
6C LEU* 1.4 56.4 + - - +
8C VAL* 3.3 10.7 + - + +
9C MET* 2.9 31.3 + - - +
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 4.8 8.3 - - + -
84B GLN* 4.5 20.2 - - + +
110B PRO* 3.2 14.7 + - + -
111B GLU* 3.7 31.6 - - + +
4C CYS* 3.3 4.4 - - - -
5C VAL* 1.4 73.1 - - - +
7C ASP* 1.3 53.2 + - - +
9C MET* 3.2 10.4 + - + +
10C HIS* 2.8 63.7 + - + +
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Residues in contact with ASP 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASP* 5.4 3.9 - - + +
4C CYS* 3.0 32.0 + - + +
6C LEU* 1.3 74.4 - - - +
8C VAL* 1.3 65.0 + - + +
10C HIS* 3.2 17.7 + - - +
11C ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.7 32.1 - - + -
28B LEU* 6.4 0.2 - - + -
115B MET* 4.9 12.3 - - + -
1C ARG* 5.9 4.5 - - + -
3C ASP* 4.1 21.8 - - + +
4C CYS 3.1 15.6 + - - +
5C VAL* 3.5 11.0 - - + +
7C ASP* 1.3 73.9 - - + +
9C MET* 1.3 62.6 + - + +
11C ALA* 3.3 9.7 + - - +
12C ILE* 3.2 21.4 + - + +
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Residues in contact with MET 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.5 14.6 - - + -
24B CYS* 4.0 18.6 - - - -
27B LEU* 6.2 1.1 - - + -
28B LEU* 4.5 12.8 - - + -
47B VAL* 5.7 0.9 - - - -
49B TRP* 3.5 32.5 - - + -
84B GLN* 5.7 1.1 - - + -
85B PRO* 3.5 22.9 - - + -
87B LEU* 5.3 1.6 - - - -
110B PRO* 4.0 29.2 - - - -
5C VAL* 2.9 22.7 + - + +
6C LEU* 3.4 12.8 - - + +
8C VAL* 1.3 77.0 - - + +
10C HIS* 1.4 52.2 + - + +
12C ILE* 3.3 1.8 + - - -
13C TYR* 2.8 34.4 + - - +
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Residues in contact with HIS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 5.1 10.4 - - + +
84B GLN* 6.4 0.2 - - + -
6C LEU* 2.8 45.1 + - + +
7C ASP* 3.2 19.9 + - - +
9C MET* 1.4 73.1 - - + +
11C ALA* 1.4 57.6 + - - +
13C TYR* 3.3 12.8 + - - +
14C GLN* 2.9 31.2 + - - +
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Residues in contact with ALA 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASP 3.1 12.3 + - - +
8C VAL* 3.5 12.3 - - - +
9C MET 3.3 0.2 - - - -
10C HIS* 1.4 75.3 - - - +
12C ILE* 1.4 61.0 + - - +
14C GLN* 3.5 7.7 + - - +
15C GLN* 3.2 24.6 + - - +
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.1 2.9 - - + -
23B GLU* 5.0 13.2 - - + -
24B CYS* 4.1 20.0 - - - -
27B LEU* 6.5 0.7 - - + -
8C VAL* 3.2 12.9 + - + +
9C MET 3.3 6.9 + - - +
11C ALA* 1.4 72.5 - - - +
13C TYR* 1.4 64.2 + - - +
15C GLN* 3.4 6.1 + - - +
16C ASN* 2.8 35.8 + - - +
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Residues in contact with TYR 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 4.3 21.2 + + - -
20B PHE* 3.7 39.2 - + + -
9C MET 2.8 13.8 + - - +
10C HIS* 3.4 17.0 - - - +
12C ILE* 1.4 75.6 - - - +
14C GLN* 1.3 71.7 + - - +
16C ASN* 3.2 4.8 + - + +
17C LYS* 2.8 56.5 + - + +
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Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C HIS 2.9 16.6 + - - +
11C ALA* 3.6 8.5 - - - +
12C ILE 3.4 0.2 - - - -
13C TYR* 1.3 97.5 - - - +
15C GLN* 1.3 60.9 + - - +
17C LYS* 3.4 26.9 + - - +
18C GLU* 3.2 24.3 + - - +
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Residues in contact with GLN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 6.5 0.2 - - - -
11C ALA 3.2 14.7 + - - +
12C ILE* 3.8 9.9 - - - +
13C TYR 3.3 0.2 - - - -
14C GLN* 1.3 76.3 - - - +
16C ASN* 1.3 59.3 + - - +
18C GLU* 3.6 6.4 + - - +
19C HIS* 3.2 25.6 + - - +
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Residues in contact with ASN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASN* 3.5 20.1 - - - +
19B HIS* 2.8 26.8 + - - +
20B PHE* 3.4 32.8 + - + +
23B GLU* 3.9 23.2 - - - -
12C ILE* 2.8 27.0 + - - +
13C TYR* 3.5 7.9 - - + +
15C GLN* 1.3 77.0 - - - +
17C LYS* 1.4 57.8 + - - +
19C HIS* 3.5 6.4 + - - +
20C PHE* 3.0 27.9 + - - +
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 2.8 43.5 + - + +
14C GLN* 3.5 29.1 + - - +
15C GLN 3.4 0.2 - - - -
16C ASN* 1.4 72.4 - - - +
18C GLU* 1.4 58.7 + - - +
20C PHE* 3.2 13.7 + - + +
21C GLN* 3.0 59.4 + - + +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLN* 3.2 14.0 + - - +
15C GLN* 3.7 7.2 - - - +
17C LYS* 1.4 74.6 - - - +
19C HIS* 1.3 60.1 + - - +
21C GLN* 3.3 9.9 + - - +
22C ASP* 2.9 41.3 + - - +
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Residues in contact with HIS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASN* 2.8 20.7 + - - +
15C GLN 3.2 15.1 + - - +
16C ASN* 3.6 12.3 - - - +
17C LYS 3.3 0.2 - - - -
18C GLU* 1.3 76.2 - - - +
20C PHE* 1.4 56.1 + - - +
22C ASP* 3.5 7.6 + - + +
23C GLU* 2.9 52.6 + - + +
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Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET* 3.6 22.0 - - + -
12B ILE* 4.0 5.8 - - + -
13B TYR* 3.6 45.5 - + + -
16B ASN* 3.4 22.2 + - + +
16C ASN 3.0 13.6 + - - +
17C LYS* 3.2 19.3 + - + +
19C HIS* 1.4 73.9 - - - +
21C GLN* 1.3 68.6 + - + +
23C GLU* 3.3 3.6 + - - +
24C CYS* 3.0 45.8 + - - +
49C TRP* 3.8 33.2 - + - -
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Residues in contact with GLN 21 (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 LYS* 3.0 48.5 + - - +
18C GLU* 3.8 7.9 - - - +
20C PHE* 1.3 85.6 - - + +
22C ASP* 1.3 61.5 + - - +
24C CYS 3.4 1.6 + - - -
25C THR* 3.0 34.7 + - - +
49C TRP* 3.6 61.2 - - + +
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 2.9 26.8 + - - +
19C HIS* 3.8 7.1 + - + +
21C GLN* 1.3 75.7 - - - +
23C GLU* 1.3 57.5 + - - +
25C THR* 2.9 10.6 + - - +
26C LYS* 2.9 31.9 + - - +
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.7 24.6 - - + +
15B GLN* 5.8 2.4 - - - +
16B ASN* 2.9 22.1 + - - -
19C HIS* 2.9 39.8 + - + +
20C PHE 3.3 5.8 + - - +
22C ASP* 1.3 72.1 - - - +
24C CYS* 1.4 64.2 + - - +
26C LYS* 3.7 5.8 + - - +
27C LEU* 3.2 24.1 + - - +
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Residues in contact with CYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET* 4.0 23.1 - - + -
12B ILE* 4.2 15.7 - - - -
20C PHE* 3.0 43.1 + - - +
21C GLN 3.6 5.2 - - - +
23C GLU* 1.4 73.7 - - - +
25C THR* 1.4 54.3 + - - +
27C LEU* 3.3 8.3 + - - +
28C LEU* 2.8 49.4 + - + +
47C VAL* 6.1 0.7 - - + -
49C TRP* 3.6 17.0 - - + -
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Residues in contact with THR 25 (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 3.0 14.4 + - - +
22C ASP* 2.9 25.2 + - - +
24C CYS* 1.4 71.8 - - - +
26C LYS* 1.3 60.5 + - - +
28C LEU* 3.1 2.0 + - - -
29C VAL* 2.7 45.1 + - - +
46C ASP* 4.6 11.7 - - - +
47C VAL* 4.2 16.6 - - + +
49C TRP* 3.6 21.5 - - + +
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Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP 2.9 21.9 + - - +
23C GLU* 3.8 7.2 - - - +
24C CYS 3.4 0.2 - - - -
25C THR* 1.3 74.0 + - - +
27C LEU* 1.3 60.6 + - - +
29C VAL 3.9 10.1 - - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.7 29.4 - - + -
12B ILE* 5.0 11.0 - - + -
23C GLU 3.2 15.7 + - - +
24C CYS* 3.6 6.7 - - - +
26C LYS* 1.3 78.6 - - - +
28C LEU* 1.3 71.1 + - + +
31C ASN* 3.8 19.4 + - - +
115C MET* 5.0 7.6 - - - +
118C ILE* 3.9 26.9 - - + +
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.6 25.8 - - + -
8B VAL* 6.0 1.8 - - + -
9B MET* 3.6 35.2 - - + -
24C CYS* 2.8 29.7 + - + +
25C THR* 4.2 1.3 - - - +
27C LEU* 1.3 85.8 - - + +
29C VAL* 1.4 56.4 + - - +
30C GLY 3.0 0.9 + - - -
31C ASN* 2.8 34.6 + - - +
33C VAL* 5.8 0.2 - - + -
44C ILE* 3.8 20.0 - - + +
47C VAL* 6.1 3.8 - - + -
87C LEU* 4.4 13.0 - - + -
115C MET* 3.7 25.1 - - + -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 2.7 28.4 + - - +
26C LYS* 3.9 11.5 - - - +
28C LEU* 1.4 68.7 - - - +
30C GLY* 1.3 57.8 + - - +
31C ASN 4.1 0.3 + - - -
44C ILE* 3.4 9.4 - - - -
45C ASP 3.6 22.9 - - - +
46C ASP* 4.4 8.7 - - - +
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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
------------------------------------------------------------
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