Contacts of the helix formed by residues 7 - 35 (chain C) in PDB entry 3ITX
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 7 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PHE* 4.4 3.5 + - - -
5C ARG 4.1 2.0 + - - -
6C ILE* 1.3 75.1 - - - +
8C GLN* 1.3 65.1 - - - +
9C ASP* 2.9 21.8 - - - +
10C VAL* 3.0 26.7 + - + +
11C VAL* 3.3 10.9 + - - +
409C SER* 5.5 1.0 - - - -
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PHE* 3.0 54.9 - - + +
6C ILE 3.3 2.5 + - - +
7C ALA* 1.3 71.6 - - - +
9C ASP* 1.3 56.8 + - - +
11C VAL* 3.3 10.1 + - - +
12C ALA* 3.0 29.6 + - - +
90C GLN* 5.4 1.8 - - - +
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Residues in contact with ASP 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 2.9 34.1 - - - +
8C GLN* 1.3 78.4 - - - +
10C VAL* 1.3 61.9 + - - +
12C ALA* 3.8 6.0 - - - +
13C ARG* 3.0 53.7 + - - +
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.7 3.6 - - + -
7C ALA* 3.0 18.1 + - + +
9C ASP* 1.3 88.8 - - - +
11C VAL* 1.3 66.2 + - - +
13C ARG* 3.2 22.6 + - - +
14C GLU* 2.9 33.6 + - + +
405C THR* 4.1 26.5 - - + +
408C ALA* 4.3 7.4 - - + +
409C SER* 4.1 24.2 - - - +
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.9 18.6 - - + -
7C ALA 3.3 12.5 + - - +
8C GLN* 3.3 10.1 + - - +
10C VAL* 1.3 77.0 - - - +
12C ALA* 1.3 62.3 + - - +
14C GLU* 3.9 1.0 - - - +
15C ASN* 3.0 48.0 + - - +
90C GLN* 4.0 15.3 - - - +
91C LEU* 4.1 12.3 - - + -
397C GLY 4.3 9.0 - - - +
398C GLY 3.7 18.6 - - - +
399C ALA* 4.5 4.3 - - - -
405C THR* 4.0 9.0 - - + -
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN 3.0 16.8 + - - +
9C ASP* 3.8 6.7 - - - +
11C VAL* 1.3 77.6 - - - +
13C ARG* 1.3 57.8 + - - +
15C ASN* 3.2 7.1 + - - +
16C ASP* 2.8 42.2 + - - +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 3.0 42.1 + - - +
10C VAL* 3.7 23.7 - - - +
12C ALA* 1.3 78.0 - - - +
14C GLU* 1.3 71.0 + - - +
16C ASP* 3.4 7.7 + - - +
17C ARG* 3.1 45.2 + - - +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 2.9 23.4 + - + +
11C VAL 4.1 1.3 - - - +
13C ARG* 1.3 85.3 + - - +
15C ASN* 1.3 61.5 - - - +
17C ARG* 3.2 28.9 + - - -
18C ARG* 2.8 60.0 + - - +
400C VAL* 5.1 0.2 - - - +
401C ASP 5.8 0.6 + - - -
404C ALA 5.1 0.7 - - - +
405C THR* 3.4 31.0 - - - +
408C ALA* 3.9 31.3 - - + +
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Residues in contact with ASN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 3.0 33.2 + - - +
12C ALA* 3.2 6.2 + - - +
14C GLU* 1.3 76.1 - - - +
16C ASP* 1.3 56.6 + - - +
17C ARG 3.1 1.3 - - - -
18C ARG* 3.0 3.6 + - - +
19C ALA* 2.7 37.4 + - - +
394C ARG* 4.5 16.6 + - + +
398C GLY 3.3 20.4 + - - -
399C ALA* 3.5 5.3 - - - +
400C VAL* 2.8 44.2 + - + +
401C ASP 4.7 0.3 + - - -
405C THR* 4.8 0.5 + - - -
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Residues in contact with ASP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 2.8 31.4 + - - +
13C ARG* 3.8 6.5 + - - +
15C ASN* 1.3 79.2 - - - +
17C ARG* 1.3 61.9 + - - +
18C ARG 3.2 0.7 + - - -
19C ALA* 3.4 19.3 + - - +
20C SER* 4.6 2.4 + - - -
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Residues in contact with ARG 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 3.1 37.9 + - - +
14C GLU* 3.2 36.3 + - - +
15C ASN 3.1 0.2 - - - -
16C ASP* 1.3 78.1 - - - +
18C ARG* 1.3 77.8 + - + +
20C SER* 5.3 2.5 + - - -
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 2.8 60.3 + - - +
15C ASN 3.0 4.6 + - - +
17C ARG* 1.3 96.7 - - + +
19C ALA* 1.3 63.2 + - - +
20C SER 3.3 2.9 + - - -
21C ALA* 3.5 10.9 + - + +
22C LEU* 3.1 23.9 + - - +
400C VAL* 4.0 20.0 - - + -
401C ASP* 3.6 30.7 + - - +
404C ALA* 3.4 26.2 - - - +
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASN 2.7 15.5 + - - +
16C ASP* 3.4 17.7 + - - +
18C ARG* 1.3 77.8 - - - +
20C SER* 1.3 57.8 + - - +
22C LEU* 3.3 9.5 + - - +
23C LYS* 2.9 31.4 + - - +
394C ARG* 5.3 9.4 - - - +
400C VAL* 5.6 0.9 - - - -
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP 4.6 2.5 + - - -
17C ARG 5.3 2.2 + - - -
18C ARG 3.3 0.6 - - - -
19C ALA* 1.3 80.6 - - - +
21C ALA* 1.3 62.1 + - - +
23C LYS* 3.4 7.8 + - - +
24C GLU* 3.3 27.0 + - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 4.5 21.1 - - + +
18C ARG* 3.5 12.3 + - + +
20C SER* 1.3 76.3 - - - +
22C LEU* 1.3 65.6 + - - +
24C GLU* 3.2 9.0 + - - +
25C ASP* 3.0 34.3 + - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG 3.1 18.2 + - - +
19C ALA* 3.6 5.4 - - - +
21C ALA* 1.3 75.3 - - - +
23C LYS* 1.3 60.7 + - - +
25C ASP* 4.6 3.8 - - + +
26C TYR* 2.8 37.8 + - + +
387C PRO* 3.7 34.1 - - + +
390C ALA* 3.8 11.0 - - + -
391C GLU* 3.5 35.0 - - + +
394C ARG* 4.2 8.7 - - - +
400C VAL* 4.0 32.1 - - + -
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 2.9 17.6 + - - +
20C SER* 3.5 9.0 - - - +
21C ALA 3.3 0.2 - - - -
22C LEU* 1.3 77.7 - - - +
24C GLU* 1.3 64.3 + - - +
26C TYR* 3.8 4.1 - - - +
27C GLU* 2.8 70.3 + - + +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 3.8 31.0 + - - +
20C SER* 3.3 16.7 + - - +
21C ALA* 3.2 8.9 + - - +
22C LEU 3.2 0.4 - - - -
23C LYS* 1.3 85.4 + - - +
25C ASP* 1.3 63.5 + - - +
27C GLU* 3.8 16.3 - - - +
28C ALA* 3.0 24.9 + - - +
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Residues in contact with ASP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 2.8 25.0 + - - +
35B ARG* 2.8 28.1 + - - -
21C ALA* 3.0 26.7 + - - +
22C LEU* 4.0 5.7 + - + +
24C GLU* 1.3 75.5 - - - +
26C TYR* 1.3 57.2 + - - +
28C ALA* 3.7 6.2 - - - +
29C LEU* 2.9 30.5 + - - +
387C PRO* 3.7 23.3 - - + +
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 2.8 22.7 + - + +
23C LYS* 3.8 5.2 - - - +
25C ASP* 1.3 78.6 - - - +
27C GLU* 1.3 63.7 + - + +
29C LEU* 3.4 1.0 + - - -
30C GLY* 2.8 25.1 + - - -
40C ILE* 3.6 36.7 - - + +
41C GLU* 2.8 31.2 + - - -
44C THR* 2.8 27.0 + - - +
387C PRO* 3.6 30.2 - - + +
388C ILE* 4.1 3.6 - - - -
391C GLU* 3.6 28.9 - - + +
395C ARG* 3.9 9.3 + - - -
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LYS* 2.8 57.1 + - + +
24C GLU* 3.8 17.6 - - - +
26C TYR* 1.3 80.0 - - + +
28C ALA* 1.3 60.3 + - - +
30C GLY* 3.3 2.6 + - - +
31C ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 4.5 24.0 - - + +
35B ARG* 6.1 1.3 - - - +
24C GLU 3.0 18.2 + - - +
25C ASP* 3.7 8.3 - - - +
27C GLU* 1.3 77.3 - - - +
29C LEU* 1.3 60.4 + - - +
31C ALA* 3.4 5.9 + - - +
32C ASN* 3.1 22.5 + - - +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASP 2.9 18.2 + - - +
26C TYR 3.8 3.6 - - - +
28C ALA* 1.3 73.6 - - - +
30C GLY* 1.3 59.7 + - - +
32C ASN* 3.2 10.9 + - + +
33C LEU* 2.8 40.8 + - + +
40C ILE* 4.0 7.4 - - + -
383C THR* 3.7 27.4 - - + -
384C ASP 3.5 22.0 - - - +
385C VAL* 4.2 2.7 - - + -
387C PRO* 4.1 15.3 - - + -
388C ILE* 3.7 33.2 - - + -
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR 2.8 17.6 + - - -
27C GLU* 3.3 3.3 + - - -
28C ALA 3.2 0.4 - - - -
29C LEU* 1.3 78.4 - - - +
31C ALA* 1.3 54.9 + - - +
33C LEU* 3.4 2.4 + - - +
34C ALA* 3.0 28.9 + - - +
38C VAL 4.7 0.7 - - - +
40C ILE* 3.7 30.3 + - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 4.5 14.6 - - - +
27C GLU 3.0 16.3 + - - +
28C ALA* 3.7 6.3 - - - +
29C LEU 3.3 0.2 - - - -
30C GLY* 1.3 73.2 - - - +
32C ASN* 1.3 65.8 + - - +
34C ALA* 3.3 8.6 + - - +
35C ARG* 3.2 28.6 + - - +
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Residues in contact with ASN 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 3.4 25.0 + - - +
384B ASP* 5.7 3.2 + - - -
28C ALA 3.1 15.2 + - - +
29C LEU* 3.2 17.4 + - + +
31C ALA* 1.3 77.3 - - - +
33C LEU* 1.3 63.0 + - - +
35C ARG* 3.2 33.8 + - - +
36C ARG* 2.9 42.7 + - - +
383C THR* 6.1 0.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 2.8 37.4 + - + +
30C GLY* 3.9 3.6 - - - +
32C ASN* 1.3 74.0 - - - +
34C ALA* 1.3 64.6 + - - +
36C ARG* 2.9 39.7 + - - +
38C VAL* 2.8 44.5 + - + +
40C ILE* 3.9 32.5 - - + +
43C VAL* 4.9 0.2 - - + -
355C LEU* 3.9 32.5 - - + -
388C ILE* 4.2 11.0 - - + -
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY 3.0 17.6 + - - +
31C ALA* 3.5 10.3 - - - +
32C ASN 3.2 0.2 - - - -
33C LEU* 1.3 76.4 - - - +
35C ARG* 1.3 58.1 + - + +
36C ARG 3.0 0.2 - - - -
37C GLY* 3.0 18.9 + - - -
38C VAL 3.4 10.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.7 28.3 + - - +
24B GLU* 4.1 30.3 + - - +
25B ASP* 2.7 44.5 + - - -
31C ALA 3.2 14.8 + - - +
32C ASN* 3.2 22.6 + - - +
33C LEU 3.2 0.8 - - - -
34C ALA* 1.3 76.7 - - + +
36C ARG* 1.3 61.3 + - + +
37C GLY 3.3 1.3 + - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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