Contacts of the helix formed by residues 22 - 49 (chain D) in PDB entry 2Q7N
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 LEU 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D CYS* 4.8 6.1 - - + -
19D HIS 5.1 7.4 - - - +
20D ASN* 3.4 7.5 + - - +
21D ASN* 1.3 88.7 - - - +
23D MET* 1.3 60.0 + - + +
24D ASN 3.1 0.7 - - - -
25D GLN* 2.6 35.3 + - - +
26D ILE* 2.8 20.5 + - + +
128D ASN* 4.0 17.0 - - - +
131D CYS* 3.9 20.2 - - + -
132D ARG* 3.9 47.1 - - + +
135D SER* 5.9 4.9 - - - +
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASN* 2.6 12.0 + - - +
22D LEU* 1.3 75.4 - - - +
24D ASN* 1.3 62.1 + - - +
25D GLN 3.1 1.2 + - - -
26D ILE* 3.2 38.1 - - + +
27D ARG* 3.3 36.8 + - - +
76D GLU* 3.4 37.0 - - + +
80D LEU* 4.4 4.9 - - + -
132D ARG* 3.3 47.1 - - - +
180D PHE* 4.8 15.9 - - + +
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Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN* 3.4 36.4 + - + +
22D LEU 3.1 0.6 - - - -
23D MET* 1.3 78.1 - - - +
25D GLN* 1.3 56.7 + - - +
27D ARG* 3.8 26.3 + - - +
28D SER* 3.4 24.6 + - - -
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Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D HIS* 4.4 23.2 - - - +
20D ASN 3.6 22.2 + - - -
21D ASN* 5.2 1.8 - - - +
22D LEU* 2.6 24.8 + - - +
24D ASN* 1.3 69.9 - - - +
26D ILE* 1.3 53.4 + - - +
27D ARG 2.8 14.2 + - - -
28D SER* 3.0 9.6 + - - -
29D GLN* 2.8 34.4 + - + +
128D ASN* 4.1 28.9 + - - +
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Residues in contact with ILE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU 2.8 17.6 + - - +
23D MET* 3.2 49.6 - - + +
25D GLN* 1.3 71.9 - - - +
27D ARG* 1.3 55.5 + - - +
29D GLN* 4.1 9.2 + - - +
30D LEU* 2.9 32.2 + - + +
80D LEU* 3.9 20.6 - - + -
83D LEU* 6.1 0.2 - - + -
125D LEU* 3.9 8.7 - - + +
128D ASN* 3.9 23.1 - - + -
129D VAL* 3.3 31.0 - - + +
132D ARG* 5.5 3.1 - - + -
180D PHE* 4.6 12.2 - - + -
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Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D MET* 3.3 46.5 + - - +
24D ASN* 3.8 23.6 + - - +
25D GLN 2.8 1.2 + - - -
26D ILE* 1.3 76.9 - - - +
28D SER* 1.3 54.8 + - - +
29D GLN 2.8 14.0 + - - -
30D LEU* 3.8 3.7 - - - +
31D ALA* 2.8 31.5 + - + +
177D ALA 5.5 5.4 - - - +
180D PHE* 4.1 32.9 + - - +
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASN 3.4 15.8 + - - -
25D GLN* 3.0 5.8 + - - -
27D ARG* 1.3 75.7 - - - +
29D GLN* 1.3 58.2 + - - +
31D ALA* 4.7 5.6 - - - -
32D GLN* 3.5 25.8 + - - +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLN* 2.8 27.7 + - + +
26D ILE* 4.1 4.9 - - - -
27D ARG 2.8 0.4 + - - -
28D SER* 1.3 79.1 - - - +
30D LEU* 1.3 55.4 + - - +
31D ALA 3.2 0.9 - - - -
32D GLN* 2.9 13.9 + - - +
33D LEU* 2.8 34.5 + - - +
121D ILE* 3.6 24.1 + - + +
124D GLY* 4.3 4.9 - - - -
125D LEU* 3.0 43.8 - - + +
128D ASN* 3.6 17.4 + - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 2.9 18.9 + - + +
27D ARG* 3.8 4.5 - - - +
29D GLN* 1.3 77.9 - - - +
31D ALA* 1.3 58.7 + - - +
33D LEU* 3.1 6.4 + - + +
34D ASN* 2.9 28.8 + - - +
83D LEU* 3.9 14.6 - - + -
125D LEU* 3.5 34.6 - - + +
173D ILE* 4.1 17.2 - - + +
176D LEU* 3.3 42.4 - - + +
177D ALA* 3.5 9.9 - - - +
180D PHE* 3.7 20.4 - - + +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG* 2.8 20.6 + - + +
28D SER* 4.7 5.2 - - - -
30D LEU* 1.3 78.6 - - - +
32D GLN* 1.3 59.1 + - - +
34D ASN* 3.7 9.1 + - - +
35D GLY* 3.3 16.5 + - - -
177D ALA* 4.6 11.1 - - + +
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER 3.5 18.6 + - - +
29D GLN* 2.9 23.9 + - - +
31D ALA* 1.3 76.3 - - - +
33D LEU* 1.3 64.2 + - - +
35D GLY* 2.9 15.0 + - - -
36D SER* 3.5 6.6 + - - -
121D ILE* 3.9 26.8 - - + +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN 2.8 11.5 + - - +
30D LEU 3.1 8.9 + - - +
32D GLN* 1.3 67.8 - - - +
34D ASN* 1.3 55.9 + - - +
35D GLY 2.7 14.9 + - - -
36D SER* 3.2 6.5 + - - +
37D ALA 3.0 19.1 + - - -
118D THR* 3.6 22.2 - - + +
121D ILE* 3.5 37.4 - - + +
122D LEU* 3.8 28.5 - - + +
125D LEU* 4.5 14.1 - - + -
169D TYR* 3.3 23.0 + - + +
173D ILE* 3.6 23.8 - - + -
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU 2.9 12.1 + - - +
31D ALA* 3.8 7.6 - - - +
33D LEU* 1.3 79.3 - - - +
35D GLY* 1.3 65.4 + - - +
37D ALA* 3.2 11.1 - - - +
38D ASN* 4.6 0.7 + - - +
170D LYS 4.6 1.0 + - - -
173D ILE* 3.4 23.6 - - + +
174D ALA* 2.9 45.3 - - - +
177D ALA* 4.1 11.6 - - + +
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Residues in contact with GLY 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA 3.3 8.1 + - - -
32D GLN 2.9 9.0 + - - -
33D LEU 2.7 7.1 + - - -
34D ASN* 1.3 78.8 - - - +
36D SER* 1.3 71.5 + - - +
37D ALA* 4.0 0.3 - - - +
38D ASN* 4.0 4.2 + - - +
39D ALA* 5.3 0.5 - - - +
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Residues in contact with SER 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN 3.5 6.2 + - - -
33D LEU* 3.2 11.2 + - - +
35D GLY* 1.3 75.3 - - - +
37D ALA* 1.3 79.5 + - - +
39D ALA* 2.8 22.1 + - - +
40D LEU* 4.3 2.6 - - - +
114D LYS* 4.0 29.8 - - - +
118D THR* 3.2 24.1 + - - +
169D TYR* 3.9 2.6 + - - -
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU 3.0 7.6 + - - +
34D ASN* 3.2 22.9 - - - +
36D SER* 1.3 77.6 + - - +
38D ASN* 1.3 69.1 + - - +
40D LEU* 2.9 19.4 + - - +
41D PHE* 3.0 11.2 + - - +
169D TYR* 3.8 20.9 - - + -
170D LYS* 4.4 9.2 - - + +
173D ILE* 3.8 22.0 - - + -
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Residues in contact with ASN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN 5.6 0.7 - - - +
35D GLY 4.0 4.0 + - - +
36D SER 2.8 3.7 + - - +
37D ALA* 1.3 75.5 - - - +
39D ALA* 1.3 59.8 + - - +
41D PHE* 2.9 11.7 + - - +
42D ILE* 2.7 58.2 + - - +
170D LYS* 4.4 25.7 - - + +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLY 5.3 0.4 - - - +
36D SER* 2.8 16.6 + - - +
38D ASN* 1.3 79.1 + - - +
40D LEU* 1.3 51.4 + - - +
42D ILE* 3.2 7.8 + - - +
43D LEU* 2.7 47.1 + - + +
114D LYS* 3.9 16.4 - - - +
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER 3.7 2.2 + - - -
37D ALA* 2.9 17.1 + - - +
39D ALA* 1.3 73.9 - - - +
41D PHE* 1.3 67.1 + - + +
43D LEU* 2.9 9.1 + - - +
44D TYR* 2.9 20.6 + - - +
94D LEU* 5.5 2.0 - - + -
111D LEU* 4.2 2.7 - - + +
114D LYS* 3.4 44.8 - - + +
115D LEU* 3.6 17.9 - - + +
118D THR* 3.3 31.4 - - + +
166D LEU* 3.1 45.1 - - + -
169D TYR* 4.8 4.9 - - + -
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ALA 3.0 6.8 + - - +
38D ASN* 2.9 15.3 + - - +
40D LEU* 1.3 89.3 - - + +
42D ILE* 1.3 80.0 + - + +
44D TYR* 3.0 14.8 + - + +
45D TYR* 3.1 37.3 + + - -
56D LEU* 4.3 21.5 - - + -
60D CYS 4.2 11.9 - - - -
163D CYS* 4.5 14.4 - - - -
166D LEU* 4.0 9.6 - - + -
167D GLY* 3.9 35.4 - - - -
169D TYR* 6.3 0.7 - - + -
170D LYS* 4.6 26.2 - - + -
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASN* 2.7 42.0 + - - +
39D ALA* 3.6 9.0 - - - +
41D PHE* 1.3 80.7 - - + +
43D LEU* 1.3 62.4 + - + +
44D TYR 3.1 0.2 + - - -
45D TYR* 3.2 49.5 - - + +
46D THR* 2.6 29.3 + - - +
56D LEU* 5.8 0.9 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 2.7 30.1 + - + +
40D LEU* 2.9 15.2 + - - +
42D ILE* 1.3 76.3 - - + +
44D TYR* 1.3 59.9 + - - +
46D THR* 3.5 7.5 + - - +
47D ALA* 3.5 18.0 + - - +
108D ALA* 6.3 0.7 - - + -
110D SER* 4.2 28.0 - - - +
111D LEU* 4.0 27.5 - - + +
114D LYS* 4.8 9.4 - - + -
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Residues in contact with TYR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU 2.9 10.9 + - - +
41D PHE* 3.0 8.5 + + + +
43D LEU* 1.3 69.4 - - - +
45D TYR* 1.3 69.4 + - - +
46D THR 3.1 1.6 - - - -
47D ALA* 2.9 12.8 + - - +
48D GLN* 3.1 42.7 + - + -
97D ILE* 3.7 14.7 - - + +
100D ASP* 5.2 0.3 + - - -
101D GLN* 3.1 40.1 + - + -
111D LEU* 3.9 24.0 - - + -
115D LEU* 4.8 2.9 - - + -
158D LYS 3.3 19.6 + - - -
159D LYS 3.4 4.0 + - - -
162D GLY* 3.6 7.5 - - - -
163D CYS* 3.0 40.6 - - + -
166D LEU* 3.7 24.0 - - + -
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Residues in contact with TYR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 3.1 32.5 + + - +
42D ILE* 3.2 61.7 - - + +
44D TYR* 1.3 82.4 - - - +
46D THR* 1.3 73.1 + - + +
48D GLN* 3.2 23.9 + - - +
52D PHE* 3.6 15.2 - - + +
53D PRO* 3.7 38.2 - - + +
56D LEU* 3.8 23.0 - - + +
163D CYS* 3.6 23.1 - - - -
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 2.6 30.5 + - - +
43D LEU* 3.5 10.9 + - - +
44D TYR 3.1 0.2 - - - -
45D TYR* 1.3 91.4 - - + +
47D ALA* 1.3 63.8 + - - +
49D GLY* 3.1 17.0 + - - -
53D PRO* 5.3 6.9 - - + +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLU* 5.0 1.9 - - - +
262C SER* 3.4 8.1 - - - -
43D LEU 3.5 10.0 + - - +
44D TYR 2.9 9.5 + - - +
46D THR* 1.3 81.4 - - - +
48D GLN* 1.3 64.8 + - - +
49D GLY* 3.2 2.1 + - - -
105D ASN* 2.8 41.6 + - + +
108D ALA* 5.3 8.1 - - + -
111D LEU* 4.4 11.9 - - + -
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Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C SER* 3.2 5.9 + - - -
263C GLY 4.5 0.2 - - - +
265C ASN* 3.0 8.5 + - - -
44D TYR* 3.1 55.0 + - + +
45D TYR* 3.5 11.4 - - - +
46D THR 3.1 1.0 - - - -
47D ALA* 1.3 83.4 - - - +
49D GLY* 1.3 58.5 + - - +
52D PHE* 3.7 22.4 - - + -
101D GLN* 2.8 43.3 + - - +
105D ASN* 4.7 0.7 - - - -
159D LYS* 2.7 53.4 + - + +
163D CYS* 5.1 0.2 - - - -
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Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLU* 4.3 15.0 - - - -
263C GLY 5.4 1.6 - - - -
265C ASN* 2.9 10.4 + - - -
45D TYR 3.8 1.4 + - - -
46D THR 3.1 14.1 + - - -
47D ALA 3.1 3.0 - - - -
48D GLN* 1.3 77.3 - - - +
50D GLU* 1.3 61.0 + - - -
52D PHE* 2.7 30.2 + - - +
53D PRO* 4.3 4.0 - - - -
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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
------------------------------------------------------------
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