Contacts of the helix formed by residues 18 - 43 (chain D) in PDB entry 1VF5
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 PHE 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D ARG* 3.0 49.4 - - + -
16D ARG* 2.5 52.7 + - + +
17D GLN* 1.3 78.3 - - + +
19D MET* 1.3 57.4 + - - -
20D ASN 3.6 0.9 - - - -
21D LEU* 3.3 31.7 - - + +
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Residues in contact with MET 19 (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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271C MET* 4.1 8.3 - - + +
274C LEU* 4.5 9.6 - - + -
275C LYS* 3.6 44.0 - - + +
279C VAL* 4.9 8.7 - - + -
16D ARG 3.4 10.6 + - - +
17D GLN* 3.2 0.6 - - - -
18D PHE* 1.3 77.6 - - - +
20D ASN* 1.3 54.3 + - - +
21D LEU 2.4 20.2 + - - -
22D LEU* 2.6 61.9 + - + +
27H ASN* 4.7 26.9 - - - +
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Residues in contact with ASN 20 (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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275C LYS* 3.4 37.6 - - + +
17D GLN* 2.8 30.4 + - - +
19D MET* 1.3 79.2 - - - +
21D LEU* 1.3 75.2 + - - +
22D LEU 2.6 14.4 + - - +
23D ALA* 3.5 13.7 - - + +
24D PHE* 3.0 50.7 + - + +
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Residues in contact with LEU 21 (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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17D GLN 5.4 0.2 - - - +
18D PHE* 3.3 31.0 - - + +
19D MET 2.4 13.3 + - - +
20D ASN* 1.3 87.0 + - - +
22D LEU* 1.3 55.2 + - - +
24D PHE* 5.5 0.7 - - - -
25D GLY* 4.3 9.9 - - - +
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Residues in contact with LEU 22 (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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271C MET* 3.0 38.6 - - + -
19D MET* 2.6 42.8 + - + +
20D ASN 2.6 1.4 - - - -
21D LEU* 1.3 80.3 - - - +
23D ALA* 1.3 76.2 + - - +
25D GLY* 3.3 5.8 - - - +
26D THR* 2.8 38.9 + - + +
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Residues in contact with ALA 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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268C ALA 4.5 0.2 - - - +
271C MET* 3.6 38.1 - - + +
272C LEU* 4.5 7.2 - - + +
275C LYS* 4.3 7.4 - - + -
20D ASN* 3.1 18.0 + - + +
22D LEU* 1.3 84.9 - - + +
24D PHE* 1.3 65.9 + - + +
26D THR* 3.3 3.5 + - - -
27D VAL* 3.0 33.3 + - - +
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Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PL9 5.0 28.7 - - + -
38B TYR* 4.3 32.3 - + - -
41B PRO* 6.4 0.2 - - + -
307B OPC 5.1 12.1 - - + -
272C LEU* 4.5 16.6 - - + -
275C LYS* 4.7 3.1 - - + -
276C LYS* 4.5 15.7 - - + -
20D ASN* 3.0 46.0 + - + +
21D LEU* 5.5 1.1 - - + -
23D ALA* 1.3 76.6 - - + +
25D GLY* 1.3 62.7 + - - +
27D VAL* 3.8 14.3 - - + +
28D THR* 2.9 31.8 + - - +
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Residues in contact with GLY 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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20D ASN 4.0 0.2 + - - -
21D LEU 4.3 6.4 - - - -
22D LEU* 3.1 18.3 + - - +
23D ALA 2.9 1.6 - - - -
24D PHE* 1.3 81.7 - - - +
26D THR* 1.3 62.0 + - - +
28D THR* 3.5 4.5 + - - -
29D GLY* 3.1 16.5 + - - -
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Residues in contact with THR 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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264C LEU* 3.7 20.0 - - + +
267C LEU* 4.4 7.0 + - + -
268C ALA* 3.0 25.2 + - - -
271C MET* 4.5 19.6 - - + +
22D LEU* 2.8 24.7 + - + +
23D ALA 3.3 6.9 + - - -
25D GLY* 1.3 69.2 - - - -
27D VAL* 1.3 66.4 + - - +
29D GLY* 3.0 5.5 + - - +
30D VAL* 2.9 23.9 + - - +
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Residues in contact with VAL 27 (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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305A PL9 4.1 27.4 - - + -
41B PRO* 5.8 6.3 - - + -
45B MET* 3.6 29.1 - - + +
268C ALA* 4.1 13.9 - - - +
272C LEU* 4.3 17.5 - - + -
23D ALA 3.0 24.2 + - - +
24D PHE* 3.9 12.8 - - + -
25D GLY 3.2 0.2 - - - -
26D THR* 1.3 73.2 + - - +
28D THR* 1.3 58.4 + - - +
29D GLY 2.8 3.8 - - - -
30D VAL* 2.7 26.2 + - - +
31D ALA* 2.9 11.4 + - + +
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Residues in contact with THR 28 (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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305A PL9 3.2 44.6 - - + +
24D PHE* 2.9 20.7 + - - +
25D GLY* 3.7 4.5 - - - -
27D VAL* 1.3 79.7 - - - +
29D GLY* 1.3 62.1 + - - +
31D ALA* 3.1 9.3 + - - +
32D LEU* 3.0 42.9 + - + +
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Residues in contact with GLY 29 (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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264C LEU* 3.6 15.3 - - - +
25D GLY 3.1 10.3 + - - -
26D THR* 3.0 11.7 + - - -
27D VAL 2.8 2.6 - - - -
28D THR* 1.3 78.7 - - - +
30D VAL* 1.3 60.4 + - - -
32D LEU* 3.5 9.0 + - - +
33D GLY* 3.1 18.0 + - - -
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Residues in contact with VAL 30 (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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45B MET* 3.7 21.5 - - + -
48B PHE* 5.8 1.3 - - + -
261C PHE* 3.3 29.4 - - + -
264C LEU* 3.7 17.0 - - + -
265C VAL* 3.9 20.9 - - + -
268C ALA* 3.7 22.2 - - + -
26D THR 2.9 15.5 + - - +
27D VAL 2.7 12.3 + - - +
29D GLY* 1.3 70.8 - - - -
31D ALA* 1.3 63.7 + - - +
33D GLY* 3.1 2.6 + - - -
34D ALA* 2.9 23.1 + - + +
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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
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305A PL9 4.3 18.8 - - + -
45B MET* 5.3 0.6 - - + +
27D VAL* 2.9 10.3 + - + +
28D THR* 3.2 18.6 - - - +
30D VAL* 1.3 78.8 - - - +
32D LEU* 1.3 58.7 + - + +
34D ALA* 3.4 5.6 + - - +
35D LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 32 (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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305A PL9 5.5 9.0 - - + -
28D THR* 3.0 36.6 + - + +
29D GLY* 4.0 7.2 - - - +
31D ALA* 1.3 74.4 - - + +
33D GLY* 1.3 62.7 + - - +
35D LEU* 2.9 16.7 + - + +
36D TYR* 2.7 33.7 + - - +
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Residues in contact with GLY 33 (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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261C PHE* 4.8 11.0 - - - -
264C LEU* 6.0 0.9 - - - -
29D GLY 3.1 9.6 + - - -
30D VAL 3.1 7.0 + - - -
32D LEU* 1.3 80.0 - - - +
34D ALA* 1.3 56.6 + - - +
36D TYR* 3.5 5.0 + - - +
37D PRO* 3.1 23.2 - - - +
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Residues in contact with ALA 34 (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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48B PHE* 3.7 35.3 - - + -
261C PHE* 4.3 9.0 - - + -
30D VAL* 2.9 15.9 + - + +
31D ALA* 3.9 4.9 - - - +
33D GLY* 1.3 76.2 - - - +
35D LEU* 1.3 59.5 + - - +
36D TYR 3.4 0.2 - - - -
37D PRO* 3.5 16.3 - - - +
38D LEU* 4.1 9.4 + - - +
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Residues in contact with LEU 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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305A PL9 6.3 2.2 - - + -
31D ALA 3.0 17.6 + - - +
32D LEU* 2.9 19.6 + - + +
34D ALA* 1.3 79.1 - - - +
36D TYR* 1.3 65.5 + - - +
37D PRO 3.5 0.2 - - - -
38D LEU* 3.2 7.5 + - + -
39D VAL* 3.0 34.2 + - + +
306D OPC 3.6 31.4 - - - +
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Residues in contact with TYR 36 (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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78A PHE* 4.2 15.0 - + - -
32D LEU 2.7 14.3 + - - +
33D GLY* 3.7 5.4 - - - +
35D LEU* 1.3 76.7 - - - +
37D PRO* 1.3 73.1 - - + +
39D VAL* 3.0 11.3 + - + +
40D LYS* 2.9 64.2 + - + +
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Residues in contact with PRO 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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78A PHE* 3.3 53.9 - - + -
81A LEU* 5.3 10.5 - - + -
82A ILE* 5.1 2.9 - - + -
33D GLY 3.1 17.3 - - - +
34D ALA* 3.5 13.5 - - - +
36D TYR* 1.3 95.6 - - + +
38D LEU* 1.3 57.8 + - - +
41D TYR* 2.7 31.0 + - - +
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Residues in contact with LEU 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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49A ALA* 5.2 15.5 - - + +
50A THR* 6.0 4.0 - - + -
53A ALA* 4.3 18.8 - - + -
82A ILE* 4.5 17.2 - - + +
34D ALA 4.1 10.1 - - - +
35D LEU* 3.2 14.6 + - + +
36D TYR 3.2 0.8 - - - -
37D PRO* 1.3 80.8 - - - +
39D VAL* 1.3 60.8 + - - +
41D TYR* 3.2 14.7 - - + +
42D PHE* 3.2 35.5 - - + -
306D OPC 2.7 35.7 - - - +
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Residues in contact with VAL 39 (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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35D LEU* 3.0 38.4 - - + +
36D TYR* 3.0 9.4 + - + +
38D LEU* 1.3 75.1 - - - +
40D LYS* 1.3 66.8 + - + +
42D PHE* 3.2 8.9 + - - +
43D ILE* 3.0 34.8 + - + +
306D OPC 3.5 29.4 - - - -
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Residues in contact with LYS 40 (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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77A SER* 3.5 18.1 + - - -
78A PHE* 3.4 32.5 - - + -
36D TYR* 2.9 59.9 + - + +
37D PRO 3.3 1.1 + - - +
39D VAL* 1.3 76.3 - - + +
41D TYR* 1.3 68.1 + - - +
43D ILE* 2.9 38.8 + - + +
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Residues in contact with TYR 41 (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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53A ALA* 2.3 51.0 + - + -
54A MET* 3.3 10.7 - - - +
57A TYR* 2.7 58.9 + + - +
72A ILE* 4.7 6.2 - - + +
76A VAL* 3.4 22.6 - - + +
77A SER* 3.0 21.0 + - - +
79A GLY* 3.9 18.2 - - - -
82A ILE* 3.7 28.9 - - + -
37D PRO 2.7 17.5 + - - +
38D LEU* 3.2 11.4 - - + +
40D LYS* 1.3 77.1 - - - +
42D PHE* 1.3 67.4 + + - +
43D ILE 3.4 1.9 + - - +
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Residues in contact with PHE 42 (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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52A PHE* 3.7 26.5 - + - -
53A ALA* 4.2 13.9 - - + -
56A PHE* 3.6 46.0 - + - -
57A TYR* 4.0 2.2 - + - -
38D LEU* 3.2 35.1 + - + -
39D VAL 3.2 8.4 + - - +
40D LYS 3.1 0.8 - - - -
41D TYR* 1.3 88.0 - + - +
43D ILE* 1.3 59.7 + - - +
44D PRO* 3.0 13.7 - - - +
306D OPC 3.3 57.7 - - - -
168N LEU* 3.1 11.0 - - + +
182N ARG* 3.2 13.0 + - - -
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Residues in contact with ILE 43 (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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57A TYR* 4.2 0.2 + - - -
77A SER* 4.3 9.6 + - - +
39D VAL* 3.0 36.3 - - + +
40D LYS* 2.9 31.0 + - + +
41D TYR 3.7 3.9 - - - +
42D PHE* 1.3 76.3 - - + +
44D PRO* 1.3 78.4 - - + +
45D PRO* 4.4 0.9 - - - +
306D OPC 4.9 2.5 - - - -
164N LEU* 4.2 24.2 - - + -
168N LEU* 3.9 14.4 - - + -
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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
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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