Contacts of the helix formed by residues 18 - 44 (chain Y) in PDB entry 1OCR
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 LYS 18 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473N TRP* 2.7 34.5 + - + +
477N ALA* 3.5 41.3 - - + +
15Y VAL 4.8 2.3 + - - -
16Y GLU 4.1 2.2 + - - -
17Y ASN* 1.3 72.9 + - - +
19Y TRP* 1.3 86.6 + - + +
21Y LEU* 3.6 8.4 - - - +
22Y LEU 3.0 7.1 + - - -
8Z THR* 2.8 30.2 + - - -
9Z PRO 3.3 11.5 + - - -
10Z THR* 3.0 19.0 + - - +
14Z GLU* 3.6 23.1 + - - +
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Residues in contact with TRP 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473N TRP* 3.9 14.8 - + - -
17Y ASN* 2.7 20.0 + - - +
18Y LYS* 1.3 92.9 - - + +
20Y ARG* 1.3 62.3 + - - +
21Y LEU 3.2 1.1 - - - -
22Y LEU* 3.3 33.8 - - + +
23Y ALA* 3.1 19.9 + - - +
14Z GLU* 3.5 58.0 + - + -
17Z ILE* 3.9 25.1 - - + -
18Z GLY 4.4 0.4 - - - -
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Residues in contact with ARG 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y SER* 3.7 33.0 + - - +
17Y ASN* 3.0 29.7 + - + +
19Y TRP* 1.3 74.2 - - - +
21Y LEU* 1.3 65.3 + - - +
23Y ALA* 3.1 9.9 + - + +
24Y MET* 2.9 63.4 + - + +
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Residues in contact with LEU 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473N TRP* 3.9 18.2 - - + +
476N PHE* 3.5 34.5 - - + -
477N ALA 4.4 0.7 - - - +
13Y PHE* 3.7 35.7 - - + -
14Y SER 3.8 12.3 - - - +
15Y VAL* 3.6 10.1 - - + +
17Y ASN 2.9 15.8 + - - +
18Y LYS* 3.6 8.1 - - - +
20Y ARG* 1.3 74.6 - - - +
22Y LEU* 1.3 65.5 + - - +
24Y MET* 3.0 13.2 + - + +
25Y MET* 2.8 47.5 + - + +
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Residues in contact with LEU 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473N TRP* 3.5 38.3 - - + +
18Y LYS 3.0 10.7 + - - +
19Y TRP* 3.3 35.7 - - + +
20Y ARG 3.3 0.2 - - - -
21Y LEU* 1.3 73.0 - - - +
23Y ALA* 1.3 59.8 + - - +
25Y MET* 4.0 3.4 - - + +
26Y THR* 3.0 32.0 + - - +
18Z GLY* 4.0 10.1 - - - +
21Z VAL* 3.6 39.9 - - + -
22Z THR* 4.1 19.7 - - - +
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Residues in contact with ALA 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y TRP 3.1 8.6 + - - +
20Y ARG* 3.1 13.8 + - + +
21Y LEU 3.0 0.2 - - - -
22Y LEU* 1.3 78.6 - - - +
24Y MET* 1.3 59.8 + - + +
26Y THR* 3.2 10.4 + - - +
27Y LEU* 2.9 36.6 + - + +
21Z VAL* 6.1 0.7 - - - -
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Residues in contact with MET 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Y PHE* 4.4 15.7 - - + -
14Y SER 3.3 31.0 - - - +
20Y ARG* 2.9 45.6 + - + +
21Y LEU* 3.7 20.2 - - + +
23Y ALA* 1.3 76.7 - - + +
25Y MET* 1.3 60.9 + - + +
27Y LEU* 3.2 10.7 + - + +
28Y PHE* 2.8 30.9 + - - +
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Residues in contact with MET 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469N VAL* 3.5 31.4 - - + +
472N ILE* 4.1 14.8 - - + +
473N TRP* 3.7 41.5 - - + +
476N PHE* 5.4 2.5 - - - -
13Y PHE* 5.9 3.1 - - + -
21Y LEU* 2.8 40.1 + - + +
22Y LEU* 4.0 5.4 - - + +
24Y MET* 1.3 72.1 - - + +
26Y THR* 1.3 64.8 + - - +
28Y PHE* 3.2 5.9 + - - -
29Y PHE* 3.0 54.4 + - + +
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Residues in contact with THR 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469N VAL* 6.2 1.6 - - - -
22Y LEU* 3.0 22.9 + - - +
23Y ALA* 3.4 9.0 - - - +
25Y MET* 1.3 75.3 - - - +
27Y LEU* 1.3 69.6 + - + +
29Y PHE* 5.6 0.9 - - - -
30Y GLY* 2.8 30.8 + - - -
21Z VAL* 3.5 24.8 + - + +
22Z THR* 4.4 3.3 + - - -
25Z SER* 3.4 30.7 + - - -
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Residues in contact with LEU 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y ALA* 2.9 20.3 + - + +
24Y MET* 3.6 12.1 - - + +
26Y THR* 1.3 86.5 - - + +
28Y PHE* 1.3 56.9 + - - +
30Y GLY* 4.9 0.2 - - - -
31Y SER* 2.8 37.4 + - - -
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Residues in contact with PHE 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N LEU* 3.6 47.3 - - + -
22N PHE* 5.5 0.2 - - - -
24N ALA* 4.8 1.1 - - + -
25N TRP* 3.0 41.0 + + + -
24Y MET 2.8 17.6 + - - +
25Y MET* 3.4 6.7 - - - +
27Y LEU* 1.3 75.3 - - - +
29Y PHE* 1.3 92.3 + + - +
31Y SER* 2.7 23.4 + - - -
32Y GLY 3.2 0.2 + - - -
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Residues in contact with PHE 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N LEU* 6.2 1.6 - - + -
24N ALA* 3.9 28.0 - - + -
25N TRP* 4.7 1.6 - - - -
28N MET* 3.6 33.5 - - + +
468N MET* 5.8 3.8 - - + -
469N VAL* 3.9 24.5 - - + -
472N ILE* 5.1 13.9 - - + -
25Y MET* 3.0 51.1 + - + +
26Y THR* 4.8 0.9 - - - +
28Y PHE* 1.3 101.9 - + - +
30Y GLY* 1.3 63.7 + - - +
32Y GLY* 3.2 1.7 + - - -
33Y PHE* 2.9 25.0 + - - +
26Z PHE* 4.2 21.0 - - + -
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Residues in contact with GLY 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Y THR 2.8 21.8 + - - -
27Y LEU 3.8 0.2 - - - -
29Y PHE* 1.3 78.2 - - - +
31Y SER* 1.3 62.1 + - - +
33Y PHE* 3.1 6.9 + - - +
34Y ALA* 2.8 26.6 + - - +
25Z SER* 4.2 22.7 + - - +
26Z PHE* 5.2 2.6 - - - -
29Z PRO* 6.3 1.1 - - - -
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Residues in contact with SER 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TRP* 3.2 15.9 + - - -
27Y LEU 2.8 18.4 + - - -
28Y PHE* 2.7 23.0 + - - -
30Y GLY* 1.3 70.1 - - - +
32Y GLY* 1.3 61.5 + - - +
34Y ALA* 3.7 6.1 - - - +
35Y ALA* 3.0 26.5 + - - +
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Residues in contact with GLY 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TRP* 3.5 26.9 - - - -
28N MET* 3.8 13.7 - - - -
29N VAL* 3.3 22.6 - - - +
28Y PHE 3.2 2.0 + - - -
29Y PHE 3.2 6.4 + - - -
30Y GLY 3.1 1.0 - - - -
31Y SER* 1.3 84.4 + - - +
33Y PHE* 1.3 61.2 + - - +
34Y ALA 3.4 0.2 + - - -
35Y ALA* 3.6 0.9 + - - +
36Y PRO* 3.5 9.2 - - - +
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Residues in contact with PHE 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N MET* 3.6 22.2 - - + +
31N THR* 4.2 6.5 - - + -
32N ALA* 3.1 39.6 - - + +
35N LEU* 3.7 14.8 - - + -
462N LEU* 3.6 37.7 - - + -
29Y PHE 2.9 16.3 + - - +
30Y GLY* 3.7 4.0 - - - +
32Y GLY* 1.3 74.5 - - - +
34Y ALA* 1.3 63.8 + - - +
36Y PRO* 3.3 1.6 - - - +
37Y PHE* 3.3 28.3 - + - -
25Z SER 5.7 0.2 - - - +
26Z PHE* 3.5 55.9 - + + -
27Z LEU* 5.8 0.9 - - + -
29Z PRO* 6.5 0.4 - - + -
30Z ALA* 4.2 7.6 - - + -
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Residues in contact with ALA 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Y GLY 2.8 18.7 + - - +
31Y SER* 3.7 7.2 - - - +
33Y PHE* 1.3 79.3 - - - +
35Y ALA* 1.3 67.8 + - - +
37Y PHE* 3.0 19.9 + - - +
38Y PHE* 3.3 23.2 + - + -
29Z PRO* 4.2 25.8 - - + -
30Z ALA 5.9 0.2 - - - +
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Residues in contact with ALA 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TRP* 5.2 7.0 - - + -
29N VAL* 4.8 8.7 - - + -
113N LEU* 5.6 6.7 - - + -
31Y SER 3.0 16.5 + - - +
32Y GLY* 3.8 4.0 - - - +
34Y ALA* 1.3 73.9 - - - +
36Y PRO* 1.3 70.6 - - + +
38Y PHE* 3.0 17.6 + - - +
39Y ILE* 3.1 24.8 + - + +
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Residues in contact with PRO 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 3.3 38.4 - - + +
32N ALA* 3.4 13.2 - - + -
33N LEU* 3.7 26.6 - - + +
36N LEU* 4.1 7.2 - - + -
32Y GLY 3.5 8.1 - - - +
33Y PHE 3.3 15.3 - - - +
35Y ALA* 1.3 91.9 - - + +
37Y PHE* 1.3 61.5 + - - +
39Y ILE* 3.2 12.2 + - + +
40Y VAL* 3.0 28.4 + - - +
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Residues in contact with PHE 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ALA* 3.6 26.9 - - + -
35N LEU* 4.8 8.1 - - + -
36N LEU* 3.6 33.0 - - + -
33Y PHE* 3.3 44.6 - + - -
34Y ALA* 3.0 9.9 + - - +
36Y PRO* 1.3 77.7 - - - +
38Y PHE* 1.3 60.4 + - + +
40Y VAL* 3.4 4.1 + - - +
41Y ARG 3.0 20.8 + - - -
30Z ALA* 3.8 29.4 - - + -
33Z VAL* 3.5 32.4 - - + +
34Z LEU* 4.4 21.1 - - + -
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Residues in contact with PHE 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Y ALA* 3.3 28.9 + - + -
35Y ALA* 3.0 9.1 + - - +
37Y PHE* 1.3 77.0 - - + +
39Y ILE* 1.3 62.1 + - - +
41Y ARG* 3.4 22.5 + - - +
42Y HIS* 2.8 28.9 + - - +
29Z PRO* 4.3 16.8 - - + -
32Z TRP* 4.0 22.7 - + - -
33Z VAL* 3.7 26.9 - - + -
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Residues in contact with ILE 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 6.4 0.2 - - + -
33N LEU* 6.4 0.9 - - + -
56N VAL* 5.9 2.5 - - + -
113N LEU* 4.0 26.2 - - + +
116N SER* 3.6 43.5 - - - +
117N MET* 4.4 20.9 - - + -
35Y ALA* 3.1 22.7 + - + +
36Y PRO* 3.6 10.8 - - + +
38Y PHE* 1.3 76.9 - - + +
40Y VAL* 1.3 68.0 + - + +
42Y HIS* 3.0 8.4 + - + +
43Y GLN* 2.9 26.0 + - + +
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Residues in contact with VAL 40 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N LEU* 5.9 0.4 - - + -
36N LEU* 3.6 26.2 - - + -
48N LEU* 3.8 27.6 - - + -
53N ILE* 4.2 14.8 - - + -
57N VAL* 4.0 20.9 - - + -
36Y PRO 3.0 14.3 + - - +
37Y PHE* 3.6 9.4 - - - +
39Y ILE* 1.3 78.8 - - + +
41Y ARG* 1.3 62.0 + - - +
43Y GLN* 3.4 4.1 + - - +
44Y LEU* 3.0 33.6 + - + +
33Z VAL* 5.8 2.5 - - + -
37Z LEU* 5.1 3.6 - - + -
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Residues in contact with ARG 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y PHE 3.0 14.3 + - - +
38Y PHE* 3.4 27.4 + - - +
39Y ILE 3.1 0.2 - - - -
40Y VAL* 1.3 77.3 - - - +
42Y HIS* 1.3 67.0 - - - +
44Y LEU* 3.1 8.0 + - - +
45Y LEU* 3.0 40.4 + - + +
32Z TRP* 3.6 25.5 - - - -
33Z VAL* 4.1 9.4 - - + -
37Z LEU* 6.2 0.4 - - - -
40Z TYR* 3.1 60.1 + - + -
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Residues in contact with HIS 42 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N MET* 3.3 39.6 + - + +
54W SER* 3.1 34.5 + - - -
55W PHE* 4.0 31.7 - + - -
38Y PHE 2.8 21.0 + - - +
39Y ILE* 3.0 8.7 + - - +
41Y ARG* 1.3 73.8 - - - +
43Y GLN* 1.3 66.6 + - + +
45Y LEU* 3.3 16.3 + - - +
46Y LYS* 3.4 26.4 - - + +
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Residues in contact with GLN 43 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N ASP* 5.6 0.6 - - - +
53N ILE* 3.4 36.2 - - + +
56N VAL* 5.9 4.0 - - + -
116N SER 3.1 27.9 + - - +
117N MET* 3.6 14.3 + - - +
118N VAL 4.1 0.2 + - - -
119N GLU 3.1 21.9 + - - +
120N ALA* 3.5 22.3 - - - +
121N GLY* 5.4 0.2 - - - -
39Y ILE* 2.9 20.3 + - + +
40Y VAL* 3.8 5.2 - - - +
42Y HIS* 1.3 75.5 - - + +
44Y LEU* 1.3 66.3 + - - +
45Y LEU 3.0 3.0 + - - -
46Y LYS* 3.3 23.7 + - - +
47Y LYS* 4.0 9.5 + - - +
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Residues in contact with LEU 44 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N LEU* 3.6 26.0 - - - +
50N ASP* 3.8 19.1 - - - +
53N ILE* 3.9 14.4 - - + -
40Y VAL* 3.0 28.3 + - + +
41Y ARG* 3.1 6.9 + - - +
43Y GLN* 1.3 75.8 - - - +
45Y LEU* 1.3 58.3 + - - +
46Y LYS 3.4 1.4 + - - -
47Y LYS* 3.4 22.7 + - - +
37Z LEU* 3.5 31.9 - - + -
40Z TYR* 3.6 29.0 - - + +
41Z LYS* 4.4 12.3 - - + +
43Z SER* 5.2 2.1 - - - -
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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