Contacts of the helix formed by residues 26 - 54 (chain D) in PDB entry 3PJV
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 SER 26 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.3 23.7 + - - +
24D MSE 3.2 0.2 - - - -
25D VAL* 1.3 79.7 - - - +
27D LEU* 1.3 65.5 + - - +
28D GLU 3.4 2.0 - - - -
29D SER* 3.2 14.2 + - - -
30D SER* 2.9 31.9 + - - -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE 3.1 15.6 + - - +
24D MSE 3.3 44.3 + - + +
25D VAL 3.4 0.4 - - - -
26D SER* 1.3 77.4 - - - +
28D GLU* 1.3 60.8 + - - +
30D SER* 3.6 3.7 - - - -
31D ARG* 2.8 39.5 + - + +
106F PHE* 6.2 0.9 - - + -
109F LEU 6.2 0.2 - - - +
110F ILE* 4.0 27.8 - - + -
144F LEU* 4.9 11.0 - - + -
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D MSE 4.9 0.8 + - - -
25D VAL 5.0 1.8 + - - +
26D SER 3.4 0.6 - - - -
27D LEU* 1.3 79.0 - - - +
29D SER* 1.3 63.8 + - - +
31D ARG* 3.5 9.4 + - + +
32D THR* 3.1 30.5 + - - +
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D SER* 3.2 19.7 + - - -
28D GLU* 1.3 74.5 - - - +
30D SER* 1.3 68.6 + - - +
32D THR* 3.3 8.3 + - - -
33D GLN* 3.0 32.1 + - - +
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Residues in contact with SER 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D SER* 2.9 30.3 + - - -
27D LEU* 3.6 6.1 - - - -
29D SER* 1.3 77.4 + - - +
31D ARG* 1.3 62.8 + - - +
33D GLN* 3.2 19.3 + - - +
34D TYR* 3.1 32.6 + - - -
144F LEU* 4.7 13.7 - - - -
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Residues in contact with ARG 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 2.8 27.6 + - + +
28D GLU* 3.7 9.2 - - - +
30D SER* 1.3 75.9 - - - +
32D THR* 1.3 69.3 + - - +
34D TYR* 3.1 9.8 + - - +
35D VAL* 2.9 40.3 + - - +
110F ILE* 2.8 39.8 + - + +
111F GLY 2.9 29.7 + - - -
112F LEU* 3.8 15.9 - - + +
113F GLU* 4.6 4.9 - - - +
144F LEU* 4.9 6.4 - - + +
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Residues in contact with THR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU* 3.1 17.4 + - - +
29D SER* 3.6 11.2 - - - -
30D SER 3.3 0.2 - - - -
31D ARG* 1.3 83.7 + - - +
33D GLN* 1.3 55.5 + - + +
35D VAL* 3.2 9.0 + - + +
36D ASN* 2.8 48.3 + - - +
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Residues in contact with GLN 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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29D SER* 3.0 27.0 + - - +
30D SER* 3.2 21.2 + - - +
32D THR* 1.3 76.8 - - + +
34D TYR* 1.3 63.5 + - + +
36D ASN* 3.4 8.1 + - - +
37D GLN* 2.9 30.5 + - - +
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D SER* 3.1 26.1 + - - -
31D ARG* 3.1 7.0 + - - +
33D GLN* 1.3 81.2 - - + +
35D VAL* 1.3 62.1 + - - +
37D GLN* 3.7 25.6 - - - +
38D LEU* 2.9 36.7 + - - +
112F LEU* 5.5 5.2 - - + -
140F ALA* 4.0 25.1 - - + -
143F LYS* 3.5 54.1 + - + +
144F LEU* 3.5 40.8 - - + -
147F SER* 4.5 6.5 + - - -
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ARG* 2.9 37.3 + - - +
32D THR* 3.5 11.0 - - + +
34D TYR* 1.3 76.0 - - - +
36D ASN* 1.3 68.0 + - - +
38D LEU* 4.0 5.6 - - - +
39D ARG* 3.0 46.3 + - + +
112F LEU* 3.7 25.8 - - + -
113F GLU 5.9 2.0 - - - +
115F ALA* 5.1 1.4 - - - +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D THR* 2.8 38.4 + - - +
33D GLN* 3.8 6.7 - - - +
35D VAL* 1.3 77.9 - - - +
37D GLN* 1.3 58.2 + - - +
39D ARG* 3.0 30.4 + - - +
40D SER* 2.9 35.1 + - - +
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Residues in contact with GLN 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLN 2.9 17.6 + - - +
34D TYR* 3.7 33.0 + - - +
36D ASN* 1.3 77.1 - - - +
38D LEU* 1.3 59.3 + - + +
40D SER* 3.3 6.8 + - - -
41D HIS* 2.9 28.1 + - + +
72F ASP 3.0 25.7 + - - +
73F SER* 3.8 13.6 - - - +
75F TYR* 6.5 1.1 - - - -
140F ALA* 5.8 1.4 - - - +
143F LYS* 4.8 5.7 - - - +
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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
----------------------------------------------------------
34D TYR 2.9 21.2 + - - +
35D VAL* 4.0 4.3 - - - +
37D GLN* 1.3 75.5 - - + +
39D ARG* 1.3 63.3 + - - +
41D HIS* 3.1 6.7 + - + +
42D ALA* 3.0 23.2 + - - +
75F TYR* 3.9 21.5 - - + +
112F LEU* 4.2 12.6 - - + -
113F GLU 5.9 1.6 - - - +
115F ALA* 3.6 20.4 - - + +
135F SER* 3.9 13.6 + - - +
136F HIS 3.9 14.4 - - - +
137F PRO* 3.9 27.4 - - + -
140F ALA* 3.9 24.2 - - + +
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D VAL* 3.0 37.4 + - + +
36D ASN* 3.0 30.9 + - - +
38D LEU* 1.3 77.1 - - - +
40D SER* 1.3 58.1 + - - +
42D ALA* 3.2 5.0 + - - +
43D GLN* 2.9 29.5 + - + +
115F ALA* 3.9 12.7 - - + +
116F GLY 3.8 20.7 - - - +
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Residues in contact with SER 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 2.9 19.8 + - - +
37D GLN* 3.6 6.5 - - - -
39D ARG* 1.3 77.3 - - - +
41D HIS* 1.3 57.6 + - - +
43D GLN* 4.4 5.6 - - - -
44D ASP* 2.9 45.3 + - - +
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Residues in contact with HIS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLN* 2.9 15.9 + - + +
38D LEU* 3.1 13.7 + - + +
40D SER* 1.3 78.3 - - - +
42D ALA* 1.3 61.3 + - - +
44D ASP* 3.5 6.0 + - - +
45D ALA* 3.2 21.5 + - - +
75D TYR* 4.0 18.6 - - + +
76D TYR* 3.3 35.7 + + - -
73F SER 5.3 8.5 - - - -
74F GLY* 6.5 0.2 - - - -
75F TYR* 3.9 33.3 - + - +
135F SER* 2.8 24.5 + - - +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU 3.0 8.3 + - - +
39D ARG 3.7 5.8 - - - +
41D HIS* 1.3 75.6 - - - +
43D GLN* 1.3 64.6 + - - +
45D ALA* 3.3 4.0 + - - +
46D ALA* 3.0 22.7 + - - +
115F ALA 3.5 23.1 - - - +
116F GLY 3.8 0.9 - - - -
117F GLY* 3.7 16.8 - - - +
133F VAL* 3.7 16.7 - - + +
135F SER* 3.2 19.5 + - - +
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Residues in contact with GLN 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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39D ARG* 2.9 20.0 + - + +
40D SER* 3.9 7.0 - - - +
42D ALA* 1.3 75.6 - - - +
44D ASP* 1.3 62.3 + - - +
46D ALA 3.2 0.5 + - - -
47D THR* 2.9 53.3 + - - +
116F GLY 5.3 0.4 - - - +
117F GLY* 3.7 10.7 - - - -
118F ASP* 3.0 41.3 + - - +
119F ALA* 4.4 0.4 - - - +
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Residues in contact with ASP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D SER* 2.9 32.2 + - - +
41D HIS* 3.9 6.0 - - - +
43D GLN* 1.3 80.6 - - - +
45D ALA* 1.3 57.1 + - - +
47D THR* 3.4 5.8 + - - -
48D ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 45 (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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41D HIS 3.2 10.5 + - - +
42D ALA 3.6 4.5 - - - +
43D GLN 3.2 0.2 - - - -
44D ASP* 1.3 75.4 - - - +
46D ALA* 1.3 60.2 + - - +
48D ALA* 3.4 4.8 + - - +
49D LEU* 2.9 31.4 + - - +
70D ILE* 4.8 9.7 - - + +
76D TYR* 3.4 43.1 - - + +
133F VAL* 4.1 9.4 - - + -
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Residues in contact with ALA 46 (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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42D ALA 3.0 16.1 + - - +
43D GLN 3.2 4.2 + - - +
45D ALA* 1.3 76.9 - - - +
47D THR* 1.3 59.0 + - - +
49D LEU* 3.3 0.7 + - - +
50D ALA* 2.8 31.4 + - - +
117F GLY 3.7 21.1 - - - +
118F ASP* 3.8 19.1 - - - -
119F ALA* 3.5 4.2 - - - +
131F VAL* 4.0 11.1 - - - +
133F VAL* 3.7 14.3 - - + +
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Residues in contact with THR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN* 2.9 35.6 + - - +
44D ASP* 3.8 7.0 - - - -
46D ALA* 1.3 78.1 - - - +
48D ALA* 1.3 62.2 + - - +
50D ALA* 3.5 2.5 + - - +
51D LEU* 3.1 23.7 + - + +
119F ALA* 3.8 11.5 - - + +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASP 2.9 19.1 + - - +
45D ALA* 3.9 5.6 - - - +
47D THR* 1.3 78.8 - - - +
49D LEU* 1.3 56.5 + - - +
51D LEU* 3.3 10.4 + - - +
52D SER* 2.9 32.0 + - - +
70D ILE* 6.4 2.9 - - + -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ALA 2.9 18.6 + - - +
46D ALA 3.9 2.7 - - - +
48D ALA* 1.3 73.7 - - - +
50D ALA* 1.3 66.6 + - - +
52D SER* 3.1 7.9 + - - -
53D LEU* 2.8 48.1 + - + +
66D LEU* 3.8 29.8 - - + +
67D VAL* 4.2 14.6 - - + -
70D ILE* 4.4 16.4 - - + -
79D ILE* 3.6 38.1 - - + -
81D VAL* 5.1 0.4 - - + -
131F VAL* 3.8 15.7 - - + -
133F VAL* 5.1 1.6 - - + -
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA 2.8 17.6 + - - +
47D THR 3.8 3.1 - - - +
49D LEU* 1.3 76.1 - - - +
51D LEU* 1.3 61.1 + - - +
53D LEU 3.3 0.3 + - - -
54D THR* 2.9 28.5 + - - -
119F ALA* 3.7 15.9 - - + -
120F LEU 3.7 23.1 - - - +
121F VAL* 3.6 18.8 - - + +
131F VAL* 3.9 9.5 - - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.1 14.8 + - + +
48D ALA* 3.4 12.3 - - - +
49D LEU 3.2 0.2 - - - -
50D ALA* 1.3 77.0 - - - +
52D SER* 1.3 63.1 + - - +
54D THR* 3.2 16.7 + - - +
55D PRO* 3.4 10.3 - - + +
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Residues in contact with SER 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA* 2.9 17.0 + - - +
49D LEU* 3.1 16.2 + - - -
51D LEU* 1.3 77.8 - - - +
53D LEU* 1.3 58.2 + - - +
55D PRO* 3.5 6.6 - - - +
56D ASN* 3.1 20.6 - - - +
66D LEU* 3.6 23.2 - - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 2.8 29.7 + - + +
50D ALA 3.8 4.0 - - - +
52D SER* 1.3 76.7 - - - +
54D THR* 1.3 64.6 + - - +
55D PRO 3.4 0.2 - - - -
56D ASN* 2.9 3.4 + - + -
57D ILE* 2.9 32.9 + - + +
63D VAL* 3.9 40.2 - - + +
66D LEU* 3.9 22.7 - - + -
67D VAL* 4.6 0.9 - - + -
81D VAL* 4.0 25.4 - - + -
121F VAL* 4.2 9.6 - - + -
131F VAL* 3.9 24.7 - - + -
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ALA 2.9 20.6 + - - -
51D LEU* 3.6 12.8 + - + +
53D LEU* 1.3 77.7 - - - +
55D PRO* 1.3 69.7 - - + +
56D ASN 3.2 1.2 + - - -
57D ILE* 3.7 15.1 + - - +
120F LEU 5.3 0.3 + - - -
121F VAL* 3.6 19.8 - - - +
122F SER 3.8 22.4 + - - +
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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
------------------------------------------------------------
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