Contacts of the helix formed by residues 28 - 59 (chain D) in PDB entry 6VSU
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 28 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.9 13.5 + - - -
50A LEU* 4.0 2.5 - - - +
53A GLU* 3.1 29.8 + - - -
27D SER* 1.3 74.4 + - - +
29D ILE* 1.3 60.3 + - - +
30D GLU 3.4 0.2 - - - -
31D LYS* 3.7 18.5 - - - +
32D GLY* 3.0 19.8 + - - -
35D ARG* 5.8 0.4 - - - -
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.4 16.1 - - + +
53A GLU* 5.8 1.3 - - - +
54A LEU* 6.2 4.7 - - + -
57A LEU* 6.0 6.5 - - + -
27D SER* 2.9 10.7 - - - +
28D SER* 1.3 77.5 + - - +
30D GLU* 1.3 55.6 + - + +
32D GLY* 3.1 3.1 + - - -
33D GLN* 2.8 54.0 + - - +
128D CYS 4.4 6.5 - - - +
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER* 2.8 19.9 + - - +
29D ILE* 1.3 72.0 - - + +
31D LYS* 1.3 63.4 + - + +
33D GLN* 3.3 16.1 + - - +
34D ASN* 3.3 36.6 + - - +
134D ARG* 3.0 35.3 + - - -
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Residues in contact with LYS 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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27D SER* 3.3 14.3 + - - +
28D SER* 3.7 21.5 - - - +
30D GLU* 1.3 71.5 - - + +
32D GLY* 1.3 66.2 + - - +
34D ASN* 3.2 21.2 + - - +
35D ARG* 3.3 44.7 + - - +
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Residues in contact with GLY 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 4.5 9.3 - - - +
49A LYS* 4.4 6.7 - - - -
50A LEU* 3.9 21.5 - - - -
28D SER 3.0 14.0 + - - -
29D ILE 3.1 5.3 + - - -
31D LYS* 1.3 80.5 - - - +
33D GLN* 1.3 59.9 + - - +
35D ARG* 3.2 5.6 + - - +
36D VAL* 3.1 25.3 + - - +
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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
----------------------------------------------------------
50A LEU* 4.7 0.6 - - + +
29D ILE* 2.8 31.8 + - - +
30D GLU* 3.3 24.3 + - - +
32D GLY* 1.3 73.1 - - - +
34D ASN* 1.3 52.0 + - - +
36D VAL* 3.3 3.5 + - - +
37D ILE* 2.8 38.8 + - - +
128D CYS* 2.8 46.9 + - + +
129D GLY* 3.3 24.2 + - - -
130D VAL* 3.9 11.2 - - + +
134D ARG* 3.3 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
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30D GLU* 3.3 25.0 + - - +
31D LYS* 3.2 13.2 + - - +
33D GLN* 1.3 71.7 - - - +
35D ARG* 1.3 57.5 + - + +
37D ILE* 3.8 7.1 - - - +
38D ASP* 2.8 40.9 + - - +
134D ARG* 3.0 26.0 + - - -
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 4.9 2.5 - - + +
46A GLU* 3.4 41.6 + - + +
49A LYS* 3.7 26.8 - - - +
28D SER* 4.9 1.0 + - - -
31D LYS* 3.3 44.3 + - - +
32D GLY 3.2 6.3 + - - +
34D ASN* 1.3 75.0 - - + +
36D VAL* 1.3 57.7 + - - +
38D ASP* 3.5 6.6 + - - +
39D ALA* 3.0 29.8 + - - +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.6 21.4 - - + +
46A GLU* 3.6 28.7 - - + -
47A ARG* 4.7 7.0 - - + +
50A LEU* 4.8 6.1 - - + -
32D GLY 3.1 15.4 + - - +
33D GLN 3.6 7.2 - - - +
34D ASN 3.3 0.2 - - - -
35D ARG* 1.3 73.2 - - - +
37D ILE* 1.3 57.2 + - - +
39D ALA* 3.4 0.8 + - - -
40D SER* 2.7 44.5 + - - +
124D GLU* 4.6 11.7 - - + +
125D ILE* 4.5 11.4 - - + -
128D CYS* 4.4 22.2 - - + -
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Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLN 2.8 23.2 + - - +
34D ASN* 3.9 5.2 - - - +
36D VAL* 1.3 70.9 - - + +
38D ASP* 1.3 56.8 + - - +
40D SER* 3.0 10.1 + - - -
41D LEU* 2.8 48.7 + - + +
125D ILE* 4.4 16.6 - - + -
130D VAL* 4.1 13.5 - - + -
134D ARG* 3.5 45.3 - - + +
138D VAL* 3.8 29.2 - - + -
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Residues in contact with ASP 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* 2.8 25.4 + - - +
35D ARG* 3.6 8.3 - - - +
36D VAL 3.3 0.2 - - - -
37D ILE* 1.3 76.2 - - - +
39D ALA* 1.3 50.5 + - - +
41D LEU* 3.3 9.9 + - - +
42D THR* 2.7 43.2 + - - +
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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
----------------------------------------------------------
39A ALA* 3.8 21.2 - - - +
42A THR* 4.0 20.0 - - + -
43A LEU* 3.7 22.2 - - + +
46A GLU* 5.8 0.2 - - + -
35D ARG 3.0 18.6 + - - +
38D ASP* 1.3 71.3 - - - +
40D SER* 1.3 60.0 + - - +
42D THR* 3.7 7.9 - - - -
43D LEU* 3.0 30.5 + - - +
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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
----------------------------------------------------------
43A LEU* 3.4 14.3 - - - +
36D VAL* 2.7 21.6 + - - +
37D ILE 3.2 11.9 - - - -
39D ALA* 1.3 79.8 - - - +
41D LEU* 1.3 59.0 + - - +
43D LEU* 3.5 10.4 + - - +
44D ILE* 3.5 18.8 + - - +
121D PRO* 3.7 30.1 - - - +
124D GLU* 5.5 0.2 - - - +
125D ILE* 3.9 25.2 - - - +
138D VAL* 5.3 3.4 - - - -
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 2.8 37.6 + - + +
38D ASP* 3.8 9.9 - - - +
40D SER* 1.3 67.5 - - - +
42D THR* 1.3 55.9 + - - +
43D LEU 3.1 1.8 - - - -
44D ILE* 3.1 5.8 + - - +
45D ARG* 2.8 52.0 + - - +
138D VAL* 3.9 21.1 - - + +
141D GLU* 3.9 22.0 - - + -
142D SER* 3.4 25.1 - - - +
145D LEU* 3.7 18.4 - - + +
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Residues in contact with THR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 5.1 5.8 - - + +
39A ALA* 3.9 17.9 - - + -
38D ASP* 2.7 29.7 + - - +
39D ALA* 3.7 9.2 - - - -
40D SER 3.4 0.2 - - - -
41D LEU* 1.3 71.9 - - - +
43D LEU* 1.3 56.8 + - - +
45D ARG* 3.3 21.5 + - - +
46D GLU* 3.1 42.8 + - + +
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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
----------------------------------------------------------
36A VAL* 3.4 43.3 - - + +
39A ALA* 3.8 12.5 - - + +
40A SER* 3.9 7.9 - - - +
43A LEU* 4.5 18.2 - - + -
121A PRO* 4.3 22.9 - - + -
124A GLU* 5.6 0.2 - - + -
39D ALA 3.0 16.6 + - - +
40D SER 3.5 5.8 - - - +
41D LEU 3.1 0.4 - - - -
42D THR* 1.3 76.3 - - - +
44D ILE* 1.3 64.7 + - + +
46D GLU* 3.6 3.0 + - - +
47D ARG* 3.0 59.5 + - - +
121D PRO* 4.9 9.9 - - + -
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D SER 3.6 14.8 - - - +
41D LEU 3.1 5.9 + - - +
43D LEU* 1.3 74.4 - - + +
45D ARG* 1.3 65.9 + - - +
46D GLU 3.3 0.2 + - - -
47D ARG* 3.3 21.9 + - - +
48D ALA* 2.9 26.8 + - + +
68D LEU* 4.1 23.8 - - + -
117D VAL* 3.8 15.4 - - + +
119D ASP 3.7 24.5 - - - +
120D VAL* 4.3 5.4 - - + +
121D PRO* 5.0 1.8 - - + -
142D SER* 4.1 33.9 - - - +
145D LEU* 4.1 13.2 - - + -
146D VAL* 4.9 1.8 - - + -
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Residues in contact with ARG 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 2.8 32.4 + - - +
42D THR* 3.3 34.5 + - - +
43D LEU 3.4 0.2 - - - -
44D ILE* 1.3 73.4 - - - +
46D GLU* 1.3 68.2 + - + +
48D ALA* 3.4 4.7 + - - +
49D LYS* 2.9 32.4 + - + +
145D LEU* 4.0 32.1 - - + +
149D GLU* 4.9 3.0 - - - +
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Residues in contact with GLU 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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31A LYS 4.9 0.3 - - - +
32A GLY* 4.9 10.4 - - - +
35A ARG* 2.9 62.3 + - + +
36A VAL* 4.2 20.6 - - + +
42D THR* 3.1 30.1 + - + +
43D LEU* 4.3 2.5 - - - +
45D ARG* 1.3 88.4 + - + +
47D ARG* 1.3 62.4 + - - +
49D LYS* 3.2 18.1 + - - +
50D LEU* 3.2 26.5 + - - +
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Residues in contact with ARG 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.1 18.6 - - + -
124A GLU* 2.8 44.7 - - - +
127A ASP* 5.4 6.1 - - - +
128A CYS* 5.6 4.7 - - + -
43D LEU* 3.0 53.6 + - - +
44D ILE* 3.7 13.4 - - - +
46D GLU* 1.3 74.2 - - - +
48D ALA* 1.3 63.6 + - - +
50D LEU* 3.1 18.9 + - - +
51D LYS* 3.1 23.9 + - - +
117D VAL* 2.5 37.1 + - - +
118D GLY* 3.1 18.6 - - - -
119D ASP 3.2 14.5 + - - +
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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 ILE* 2.9 19.5 + - + +
45D ARG* 3.7 5.4 - - - +
47D ARG* 1.3 72.1 - - - +
49D LYS* 1.3 58.7 + - - +
51D LYS* 3.3 1.5 + - - +
52D GLY 2.9 25.5 + - - -
117D VAL* 3.7 23.8 - - + +
145D LEU 4.1 23.3 - - - +
146D VAL* 4.6 6.5 - - + +
149D GLU* 3.5 16.2 - - + +
152D LEU* 4.1 2.8 - - + +
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 4.0 12.1 + - - -
31A LYS* 6.0 3.0 - - - +
32A GLY* 6.3 0.4 - - - -
35A ARG* 5.0 9.7 - - - +
45D ARG* 2.9 18.6 + - + +
46D GLU* 3.3 26.2 + - - +
48D ALA* 1.3 77.4 - - - +
50D LEU* 1.3 64.5 + - + +
52D GLY* 3.5 0.5 + - - -
53D GLU* 3.0 61.2 + - + +
56D ARG* 5.6 0.4 - - - +
149D GLU* 3.4 22.1 + - - +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 4.1 20.2 - - - +
29A ILE* 4.2 21.8 - - + +
32A GLY* 4.2 25.6 - - - -
33A GLN 4.5 1.6 - - - +
36A VAL* 4.9 4.7 - - + -
128A CYS* 3.8 32.5 - - + +
46D GLU 3.5 11.9 - - - +
47D ARG* 3.1 11.3 + - - +
49D LYS* 1.3 83.7 - - + +
51D LYS* 1.3 66.8 + - + +
53D GLU* 3.8 13.1 - - + +
54D LEU* 3.2 23.0 + - - +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP* 2.8 45.1 + - - -
128A CYS* 5.4 1.5 - - - +
47D ARG* 3.1 19.1 + - - +
48D ALA 3.3 4.7 + - - +
49D LYS 3.2 0.2 - - - -
50D LEU* 1.3 81.6 - - + +
52D GLY* 1.3 65.6 + - - +
54D LEU* 3.3 13.8 + - + +
55D VAL* 3.0 29.6 + - - +
115D THR* 3.9 32.9 - - + +
116D ASP 3.2 24.7 + - - +
117D VAL* 4.1 8.7 - - + +
152D LEU* 4.3 9.2 - - + -
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Residues in contact with GLY 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 16.8 + - - -
49D LYS 4.0 0.9 - - - -
51D LYS* 1.3 75.4 - - - +
53D GLU* 1.3 56.4 + - - +
55D VAL* 3.3 2.1 + - - +
56D ARG* 2.9 54.6 + - - +
149D GLU* 4.2 3.4 - - - -
150D GLU 4.5 1.3 - - - -
152D LEU* 4.2 17.1 - - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.2 23.4 + - - -
49D LYS* 3.0 52.9 + - + +
50D LEU* 3.8 13.8 - - - +
52D GLY* 1.3 74.7 - - - +
54D LEU* 1.3 56.6 + - - +
56D ARG* 3.4 22.4 + - - +
57D LEU* 3.0 33.4 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU 3.2 17.4 + - - +
51D LYS* 3.5 14.1 - - + +
52D GLY 3.2 0.2 - - - -
53D GLU* 1.3 75.1 - - - +
55D VAL* 1.3 65.5 + - - +
57D LEU* 3.3 10.8 + - + +
58D LEU* 3.1 36.3 + - + +
111D PRO* 3.5 32.1 - - + -
115D THR* 4.9 6.5 - - + -
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LYS 3.0 20.6 + - - +
52D GLY 3.7 4.0 - - - +
54D LEU* 1.3 74.8 - - - +
56D ARG* 1.3 62.9 + - - +
58D LEU* 3.3 7.3 + - - +
59D GLY* 3.2 16.6 + - - -
61D ALA* 4.1 3.7 - - + +
64D SER* 3.4 22.4 - - - +
111D PRO* 3.6 27.8 - - + +
112D ARG* 4.0 16.5 - - + +
115D THR* 4.2 7.0 - - + -
151D PRO* 3.5 25.4 - - + -
152D LEU* 3.9 16.8 - - + -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 5.6 0.2 - - - +
52D GLY* 2.9 27.2 + - - +
53D GLU* 3.4 34.8 + - - +
55D VAL* 1.3 76.1 - - - +
57D LEU* 1.3 61.6 + - - +
59D GLY* 3.2 15.6 + - - -
149D GLU* 3.0 28.7 + - - -
150D GLU* 2.7 49.5 + - - +
151D PRO* 4.5 4.0 - - + -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 3.0 18.1 + - - +
54D LEU* 3.7 11.0 - - + +
55D VAL 3.3 0.2 - - - -
56D ARG* 1.3 74.9 - - - +
58D LEU* 1.3 73.5 + - + +
59D GLY* 3.6 0.3 + - - -
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LEU* 3.1 27.8 + - + +
55D VAL 3.8 4.7 - - - +
57D LEU* 1.3 84.2 - - + +
59D GLY* 1.3 64.1 + - - +
110D ASP* 4.2 7.9 - - - +
111D PRO* 3.6 40.6 - - + -
112D ARG* 3.7 27.9 + - + +
----------------------------------------------------------
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Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D VAL 3.2 8.0 + - - -
56D ARG* 3.2 17.9 + - - -
57D LEU 4.5 0.7 - - - -
58D LEU* 1.3 74.8 - - - +
60D GLY* 1.3 57.3 + - - -
61D ALA 3.5 2.7 - - - -
112D ARG* 2.9 32.0 + - - -
----------------------------------------------------------
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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).
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