Contacts of the helix formed by residues 28 - 58 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 1.3 70.8 - - - +
29A ILE* 1.3 61.6 + - - +
30A GLU 3.2 2.5 - - - -
31A LYS* 4.0 12.4 + - - +
32A GLY 3.7 11.8 + - - -
49D LYS* 4.0 11.8 + - - -
50D LEU* 4.1 7.1 - - - +
53D GLU* 3.2 24.0 + - - -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.6 14.4 - - - +
28A SER* 1.3 76.5 - - - +
30A GLU* 1.3 76.4 + - - +
31A LYS 3.5 0.4 - - - -
32A GLY 3.8 0.2 - - - -
33A GLN* 2.6 55.8 + - + +
128A CYS 5.3 3.8 - - - +
50D LEU* 4.2 25.0 - - + +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 2.8 35.0 + - - +
28A SER 3.2 0.6 - - - -
29A ILE* 1.3 89.9 - - - +
31A LYS* 1.3 56.6 + - - +
33A GLN* 3.0 22.1 + - - +
34A ASN* 2.8 45.9 + - - +
134A ARG* 5.7 1.6 + - - -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 4.0 14.4 + - - +
29A ILE 3.5 0.2 - - - -
30A GLU* 1.3 76.1 - - - +
32A GLY* 1.3 57.1 + - - +
34A ASN* 3.9 7.5 - - + +
35A ARG* 3.1 75.7 + - + +
46D GLU* 5.5 0.4 - - - -
49D LYS* 6.0 3.4 - - - +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 3.7 5.2 + - - -
29A ILE 3.5 4.4 + - - -
30A GLU 3.2 0.4 - - - -
31A LYS* 1.3 74.8 - - - +
33A GLN* 1.3 66.0 + - - +
34A ASN 3.0 1.1 - - - -
35A ARG* 2.9 2.4 + - - +
36A VAL* 2.7 33.7 + - - +
46D GLU* 4.9 12.1 - - - +
49D LYS* 6.3 0.2 - - - -
50D LEU* 4.2 22.4 - - - -
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 2.6 40.4 + - + +
30A GLU* 3.0 28.9 + - - +
32A GLY* 1.3 69.9 - - - +
34A ASN* 1.3 55.6 - - - +
36A VAL* 3.5 2.3 + - - +
37A ILE* 3.0 38.6 + - + +
128A CYS* 2.8 42.2 + - + +
129A GLY* 3.5 20.0 + - - -
130A VAL* 3.7 21.0 - - + +
134A ARG* 5.0 8.7 + - - +
50D LEU* 4.5 1.8 - - + +
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Residues in contact with ASN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 2.8 29.3 + - - +
31A LYS* 3.9 8.3 - - + +
33A GLN* 1.3 77.1 - - - +
35A ARG* 1.3 62.0 + - + +
37A ILE* 3.4 2.4 + - - +
38A ASP* 2.8 37.9 + - - +
134A ARG* 2.4 37.8 + - - +
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.1 58.0 + - + +
32A GLY 2.9 3.4 + - - +
34A ASN* 1.3 77.3 - - + +
36A VAL* 1.3 57.2 + - - +
38A ASP* 3.8 13.5 - - + +
39A ALA* 2.8 36.8 + - - +
42D THR* 5.1 5.2 - - + +
46D GLU* 2.9 48.5 + - + +
49D LYS* 5.0 11.7 - - - +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY* 2.7 23.8 + - - +
33A GLN 3.5 5.2 - - - +
35A ARG* 1.3 76.7 - - - +
37A ILE* 1.3 52.4 + - + +
39A ALA 3.3 0.2 + - - -
40A SER* 2.7 40.3 + - - +
124A GLU* 4.5 8.5 - - + +
125A ILE* 4.4 13.5 - - + +
128A CYS* 4.1 25.1 - - + -
43D LEU* 3.4 20.7 - - + +
46D GLU* 4.2 15.8 - - + +
47D ARG* 4.1 27.8 - - + +
50D LEU* 4.9 2.0 - - + -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 3.0 23.2 + - - +
34A ASN* 3.7 4.0 - - - +
36A VAL* 1.3 73.8 - - + +
38A ASP* 1.3 71.3 + - - +
40A SER* 3.0 9.2 + - - -
41A LEU* 2.9 42.4 + - + +
125A ILE* 4.7 13.9 - - + -
130A VAL* 4.2 14.4 - - + -
134A ARG* 3.5 52.0 - - + +
138A VAL* 3.9 26.0 - - + -
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 2.8 30.1 + - - +
35A ARG* 3.9 13.2 - - + +
37A ILE* 1.3 78.4 - - - +
39A ALA* 1.3 51.6 + - - +
41A LEU* 3.3 10.9 + - - +
42A THR* 2.7 42.0 + - - +
45A ARG* 5.3 0.5 + - - -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 2.8 23.2 + - - +
38A ASP* 1.3 72.6 - - - +
40A SER* 1.3 56.4 + - - +
42A THR* 3.5 8.5 + - - -
43A LEU* 3.1 28.4 + - - +
39D ALA* 3.8 16.7 - - - +
42D THR* 3.9 25.8 - - + -
43D LEU* 3.8 21.3 - - + +
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 2.7 22.2 + - - +
37A ILE* 3.0 9.2 + - - -
39A ALA* 1.3 72.1 - - - +
41A LEU* 1.3 66.4 + - - +
43A LEU* 3.1 20.7 + - - +
44A ILE* 3.4 14.5 - - - +
120A VAL* 5.8 0.2 - - - -
121A PRO* 3.2 37.4 - - - +
125A ILE* 4.0 17.5 - - - +
138A VAL* 5.0 5.4 - - - -
142A SER* 5.7 0.2 - - - -
43D LEU* 3.9 7.9 - - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 2.9 31.2 + - + +
38A ASP* 3.6 11.9 - - - +
40A SER* 1.3 72.0 - - - +
42A THR* 1.3 66.2 + - - +
44A ILE* 3.0 6.9 + - - +
45A ARG* 2.9 33.9 + - - +
138A VAL* 3.6 20.6 - - + -
141A GLU* 4.1 30.7 - - + +
142A SER* 3.5 24.9 - - - +
145A LEU* 3.7 16.2 - - + +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 2.7 30.3 + - - +
39A ALA* 3.6 10.1 - - - -
41A LEU* 1.3 70.3 - - - +
43A LEU* 1.3 56.0 + - - +
45A ARG* 3.0 24.6 + - - +
46A GLU* 2.8 50.7 + - + +
35D ARG* 4.9 2.7 - - + +
39D ALA* 4.0 15.9 - - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA 3.1 10.4 + - - +
40A SER* 3.2 15.3 - - - +
41A LEU 3.1 0.2 - - - -
42A THR* 1.3 76.1 - - - +
44A ILE* 1.3 62.3 - - + +
46A GLU* 4.0 5.1 + - - +
47A ARG* 3.5 21.5 + - - +
117A VAL 5.2 0.3 - - - +
119A ASP 5.4 4.5 - - - +
121A PRO* 5.3 8.7 - - + -
36D VAL* 3.6 27.1 - - + +
39D ALA* 3.7 14.4 - - + -
40D SER* 3.4 24.2 - - - +
43D LEU* 4.5 16.2 - - + -
121D PRO* 4.3 24.7 - - + -
124D GLU* 5.0 14.6 - - + -
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER 3.4 15.5 - - - +
41A LEU* 3.0 5.1 + - - +
43A LEU* 1.3 81.7 - - + +
45A ARG* 1.3 56.9 + - - +
46A GLU 3.3 0.2 - - - -
47A ARG* 3.2 1.3 + - - +
48A ALA* 2.8 34.5 + - - +
68A LEU* 4.3 11.9 - - + -
117A VAL* 3.8 39.2 - - + +
119A ASP 4.0 26.7 - - - +
120A VAL* 4.4 4.9 - - + +
121A PRO* 5.2 1.1 - - + -
142A SER* 4.0 34.5 - - - +
145A LEU* 4.4 11.0 - - + -
146A VAL* 4.5 2.5 - - + -
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP 5.3 0.6 + - - -
41A LEU* 2.9 29.5 + - - +
42A THR* 3.3 32.6 + - - +
44A ILE* 1.3 77.5 - - - +
46A GLU* 1.3 62.4 + - - +
48A ALA* 3.1 5.6 + - - +
49A LYS* 2.8 34.5 + - + +
145A LEU* 4.3 30.8 - - + +
149A GLU* 4.2 7.7 - - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 2.8 36.5 + - + +
43A LEU* 4.1 2.7 - - - +
45A ARG* 1.3 80.3 + - - +
47A ARG* 1.3 56.6 + - - +
49A LYS* 3.1 34.9 + - - +
50A LEU* 3.2 19.3 + - - +
32D GLY* 4.5 5.0 - - - +
35D ARG* 3.4 55.2 + - + +
36D VAL* 3.6 22.2 - - + -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 3.5 14.8 + - - +
44A ILE 3.2 3.4 + - - +
45A ARG 3.2 0.8 - - - -
46A GLU* 1.3 73.8 - - - +
48A ALA* 1.3 61.0 + - - +
50A LEU* 3.2 13.2 + - + +
51A LYS* 2.9 46.3 + - - +
90A ARG* 5.4 1.6 - - - +
116A ASP* 2.6 42.4 + - - -
117A VAL* 3.4 18.8 - - - +
118A GLY* 3.5 21.7 - - - +
36D VAL* 5.1 6.5 - - + -
123D GLN 4.4 1.4 + - - -
124D GLU* 3.5 39.2 - - - +
127D ASP* 3.0 37.8 + - - +
128D CYS* 5.5 4.0 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE 2.8 22.5 + - - +
45A ARG* 3.4 4.9 - - - +
47A ARG* 1.3 70.9 - - - +
49A LYS* 1.3 53.2 + - - +
51A LYS* 3.1 2.4 + - - +
52A GLY 2.7 32.2 + - - -
117A VAL* 3.9 19.5 - - + +
145A LEU 4.0 25.4 - - - +
146A VAL* 4.5 3.8 - - + -
149A GLU* 3.4 18.3 - - + +
152A LEU* 4.0 5.6 - - + +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 2.8 18.8 + - + +
46A GLU* 3.1 24.2 + - - +
48A ALA* 1.3 71.3 - - - +
50A LEU* 1.3 67.6 + - - +
52A GLY* 3.6 0.7 + - - -
53A GLU* 3.0 56.1 + - + +
56A ARG* 4.5 1.6 + - - -
149A GLU* 3.4 22.6 + - - +
28D SER* 3.9 17.5 + - - -
32D GLY* 4.4 1.4 - - - -
35D ARG* 3.7 26.6 - - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 3.2 13.9 + - - +
47A ARG* 3.5 13.0 - - + +
49A LYS* 1.3 83.1 - - - +
51A LYS* 1.3 68.5 + - + +
53A GLU* 3.5 10.3 + - - +
54A LEU* 3.0 30.4 + - - +
28D SER 4.0 12.3 - - - +
29D ILE* 4.4 16.6 - - + +
32D GLY* 3.9 34.5 - - - +
33D GLN 4.7 1.1 - - - +
36D VAL* 4.8 4.3 - - + -
128D CYS* 3.9 31.6 - - + +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 2.9 31.5 + - - +
48A ALA* 3.7 5.6 - - - +
50A LEU* 1.3 80.3 - - - +
52A GLY* 1.3 67.2 + - - +
54A LEU* 3.2 18.4 + - + +
55A VAL* 3.1 26.4 + - - +
66A SER* 4.5 1.3 - - - +
115A THR* 3.9 31.4 - - + +
116A ASP 3.5 24.8 - - - +
117A VAL* 4.2 5.2 - - + -
152A LEU* 4.4 6.3 - - + -
127D ASP* 2.7 39.4 + - - -
128D CYS* 5.2 2.5 - - - +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA 2.7 20.0 + - - -
49A LYS 3.9 0.9 - - - -
51A LYS* 1.3 70.5 - - - +
53A GLU* 1.3 61.8 - - - +
55A VAL* 3.0 17.8 + - - +
56A ARG* 3.0 37.9 + - - +
149A GLU* 4.3 3.1 - - - -
150A GLU 4.4 2.0 - - - -
151A PRO* 5.4 0.2 - - - -
152A LEU* 4.0 15.1 - - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 3.0 47.3 + - + +
50A LEU* 3.7 12.6 - - - +
52A GLY* 1.3 71.5 - - - +
54A LEU* 1.3 53.2 + - - +
56A ARG* 3.2 19.6 + - - +
57A LEU* 2.8 53.5 + - + +
28D SER* 3.1 27.7 + - - -
29D ILE* 5.8 1.6 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU 3.0 17.4 + - - +
51A LYS* 3.5 22.9 - - + +
52A GLY 3.2 0.2 - - - -
53A GLU* 1.3 74.9 - - - +
55A VAL* 1.3 62.3 + - - +
57A LEU* 3.4 27.6 - - + +
58A LEU 3.9 4.2 + - - +
111A PRO* 3.6 34.0 - - + +
115A THR* 5.3 0.4 - - + -
29D ILE* 6.2 4.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS 3.2 15.9 - - - +
52A GLY 3.0 7.9 + - - +
54A LEU* 1.3 74.9 - - - +
56A ARG* 1.3 66.6 + - + +
57A LEU 3.3 0.5 + - - -
58A LEU 3.2 21.5 - - - +
59A GLY* 3.6 3.7 - - - -
61A ALA* 4.6 4.0 - - + -
64A SER* 3.5 21.8 - - - +
111A PRO* 3.4 29.4 - - + +
112A ARG* 3.8 16.9 - - + +
115A THR* 3.9 8.5 - - + -
151A PRO* 4.0 20.9 - - + -
152A LEU* 4.4 11.4 - - + -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 3.0 26.7 + - - +
53A GLU* 3.2 35.2 - - - +
55A VAL* 1.3 73.8 - - - +
57A LEU* 1.3 66.0 + - + +
58A LEU 3.1 1.0 + - - -
59A GLY* 3.2 18.6 + - - -
149A GLU* 4.4 14.6 + - - +
150A GLU* 2.3 45.3 + - - +
151A PRO* 4.1 15.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 2.8 40.3 + - + +
54A LEU* 3.4 21.3 - - + +
55A VAL 3.2 0.4 - - - -
56A ARG* 1.3 74.8 - - + +
58A LEU* 1.3 67.6 + - - +
29D ILE* 6.0 6.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 3.9 3.9 + - - +
55A VAL 3.2 6.4 + - - +
56A ARG 3.3 0.2 - - - -
57A LEU* 1.3 82.1 - - - +
59A GLY* 1.3 59.9 + - - +
112A ARG* 3.2 28.5 + - - +
----------------------------------------------------------
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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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