Contacts of the helix formed by residues 10 - 36 (chain D) in PDB entry 1IES
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 THR 10 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 3.6 10.0 + - - +
9D SER* 1.3 69.9 - - - +
11D GLU* 1.3 76.9 + - - +
13D GLU* 3.7 10.5 - - - +
14D ALA* 3.0 26.0 + - + +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER* 3.2 10.0 - - - +
10D THR* 1.3 87.8 + - - +
12D VAL* 1.3 57.3 + - - +
14D ALA* 3.5 5.2 + - - +
15D ALA* 2.9 27.2 + - - +
18D ARG* 5.0 2.4 + - - -
116D LEU* 3.8 24.7 - - + +
120D GLN* 3.6 26.8 + - - +
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Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.5 26.9 - - + -
9D SER* 3.2 24.7 + - - +
11D GLU* 1.3 76.2 - - - +
13D GLU* 1.3 67.4 + - - +
15D ALA* 3.0 1.9 + - - +
16D VAL* 2.8 25.9 + - + +
113D LEU* 4.3 1.1 - - + -
116D LEU* 3.9 20.4 - - + -
117D GLY* 4.5 3.6 - - - +
120D GLN* 4.1 15.7 - - + -
122D ASP* 4.4 6.7 - - - +
125D LEU* 3.7 37.5 - - + -
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 2.9 31.9 + - - -
8D TYR* 3.9 9.8 - - + -
9D SER 2.9 16.1 + - - +
10D THR* 3.7 14.5 - - - +
12D VAL* 1.3 76.3 - - - +
14D ALA* 1.3 59.9 + - - +
16D VAL 3.4 0.2 + - - -
17D ASN* 3.0 27.4 + - - +
69D GLN* 3.1 36.2 + - - +
74D GLY* 3.6 2.4 - - - -
75D ARG* 2.8 37.2 + - - +
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR 3.0 18.9 + - - +
11D GLU* 3.5 5.6 - - - +
13D GLU* 1.3 75.9 - - - +
15D ALA* 1.3 63.2 + - - +
17D ASN* 3.2 10.1 + - - +
18D ARG* 3.0 41.1 + - - +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLU 2.9 17.9 + - - +
12D VAL 3.0 4.2 + - - +
14D ALA* 1.3 75.2 - - - +
16D VAL* 1.3 52.3 + - - +
18D ARG* 3.3 25.7 + - - +
19D LEU* 2.8 34.4 + - - +
113D LEU* 3.7 26.1 - - + +
116D LEU* 3.8 11.9 - - + -
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.4 15.0 - - - +
12D VAL* 2.8 32.0 + - + +
13D GLU 3.6 4.7 - - - +
15D ALA* 1.3 70.3 - - - +
17D ASN* 1.3 63.8 + - - +
19D LEU* 3.0 8.8 + - - +
20D VAL* 2.9 25.7 + - + +
65D LEU* 4.0 31.9 - - + +
68D MET* 3.9 21.8 - - + -
69D GLN* 3.8 15.9 - - + +
113D LEU* 4.2 15.7 - - + -
125D LEU* 4.3 0.7 - - + -
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLU* 3.0 16.4 + - - +
14D ALA* 3.2 12.9 + - - +
16D VAL* 1.3 76.9 - - - +
18D ARG* 1.3 60.2 + - - +
20D VAL* 3.7 8.3 + - - +
21D ASN* 3.5 16.8 + - - +
66D LEU* 5.0 4.9 - - - +
69D GLN* 3.1 17.6 + - - +
75D ARG 2.9 23.0 + - - -
76D ALA* 3.3 6.8 - - - +
77D LEU* 3.0 48.7 + - + +
79D GLN* 4.1 10.6 + - - +
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLU 5.0 1.8 + - - -
14D ALA* 3.0 34.1 + - + +
15D ALA* 3.6 29.0 - - - +
17D ASN* 1.3 72.5 - - - +
19D LEU* 1.3 65.2 + - - +
21D ASN* 3.1 17.7 + - - +
22D LEU* 3.1 20.5 + - + +
79D GLN* 4.5 13.9 - - - +
116D LEU* 5.6 2.6 - - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA 2.8 17.7 + - - +
16D VAL* 3.0 6.2 + - - +
18D ARG* 1.3 76.7 - - - +
20D VAL* 1.3 60.8 + - - +
22D LEU* 3.2 12.6 + - + +
23D TYR* 3.0 42.4 + - + -
65D LEU* 4.0 24.0 - - + -
106D LEU* 4.8 1.6 - - + +
109D ALA* 3.5 32.5 - - + -
110D LEU* 3.6 28.3 - - + +
113D LEU* 3.6 28.0 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL* 2.9 23.1 + - + +
17D ASN* 3.7 12.6 - - - +
18D ARG 3.3 0.2 - - - -
19D LEU* 1.3 73.3 - - - +
21D ASN* 1.3 63.4 + - - +
23D TYR* 3.4 4.6 + - - +
24D LEU* 2.9 41.7 + - + +
62D ALA* 4.1 6.9 - - + +
65D LEU* 3.8 29.2 - - + -
66D LEU* 3.7 40.4 - - + +
69D GLN* 6.0 0.2 - - - +
77D LEU 5.7 1.8 - - - +
78D PHE* 4.2 8.5 - - + -
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN 3.5 5.1 + - - +
18D ARG* 3.1 11.0 + - - +
20D VAL* 1.3 80.3 - - - +
22D LEU* 1.3 62.6 + - + +
24D LEU* 3.3 8.4 + - - +
25D ARG* 2.9 35.0 + - - +
79D GLN* 3.6 38.2 + - - +
80D ASP 3.2 26.1 + - - +
81D LEU* 3.8 12.1 - - - +
82D GLN 5.7 0.3 + - - -
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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
----------------------------------------------------------
18D ARG* 3.1 18.3 + - + +
19D LEU* 3.2 16.1 + - + +
21D ASN* 1.3 86.4 - - + +
23D TYR* 1.3 57.4 + - - +
25D ARG* 3.3 6.3 + - - +
26D ALA* 2.8 30.7 + - - +
105D SER* 4.9 3.6 - - - +
106D LEU* 4.0 21.4 - - + +
109D ALA* 3.6 32.3 - - + -
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Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.0 46.4 + - + +
20D VAL 3.8 0.4 - - - +
22D LEU* 1.3 76.0 - - - +
24D LEU* 1.3 57.9 + - - +
26D ALA* 3.3 6.4 + - - +
27D SER* 2.9 28.9 + - - -
57D GLU 5.3 0.4 - - - -
58D LYS* 3.5 49.1 - - + +
61D GLY* 4.2 3.8 - - - -
62D ALA* 3.7 28.0 - - + +
65D LEU* 4.0 11.9 - - + -
106D LEU* 4.1 16.6 - - + +
110D LEU* 3.7 21.3 - - + +
133D PHE* 3.4 29.1 - + - +
136D GLU* 5.6 4.7 + - - -
137D GLU* 3.7 11.1 + - - -
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 2.9 36.3 + - + +
21D ASN* 3.6 5.4 - - - +
23D TYR* 1.3 76.3 - - - +
25D ARG* 1.4 57.0 + - - +
27D SER* 3.1 8.7 - - - -
28D TYR* 2.9 26.9 + - - +
59D ARG* 4.7 15.9 - - + +
62D ALA* 3.4 25.4 - - + -
63D GLU* 6.3 0.7 - - + -
66D LEU* 5.3 2.5 - - + -
78D PHE* 4.5 17.9 - - + -
81D LEU* 3.9 32.7 - - + +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN* 2.9 28.6 + - - +
22D LEU* 3.7 7.0 - - - +
24D LEU* 1.4 73.1 - - - +
26D ALA* 1.3 55.4 + - - +
28D TYR* 3.2 7.5 + - + +
29D THR* 2.9 53.0 + - - +
81D LEU* 4.3 6.2 - - + +
82D GLN* 3.4 54.7 + - - +
83D LYS 2.7 26.4 + - - -
84D PRO* 4.3 0.9 - - - -
85D SER* 3.5 26.0 + - - +
102D LEU* 5.5 7.3 - - - +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU 2.8 19.8 + - - +
23D TYR 3.6 4.7 - - - +
25D ARG* 1.3 70.4 - - - +
27D SER* 1.3 58.0 + - - +
29D THR* 3.3 3.6 + - - -
30D TYR* 2.8 38.7 + - + -
58D LYS* 4.2 8.7 - - + -
102D LEU* 4.1 27.8 - - + +
106D LEU* 3.9 26.0 - - + -
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR 2.9 13.3 + - - -
24D LEU* 3.1 15.9 - - - -
26D ALA* 1.3 78.2 - - - +
28D TYR* 1.3 56.7 + - - -
30D TYR* 3.2 2.3 + - - +
31D LEU* 2.9 28.2 + - - +
55D ALA* 2.9 31.1 + - - +
58D LYS* 3.8 11.6 - - - +
59D ARG* 3.6 17.0 + - - +
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU 2.9 12.5 + - - +
25D ARG* 3.2 10.1 + - - +
27D SER* 1.3 73.7 - - - +
29D THR* 1.3 63.4 + - - +
31D LEU* 3.2 25.5 + - + +
32D SER* 3.0 22.4 + - - -
81D LEU* 4.4 23.6 - - + -
82D GLN 3.7 18.2 - - - -
83D LYS* 3.7 24.2 - - - +
84D PRO* 3.8 15.4 - - + +
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 2.9 34.7 + - - +
26D ALA* 3.3 9.7 + - - -
28D TYR* 1.3 75.2 - - - +
30D TYR* 1.3 57.7 + - - +
32D SER* 3.1 5.4 + - - -
33D LEU* 2.8 41.1 + - + +
84D PRO* 3.7 16.8 - - + +
85D SER* 5.4 2.2 - - - +
89D TRP* 4.1 17.8 - - + -
102D LEU* 3.7 24.1 - - + +
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Residues in contact with TYR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ALA* 2.8 30.4 + - + +
27D SER 3.6 2.2 - - - +
29D THR* 1.3 72.4 - - - +
31D LEU* 1.3 57.3 + - - +
33D LEU* 3.7 14.5 - - + +
34D GLY* 2.8 28.9 + - - -
51D PHE* 3.5 55.2 - + - +
52D ARG* 5.0 0.2 - - - -
54D LEU* 3.9 24.2 - - + -
55D ALA* 3.6 10.1 - - - +
58D LYS* 3.9 16.8 - - + -
99D ALA* 3.7 12.5 + - + +
102D LEU* 3.7 18.4 - - + +
103D GLU* 2.6 39.4 + - - +
144D MET* 3.6 8.5 - - - +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER 2.9 12.8 + - - +
28D TYR* 3.3 29.6 - - + +
30D TYR* 1.3 76.4 - - - +
32D SER* 1.3 62.0 + - - +
34D GLY* 3.8 0.7 - - - -
35D PHE* 3.0 61.1 + - + -
52D ARG* 4.6 13.0 - - - +
55D ALA* 3.8 11.5 - - + +
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Residues in contact with SER 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 3.0 8.1 + - - -
29D THR 3.4 7.6 - - - -
31D LEU* 1.3 77.7 - - - +
33D LEU* 1.3 61.7 + - - +
35D PHE* 3.5 3.0 + - - +
36D TYR* 3.2 22.5 + - - +
84D PRO* 3.8 23.5 - - - +
86D GLN 3.9 6.1 + - - -
87D ASP* 5.0 3.8 + - - -
89D TRP* 3.0 22.3 + - - -
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR* 2.8 31.8 + - + +
30D TYR* 3.7 33.9 - - + +
32D SER* 1.3 71.3 + - - +
34D GLY* 1.3 63.2 + - - +
36D TYR* 3.2 11.1 + - - +
37D PHE* 3.3 22.2 - - + -
51D PHE* 4.0 21.3 - - + -
89D TRP* 3.6 44.6 - - + +
95D ALA* 3.8 33.2 - - + +
98D ALA* 5.3 1.6 - - + -
99D ALA* 5.0 6.1 - - + +
102D LEU* 5.5 0.2 - - + -
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR 2.8 19.8 + - - -
31D LEU 3.8 1.3 - - - -
33D LEU* 1.3 74.6 - - - +
35D PHE* 1.3 61.2 + - - +
36D TYR 3.3 0.5 + - - -
37D PHE 3.5 3.8 + - - -
38D ASP 3.7 0.9 + - - -
48D CYS* 3.2 42.2 - - - +
51D PHE* 3.7 15.6 - - - +
52D ARG* 4.1 7.6 - - - -
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Residues in contact with PHE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 3.0 51.9 + - + +
32D SER* 4.4 2.9 - - - +
34D GLY* 1.3 73.8 - - - +
36D TYR* 1.3 65.3 + - - +
38D ASP* 3.5 35.2 + - + +
39D ARG* 3.6 8.5 + - - +
48D CYS* 5.5 0.9 - - - -
52D ARG* 3.4 41.5 - - - -
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Residues in contact with TYR 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D SER 3.2 13.2 + - - +
33D LEU 3.2 8.6 + - - +
35D PHE* 1.3 75.3 - - - +
37D PHE* 1.3 74.5 + + - +
38D ASP 3.0 0.2 - - - -
39D ARG* 2.8 65.4 + - - +
42D VAL* 3.7 23.4 - - + +
87D ASP 4.4 4.7 - - - +
88D GLU* 3.8 19.9 + - + +
89D TRP* 3.5 34.3 - + + -
90D GLY* 2.8 47.7 + - - -
----------------------------------------------------------
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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