Contacts of the helix formed by residues 27 - 51 (chain D) in PDB entry 1C03
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 PHE 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS* 3.8 28.8 - + - -
67B LYS* 3.9 17.7 - - + -
68B GLY* 4.1 20.9 - - - -
71B ALA* 4.7 2.7 - - + -
17D ILE* 3.7 32.1 - - + -
20D MET* 3.5 39.5 - - + +
21D ASP* 3.2 9.4 + - - +
24D ASP* 3.2 30.0 + - + +
25D SER 3.3 4.0 + - - -
26D ASP* 1.3 74.4 - - - +
28D SER* 1.3 66.5 + - - +
29D LYS 4.3 0.2 - - - +
30D GLY* 2.7 20.6 + - - -
31D LEU* 3.0 29.2 + - + +
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 5.6 2.2 - - - -
17D ILE* 4.2 23.3 - - - -
18D ILE* 4.3 8.7 - - - +
21D ASP* 2.7 36.9 + - - -
27D PHE* 1.3 75.6 - - - +
29D LYS* 1.3 65.4 + - - +
30D GLY 3.1 0.5 + - - -
31D LEU* 3.2 6.4 + - - +
32D ILE* 3.0 26.0 + - - +
73D LEU* 5.6 0.2 - - - +
163D TYR* 2.8 28.7 + - - -
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASP* 5.3 0.2 - - - -
25D SER 5.7 0.7 - - - +
26D ASP* 3.8 28.9 + - + +
27D PHE 4.3 0.6 - - - +
28D SER* 1.3 82.0 + - - +
30D GLY* 1.3 58.7 + - - +
32D ILE* 3.7 5.9 + - + +
33D ILE* 3.1 53.0 + - + +
163D TYR* 3.6 37.0 + - + +
165D THR* 3.5 31.0 - - - +
167D LEU* 5.1 5.6 - - + -
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Residues in contact with GLY 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 5.4 9.6 - - - -
26D ASP 3.2 14.1 + - - -
27D PHE 2.7 10.4 + - - -
29D LYS* 1.3 78.0 - - - +
31D LEU* 1.3 58.5 + - - -
33D ILE* 3.5 7.3 + - - +
34D GLN* 3.0 28.0 + - - +
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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
----------------------------------------------------------
64B HIS* 5.0 8.5 - - + +
68B GLY* 4.3 24.2 - - - +
17D ILE* 3.8 33.0 - - + -
27D PHE* 3.0 34.5 + - + +
28D SER 3.5 6.3 - - - +
30D GLY* 1.3 73.9 - - - +
32D ILE* 1.3 54.8 + - - +
34D GLN* 2.9 25.0 + - - +
35D PHE* 2.8 34.1 + - - +
73D LEU* 4.0 24.1 - - + +
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 5.2 8.1 - - + -
28D SER* 3.0 13.0 + - - +
29D LYS* 3.8 6.5 - - - +
31D LEU* 1.3 74.2 - - - +
33D ILE* 1.3 58.7 + - - +
35D PHE* 3.2 4.9 + - + +
36D ILE* 3.0 43.3 + - + +
73D LEU* 4.1 21.8 - - + -
159D LEU* 4.0 33.9 - - + -
163D TYR* 3.5 46.2 - - + +
167D LEU* 4.1 19.1 - - + -
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 3.1 49.8 + - + +
30D GLY* 3.9 7.0 - - - +
32D ILE* 1.3 75.8 - - - +
34D GLN* 1.3 67.1 + - - +
36D ILE* 3.7 11.8 + - + +
37D ASP* 3.6 17.2 + - - +
167D LEU* 4.5 17.3 - - + -
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Residues in contact with GLN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 5.0 12.1 + - - -
65B PHE* 5.6 9.8 - - - +
30D GLY 3.0 13.2 + - - +
31D LEU* 2.9 27.8 + - - +
33D ILE* 1.3 77.4 - - - +
35D PHE* 1.3 62.2 + - - +
37D ASP* 3.2 8.5 + - - +
38D GLN* 3.1 41.1 + - - +
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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 2.8 6.0 + - - +
32D ILE* 3.4 11.2 - - + +
34D GLN* 1.3 77.4 - - - +
36D ILE* 1.3 56.3 + - + +
38D GLN* 3.2 10.7 + - - +
39D ALA* 2.8 44.7 + - + +
66D LEU* 3.5 27.4 - - + -
69D SER* 3.8 19.5 - - - -
70D SER* 4.0 23.1 - - - -
73D LEU* 3.5 23.1 - - + -
75D LEU* 3.4 27.1 - - + -
78D ILE* 4.1 17.0 - - + -
152D PHE* 3.8 22.4 - + - -
155D ALA* 5.7 0.2 - - + -
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 3.0 38.5 + - + +
33D ILE* 3.9 12.3 - - + +
34D GLN 3.3 0.4 - - - -
35D PHE* 1.3 79.8 - - + +
37D ASP* 1.3 60.6 + - - +
40D GLN* 3.4 41.6 + - - +
152D PHE* 3.5 18.0 - - + -
156D ARG* 3.5 27.8 - - + +
159D LEU* 6.2 0.4 - - + -
167D LEU* 3.5 32.8 - - + +
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Residues in contact with ASP 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 4.1 16.0 + - - -
48A ARG* 4.5 11.3 + - - -
33D ILE 3.6 8.8 + - - +
34D GLN* 3.2 9.7 + - - +
35D PHE 3.1 1.0 - - - -
36D ILE* 1.3 78.8 - - - +
38D GLN* 1.3 64.0 + - + +
40D GLN* 3.5 12.6 + - - +
41D THR* 2.9 36.5 + - - -
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLN* 3.1 35.4 + - + +
35D PHE* 3.7 13.9 - - + +
37D ASP* 1.3 75.1 - - - +
39D ALA* 1.3 59.5 + - - +
41D THR* 2.8 22.7 + - - -
42D THR* 2.9 19.5 + - - +
65D PHE* 3.4 35.3 - - + -
66D LEU* 5.7 0.7 - - + -
69D SER* 3.5 20.0 + - - -
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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
----------------------------------------------------------
35D PHE* 2.8 35.7 + - + +
38D GLN* 1.3 71.6 - - - +
40D GLN* 1.3 63.9 + - - +
41D THR 3.1 0.2 + - - -
42D THR* 3.2 2.0 + - - -
43D PHE* 3.0 35.8 + - + -
66D LEU* 4.0 16.5 - - + +
152D PHE* 3.5 30.5 - - + -
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.2 47.1 + - - +
36D ILE* 3.4 31.4 + - - +
37D ASP* 3.8 13.6 + - - +
38D GLN 3.3 0.4 - - - -
39D ALA* 1.3 78.9 - - - +
41D THR* 1.3 62.4 + - - +
43D PHE* 3.9 9.3 + - + +
44D ALA* 3.4 14.9 + - - +
152D PHE* 3.7 10.7 - - + -
156D ARG* 3.2 26.2 + - - +
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Residues in contact with THR 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.2 25.6 - - + -
45A GLN* 4.8 5.9 + - + -
48A ARG* 3.3 21.9 + - - +
37D ASP* 2.9 24.1 + - - -
38D GLN* 2.8 11.7 + - - -
40D GLN* 1.3 78.9 - - - +
42D THR* 1.3 59.3 + - + +
44D ALA* 3.3 5.4 + - + +
45D GLN* 3.1 37.8 + - + +
48D ARG* 5.3 0.2 + - - -
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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
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38D GLN* 2.9 16.9 + - - +
39D ALA* 3.4 2.0 + - - -
41D THR* 1.3 75.3 - - + +
43D PHE* 1.3 60.1 + - - +
44D ALA 3.1 0.2 - - - -
45D GLN* 3.0 15.2 + - - +
46D MET* 2.7 42.1 + - - +
62D LEU* 4.5 15.5 - - + -
65D PHE* 3.5 36.3 - - + -
66D LEU* 3.0 28.4 - - + +
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Residues in contact with PHE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 3.0 21.1 + - + +
40D GLN* 4.0 8.1 - - + +
42D THR* 1.3 81.4 + - - +
44D ALA* 1.3 56.5 + - - +
46D MET* 3.3 7.4 + - - +
47D GLN* 2.9 29.7 + - - +
66D LEU* 3.4 29.8 - - + -
78D ILE* 5.1 6.7 - - + -
82D CYS* 5.6 0.7 - - - -
85D ILE* 6.2 0.2 - - + -
145D LEU* 3.4 25.1 - - + +
148D SER* 3.6 39.0 - - - -
149D ARG* 4.2 25.7 + - + +
152D PHE* 3.8 36.6 - + + -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 5.2 1.3 - - + -
48A ARG* 4.0 13.0 - - - +
40D GLN 3.4 11.2 + - - +
41D THR 3.3 9.9 + - - +
42D THR 3.1 0.4 - - - -
43D PHE* 1.3 80.9 - - - +
45D GLN* 1.3 56.4 + - - +
47D GLN* 3.7 6.9 - - - +
48D ARG* 3.0 51.2 + - - +
149D ARG* 5.7 0.4 - - - +
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 4.1 22.8 + - - -
41A THR* 4.8 5.5 + - - +
41D THR* 3.1 32.0 + - + +
42D THR* 3.0 15.7 + - - +
44D ALA* 1.3 72.7 - - - +
46D MET* 1.3 64.5 + - - +
48D ARG* 3.4 23.5 + - - +
49D GLN* 3.4 23.6 + - - +
62D LEU* 4.0 29.5 - - + +
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Residues in contact with MET 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D THR* 2.7 22.8 + - - +
43D PHE* 3.5 10.8 - - + +
45D GLN* 1.3 73.2 - - - +
47D GLN* 1.3 60.8 + - - +
49D GLN* 3.2 4.5 + - - +
50D LEU* 3.1 27.1 + - + +
59D LEU* 3.6 18.8 - - + +
62D LEU* 3.5 26.2 - - + +
63D GLY* 3.5 35.0 - - - +
66D LEU* 4.5 15.5 - - + -
82D CYS* 5.2 1.6 - - - -
85D ILE* 4.3 24.9 - - + -
141D ILE* 6.3 1.3 - - + -
145D LEU* 3.9 28.5 - - + -
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE 2.9 17.5 + - - +
44D ALA* 3.7 8.5 - - - +
45D GLN 3.3 0.2 - - - -
46D MET* 1.3 77.8 - - - +
48D ARG* 1.3 60.5 + - - +
50D LEU* 3.6 10.5 + - - +
51D ASP* 3.2 44.3 + - - +
122D GLU* 3.3 27.4 - - + +
123D GLU 5.3 2.8 - - - +
142D ALA* 6.3 0.2 - - - +
145D LEU* 3.8 9.9 - - + +
149D ARG* 2.6 38.4 - - - +
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 4.6 9.3 + - - -
40A GLN* 3.2 53.2 + - - +
41A THR* 3.4 30.3 + - - +
44A ALA* 4.0 12.3 - - - +
44D ALA* 3.0 42.4 + - - +
45D GLN* 3.6 23.5 - - - +
46D MET 3.2 0.2 - - - -
47D GLN* 1.3 76.2 - - - +
49D GLN* 1.3 59.8 + - - +
51D ASP* 3.9 5.5 - - - +
52D GLY* 3.2 21.8 + - - -
53D GLU 4.3 0.7 + - - -
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLN 3.4 12.9 + - - +
46D MET 3.2 9.3 + - - +
48D ARG* 1.3 78.9 - - - +
50D LEU* 1.3 66.4 + - - +
51D ASP 3.0 1.6 - - - -
52D GLY 3.0 5.9 + - - +
53D GLU* 3.1 40.7 + - - +
54D LYS* 2.8 26.8 + - - +
55D ASN* 3.3 31.1 - - - +
58D GLU* 3.5 26.8 + - + +
59D LEU* 3.9 14.8 - - + -
62D LEU* 4.8 4.6 - - - +
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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
----------------------------------------------------------
46D MET* 3.1 18.0 + - + +
47D GLN* 3.8 20.0 - - - +
49D GLN* 1.3 79.0 - - - +
51D ASP* 1.3 60.9 + - - +
54D LYS* 2.9 31.6 + - - +
59D LEU* 3.8 26.9 - - + -
126D ILE* 5.1 2.3 - - - +
138D LEU* 4.0 25.3 - - + +
141D ILE* 4.0 10.8 - - + -
142D ALA* 4.0 28.5 - - + -
145D LEU* 3.7 25.4 - - + -
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Residues in contact with ASP 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 3.2 41.0 + - - +
48D ARG* 4.0 5.1 - - - +
49D GLN 3.0 0.6 - - - -
50D LEU* 1.3 80.4 - - - +
52D GLY* 1.3 59.4 + - - +
54D LYS* 4.5 6.7 - - - +
123D GLU 5.5 2.6 - - - +
125D LYS* 5.7 6.1 + - - +
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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