Contacts of the helix formed by residues 27 - 51 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 3.7 31.6 - - + -
20B MET* 3.5 39.5 - - + -
21B ASP* 3.2 10.1 - - - +
24B ASP* 3.2 31.3 + - + +
25B SER 3.3 2.4 + - - -
26B ASP* 1.3 74.0 - - - +
28B SER* 1.3 66.1 + - - +
30B GLY* 2.7 20.8 + - - -
31B LEU* 3.0 30.8 + - + +
64D HIS* 3.7 30.8 - + - -
67D LYS* 3.9 17.5 - - + -
68D GLY* 4.1 19.7 - - - -
71D ALA* 4.7 2.2 - - + -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 5.6 2.2 - - - -
17B ILE* 4.2 24.2 - - - -
18B ILE* 4.2 8.4 - - - +
21B ASP* 2.7 35.3 + - - -
27B PHE* 1.3 76.5 - - - +
29B LYS* 1.3 65.4 + - - +
30B GLY 3.1 0.5 + - - -
31B LEU* 3.2 5.7 + - - +
32B ILE* 3.0 26.7 + - - +
163B TYR* 2.7 31.9 + - - -
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 5.7 1.3 + - - +
26B ASP* 3.8 29.3 + - - +
27B PHE 3.2 1.2 - - - +
28B SER* 1.3 82.2 + - - +
30B GLY* 1.3 56.6 + - - +
32B ILE* 3.7 6.8 + - + +
33B ILE* 3.1 54.7 + - + +
163B TYR* 3.6 35.7 + - + +
165B THR* 3.5 29.9 - - - +
167B LEU* 5.1 5.2 - - + -
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 3.2 14.8 + - - -
27B PHE 2.7 11.4 + - - -
29B LYS* 1.3 76.3 - - - +
31B LEU* 1.3 58.7 + - - -
33B ILE* 3.4 7.9 + - - +
34B GLN* 3.0 28.9 + - - +
64D HIS* 5.3 8.5 - - - -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.8 32.3 - - + -
27B PHE* 3.0 34.1 + - + +
28B SER* 3.2 6.9 + - - +
30B GLY* 1.3 73.4 - - - +
32B ILE* 1.3 54.0 - - - +
34B GLN* 3.0 24.0 + - - +
35B PHE* 2.8 34.8 + - - +
73B LEU* 4.0 23.7 - - + +
64D HIS* 5.0 9.6 - - + +
68D GLY* 4.3 24.5 - - - +
72D ALA* 6.5 0.4 - - + -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 5.2 9.2 - - + -
28B SER* 3.0 11.9 + - - +
29B LYS* 3.7 7.0 - - + +
31B LEU* 1.3 74.0 - - + +
33B ILE* 1.3 58.1 + - - +
35B PHE* 3.2 5.2 + - + +
36B ILE* 3.0 44.4 + - + +
73B LEU* 4.1 21.5 - - + +
159B LEU* 4.1 32.5 - - + -
163B TYR* 3.5 46.9 - - + +
167B LEU* 4.1 14.6 - - + -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 3.1 51.6 + - + +
30B GLY* 3.4 6.5 + - - +
31B LEU 3.2 0.2 - - - -
32B ILE* 1.3 74.8 - - - +
34B GLN* 1.3 65.8 + - - +
36B ILE* 3.7 12.5 + - + +
37B ASP* 3.6 17.0 + - - +
167B LEU* 4.5 18.6 - - + -
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY 3.0 14.5 + - - +
31B LEU* 3.0 28.5 + - - +
33B ILE* 1.3 76.8 - - - +
35B PHE* 1.3 64.0 + - - +
37B ASP* 3.2 7.6 + - - +
38B GLN* 3.1 42.7 + - + +
64D HIS* 5.1 11.7 + - - -
65D PHE* 5.6 10.4 - - - +
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 2.8 6.0 + - - +
32B ILE* 3.2 11.0 + - + +
34B GLN* 1.3 77.4 - - - +
36B ILE* 1.3 58.7 + - + +
38B GLN* 3.2 9.7 + - - +
39B ALA* 2.8 44.6 + - + +
66B LEU* 3.5 27.8 - - + -
69B SER* 3.8 19.7 - - - -
70B SER* 4.0 19.7 - - - -
73B LEU* 3.5 22.7 - - + -
75B LEU* 3.4 31.0 - - + -
78B ILE* 4.0 17.5 - - + -
152B PHE* 3.8 22.9 - + - -
155B ALA* 5.7 0.4 - - + -
159B LEU* 6.3 0.4 - - + -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.0 36.4 + - + +
33B ILE* 3.9 13.0 - - + +
34B GLN 3.3 0.4 - - - -
35B PHE* 1.3 79.0 - - + +
37B ASP* 1.3 61.0 + - - +
40B GLN* 3.3 41.3 + - - +
152B PHE* 3.5 16.9 - - + -
156B ARG* 3.5 27.6 - - + +
159B LEU* 6.2 0.7 - - + -
167B LEU* 3.5 33.4 - - + +
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE 3.6 8.7 + - - +
34B GLN* 3.2 8.8 + - - +
35B PHE 3.1 0.4 - - - -
36B ILE* 1.3 80.5 - - - +
38B GLN* 1.3 64.7 + - - +
40B GLN* 3.5 14.3 + - - +
41B THR* 2.9 34.9 + - - -
45C GLN* 4.1 17.8 + - - -
48C ARG* 4.7 8.0 + - - -
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.1 36.1 + - + +
35B PHE* 3.7 12.8 - - + +
37B ASP* 1.3 75.8 + - - +
39B ALA* 1.3 59.3 + - - +
41B THR* 2.8 23.6 + - - -
42B THR* 2.9 20.1 + - - +
65B PHE* 3.4 34.9 - - + -
66B LEU* 5.7 0.4 - - + -
69B SER* 3.5 19.8 + - - -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 2.8 35.9 + - + +
38B GLN* 1.3 72.1 - - - +
40B GLN* 1.3 63.3 + - - +
41B THR 3.1 0.7 + - - -
42B THR* 3.2 2.2 + - - -
43B PHE* 3.0 35.0 + - + -
66B LEU* 4.0 16.7 - - + +
152B PHE* 3.5 30.5 - - + -
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Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.3 29.8 + - - +
37B ASP* 3.8 13.3 + - - +
39B ALA* 1.3 78.8 - - - +
41B THR* 1.3 61.4 + - - +
43B PHE* 4.0 9.1 + - + +
44B ALA* 3.4 14.4 + - - +
152B PHE* 3.7 10.3 - - + -
156B ARG* 3.2 27.8 + - - +
48C ARG* 3.2 48.5 + - - +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASP* 2.9 22.1 + - - -
38B GLN* 2.8 12.1 + - - -
40B GLN* 1.3 76.1 - - - +
42B THR* 1.3 61.3 + - + +
44B ALA* 3.3 5.1 + - + +
45B GLN* 3.0 37.0 + - + +
48B ARG* 5.3 0.2 + - - -
41C THR* 4.2 25.1 - - + -
45C GLN* 4.7 6.5 + - + -
48C ARG* 3.3 21.1 + - - +
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN* 2.9 16.3 + - - +
39B ALA* 3.4 2.1 + - - -
41B THR* 1.3 73.8 - - + +
43B PHE* 1.3 60.6 + - - +
45B GLN* 2.9 15.0 + - - +
46B MET* 2.7 41.6 + - - +
62B LEU* 4.5 15.9 - - + -
65B PHE* 3.5 35.2 - - + -
66B LEU* 3.1 28.1 - - + +
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Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.0 20.0 + - + +
40B GLN* 4.0 8.1 - - + +
42B THR* 1.3 81.7 + - - +
44B ALA* 1.3 55.7 + - - +
46B MET* 3.3 8.0 + - + +
47B GLN* 2.9 29.4 + - - +
66B LEU* 3.4 28.5 - - + -
78B ILE* 5.1 7.0 - - + -
82B CYS* 5.6 0.7 - - - -
85B ILE* 6.1 0.2 - - + -
145B LEU* 3.4 25.8 - - + +
148B SER* 3.6 37.9 - - - -
149B ARG* 4.2 23.8 - - + +
152B PHE* 3.8 37.5 - + + -
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLN 3.4 11.4 + - - +
41B THR* 3.3 10.6 + - - +
42B THR 3.1 0.8 - - - -
43B PHE* 1.3 78.9 - - - +
45B GLN* 1.3 57.7 + - - +
47B GLN* 3.4 7.1 + - - +
48B ARG* 3.0 51.7 + - - +
149B ARG* 5.7 0.7 - - - +
44C ALA* 5.1 1.3 - - + -
48C ARG* 3.9 13.5 - - - +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.0 31.0 + - + +
42B THR* 2.9 15.7 + - - +
44B ALA* 1.3 74.1 - - - +
46B MET* 1.3 64.6 + - - +
48B ARG* 3.4 23.6 + - - +
49B GLN* 3.3 23.6 + - - +
62B LEU* 4.0 31.3 - - + +
37C ASP* 4.1 22.0 + - - -
41C THR* 4.7 7.1 + - - +
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Residues in contact with MET 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 2.7 23.5 + - - +
43B PHE* 3.5 11.0 - - + +
45B GLN* 1.3 73.2 - - - +
47B GLN* 1.3 61.3 + - - +
49B GLN* 3.2 4.5 + - - +
50B LEU* 3.1 27.4 + - + +
59B LEU* 3.6 19.1 - - + +
62B LEU* 3.5 26.0 - - + +
63B GLY* 3.5 35.0 - - - +
66B LEU* 4.5 15.3 - - + -
82B CYS* 5.2 1.6 - - - -
85B ILE* 4.3 24.7 - - + -
141B ILE* 6.3 1.1 - - + -
145B LEU* 3.9 28.0 - - + -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE 2.9 17.5 + - - +
44B ALA* 3.7 8.7 - - - +
46B MET* 1.3 77.0 - - - +
48B ARG* 1.3 61.7 + - - +
50B LEU* 3.6 10.5 + - - +
51B ASP* 3.2 43.6 + - - +
122B GLU* 3.4 27.2 - - + +
123B GLU 5.3 2.4 - - - +
142B ALA 6.0 0.2 + - - -
145B LEU* 3.7 10.0 - - + +
149B ARG* 2.7 37.7 - - - +
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 3.0 42.1 + - - +
45B GLN* 3.6 23.1 - - - +
46B MET 3.2 0.2 - - - -
47B GLN* 1.3 77.6 - - - +
49B GLN* 1.3 57.7 + - - +
51B ASP* 3.9 5.4 - - - +
52B GLY* 3.1 21.8 + - - -
53B GLU 4.3 0.9 + - - -
37C ASP* 4.5 9.6 + - - -
40C GLN* 3.2 53.6 + - + +
41C THR* 3.2 31.5 + - - +
44C ALA* 3.9 13.5 - - - +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN 3.3 12.4 + - - +
46B MET* 3.2 8.9 + - - +
47B GLN 3.2 0.4 - - - -
48B ARG* 1.3 77.1 - - - +
50B LEU* 1.3 67.4 + - - +
51B ASP 3.0 1.3 - - - -
52B GLY 3.0 5.4 + - - +
53B GLU* 3.0 42.2 + - - +
54B LYS* 2.8 26.8 + - - +
55B ASN* 3.3 30.3 - - - +
58B GLU* 3.5 26.4 + - + +
59B LEU* 3.9 15.0 - - + -
62B LEU* 4.8 4.0 - - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET 3.1 18.0 + - - +
47B GLN* 3.8 19.1 - - - +
49B GLN* 1.3 79.5 - - - +
51B ASP* 1.3 60.8 + - - +
54B LYS* 2.9 32.6 + - - +
59B LEU* 3.8 25.8 - - + -
126B ILE* 5.1 1.9 - - - +
138B LEU* 4.0 26.4 - - + +
141B ILE* 4.0 10.5 - - + -
142B ALA* 4.0 28.7 - - + +
145B LEU* 3.7 26.0 - - + -
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 3.2 40.7 + - - +
48B ARG* 4.0 5.1 - - - +
49B GLN 3.0 0.8 - - - -
50B LEU* 1.3 80.5 - - - +
52B GLY* 1.3 58.4 + - - +
54B LYS* 4.5 6.2 - - - +
123B GLU 5.5 2.6 - - - +
125B 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