Contacts of the helix formed by residues 37 - 60 (chain A) in PDB entry 1U5U
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 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A SER* 3.8 3.9 + - - +
36A VAL* 1.3 95.5 - - + +
38A GLY* 1.3 66.0 + - - +
39A GLY 3.3 3.2 + - - -
40A LEU* 3.3 7.1 + - - +
41A LYS* 3.1 38.8 + - - +
36B VAL* 3.6 32.1 - - + -
37B PHE* 3.9 21.1 - + - -
40B LEU* 3.6 29.6 - - + -
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 2.9 35.6 + - - -
36A VAL 3.7 0.4 - - - -
37A PHE* 1.3 76.4 - - - +
39A GLY* 1.3 56.6 + - - +
41A LYS* 3.3 6.1 + - - -
42A LEU* 2.9 30.3 + - - +
337A LYS 3.2 12.6 - - - -
338A SER* 3.5 10.0 - - - -
339A PRO* 3.6 1.3 - - - +
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER 4.4 1.0 + - - -
35A PRO 6.1 0.2 - - - -
36A VAL 5.0 2.4 + - - -
37A PHE 3.3 0.8 - - - -
38A GLY* 1.3 75.4 - - - +
40A LEU* 1.3 62.7 + - - +
42A LEU* 3.2 8.3 + - - +
43A LYS* 3.1 31.8 + - - +
337A LYS* 3.4 9.8 + - - -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.3 9.6 + - + +
39A GLY* 1.3 74.4 - - - +
41A LYS* 1.3 63.3 + - - +
43A LYS* 3.1 18.1 + - + +
44A LEU* 3.1 25.8 + - - +
37B PHE* 3.5 34.1 - - + -
40B LEU* 4.2 22.9 - - + +
41B LYS* 3.8 34.8 - - + +
44B LEU* 4.3 24.7 - - + +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 5.4 6.4 + - - +
37A PHE* 3.1 40.6 + - - +
38A GLY* 3.6 6.5 - - - +
39A GLY 3.3 0.2 - - - -
40A LEU* 1.3 75.4 - - - +
42A LEU* 1.3 62.1 + - - +
44A LEU* 3.2 12.7 - - + +
45A LYS* 3.1 30.9 + - + +
339A PRO* 3.7 21.3 - - + -
340A GLU* 5.3 6.3 + - - +
40B LEU* 4.2 23.1 - - + -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 2.9 16.9 + - - +
39A GLY* 3.6 7.2 - - - +
41A LYS* 1.3 76.3 - - - +
43A LYS* 1.3 63.7 + - + +
45A LYS* 3.4 3.7 + - + +
46A LYS* 3.0 34.2 + - - +
336A ALA* 3.7 39.3 - - + +
337A LYS 4.8 0.2 - - - -
338A SER* 4.1 19.1 - - - +
339A PRO* 3.8 10.1 - - + +
344A SER* 4.2 15.5 - - - +
347A GLU* 3.8 15.7 - - - +
348A LEU* 4.3 19.3 - - + -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY* 3.1 20.0 + - - +
40A LEU* 3.1 19.1 + - + +
42A LEU* 1.3 78.5 - - + +
44A LEU* 1.3 62.3 + - - +
46A LYS* 3.3 18.5 + - + +
47A GLU* 3.2 24.8 + - - +
44B LEU* 3.8 25.4 - - + -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU 3.1 16.9 + - - +
41A LYS* 3.2 18.4 - - + +
43A LYS* 1.3 74.9 - - - +
45A LYS* 1.3 86.1 + - + +
47A GLU* 3.2 5.4 + - - +
48A LYS* 2.9 29.2 + - + +
40B LEU* 3.9 30.7 - - + +
43B LYS* 3.8 32.8 - - + -
44B LEU* 3.7 25.8 - - + +
47B GLU* 4.0 9.5 - - + +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.1 22.8 + - - +
42A LEU* 3.7 6.7 - - + +
43A LYS 3.3 0.2 - - - -
44A LEU* 1.3 87.8 - - + +
46A LYS* 1.3 67.5 + - - +
48A LYS* 3.2 17.4 + - + +
49A PHE* 3.0 36.2 + - + -
147A SER* 3.6 22.7 - - - +
151A GLU* 2.7 34.1 + - - +
339A PRO* 4.1 16.4 - - + -
348A LEU* 4.2 6.1 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.0 31.4 + - - +
43A LYS* 3.4 18.2 - - + +
45A LYS* 1.3 78.0 - - - +
47A GLU* 1.3 59.1 + - + +
49A PHE* 3.6 2.4 + - - +
50A LYS* 3.0 37.5 + - + +
347A GLU* 2.6 51.5 + - - +
348A LEU* 3.8 18.4 - - + +
351A ALA* 3.9 24.4 - - + +
352A VAL* 4.6 1.5 - - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS 3.4 14.1 - - - +
44A LEU 3.2 7.1 + - - +
45A LYS 3.1 0.6 - - - -
46A LYS* 1.3 77.0 - - - +
48A LYS* 1.3 65.8 + - - +
50A LYS* 3.2 30.3 + - - +
51A THR* 3.0 14.3 + - - -
44B LEU* 4.0 17.7 - - + +
47B GLU* 3.6 19.5 - - + -
48B LYS* 3.7 21.2 - - - +
51B THR* 3.0 35.8 + - - +
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 2.9 15.3 + - + +
45A LYS* 3.6 20.4 - - + +
47A GLU* 1.3 77.0 - - - +
49A PHE* 1.3 67.6 + - + +
51A THR* 3.2 7.6 + - - -
52A LEU* 3.0 49.6 + - + +
151A GLU* 2.7 40.2 + - - +
154A VAL* 6.4 0.2 - - - -
47B GLU* 3.6 24.1 + - - +
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 3.0 38.1 + - + +
46A LYS* 4.2 0.9 - - - +
48A LYS* 1.3 79.0 - - + +
50A LYS* 1.3 66.3 + - - +
52A LEU* 4.1 19.5 - - + -
53A PHE* 2.9 44.2 + + + +
147A SER* 3.6 20.0 - - - -
150A LEU* 3.6 27.6 - - + -
151A GLU* 3.7 28.9 - - + -
154A VAL* 4.1 19.3 - - + -
348A LEU* 4.1 13.5 - - + -
352A VAL* 3.7 19.7 - - + -
999A HEM 4.2 5.8 - - + -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.0 31.7 + - + +
47A GLU* 3.2 34.7 + - - +
49A PHE* 1.3 76.6 - - - +
51A THR* 1.3 56.8 + - - +
53A PHE 4.0 0.2 - - - -
54A THR* 2.5 35.9 + - - -
351A ALA* 3.8 29.1 - - + +
352A VAL* 4.0 13.9 - - + -
355A TRP* 3.7 46.6 - - + -
356A VAL* 4.6 0.9 - - - +
51B THR* 4.0 8.2 - - + +
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 3.0 6.1 + - - -
48A LYS* 3.4 11.6 - - - +
50A LYS* 1.3 75.5 - - - +
52A LEU* 1.3 69.3 + - + +
54A THR* 3.2 6.7 + - - -
55A LEU* 3.1 21.8 + - - +
47B GLU* 4.0 4.5 + - - -
50B LYS* 3.9 7.8 - - + +
51B THR* 2.7 38.5 + - - +
54B THR* 3.6 9.8 - - - +
355B TRP* 3.4 41.3 - - + +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.0 45.2 + - + +
49A PHE* 3.3 22.6 + - + +
51A THR* 1.3 78.3 - - + +
53A PHE* 1.3 65.7 + - + +
55A LEU* 3.4 12.2 + - + +
56A GLY* 3.0 21.3 + - - -
154A VAL* 4.7 19.3 - - + -
355B TRP* 4.8 17.9 - - + -
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 2.9 43.2 + + - +
52A LEU* 1.3 80.4 - - + +
54A THR* 1.3 55.4 + - - +
56A GLY* 3.6 3.5 - - - +
57A THR* 2.7 38.6 + - - -
65A ALA* 3.8 11.9 - - + +
66A THR* 4.0 22.2 - - + -
150A LEU* 5.6 4.9 - - + -
154A VAL* 5.4 11.0 - - + -
352A VAL* 3.8 17.5 - - + -
356A VAL* 3.8 4.0 - - + -
999A HEM 3.5 59.9 - + + -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS 2.5 24.3 + - - -
51A THR* 3.5 6.1 - - - -
53A PHE* 1.3 76.2 - - - +
55A LEU* 1.3 59.6 + - - +
57A THR* 3.3 5.0 + - - -
58A THR* 2.9 32.9 + - - +
355A TRP* 2.9 27.7 + - - +
356A VAL* 3.9 7.8 - - - +
359A LEU* 4.4 22.6 - - + +
51B THR 5.6 0.2 - - - +
54B THR* 3.9 21.1 - - + -
55B LEU* 4.5 8.1 - - - +
58B THR* 4.4 9.4 - - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR 3.1 11.6 + - - +
52A LEU* 3.5 15.3 - - + +
54A THR* 1.3 79.9 - - - +
56A GLY* 1.3 57.3 + - - +
58A THR* 3.1 6.4 + - - -
59A LEU* 2.8 62.6 + - + +
54B THR* 4.6 4.7 - - + +
58B THR* 5.6 0.7 - - - -
62B PHE* 4.5 8.1 - - + -
355B TRP* 4.1 21.8 - - + -
358B HIS* 5.5 2.7 - - - +
359B LEU* 3.2 36.6 - - + -
362B LEU* 4.0 11.9 - - + -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 3.0 14.5 + - - -
53A PHE* 3.4 4.9 + - - -
54A THR 3.3 0.2 - - - -
55A LEU* 1.3 76.0 - - - +
57A THR* 1.3 63.9 + - - +
59A LEU* 3.3 9.4 + - - +
60A LYS* 3.0 28.8 + - - +
65A ALA* 4.1 12.8 - - - -
367B LEU* 5.5 2.0 - - - +
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE 2.7 27.5 + - - -
54A THR* 3.5 7.0 - - - -
56A GLY* 1.3 71.2 - - - +
58A THR* 1.3 60.3 + - - +
60A LYS* 3.2 9.4 + - - +
61A GLY 3.4 0.2 + - - -
62A PHE* 2.9 36.8 + - + -
63A ARG 3.3 20.4 - - - +
65A ALA* 3.7 15.4 + - - +
356A VAL* 3.6 21.1 - - - +
359A LEU* 4.8 8.3 - - + -
360A ARG* 3.8 23.6 - - + -
999A HEM 5.0 0.3 + - - -
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 2.9 18.5 + - - +
55A LEU* 3.3 11.4 - - - -
57A THR* 1.3 73.3 - - - +
59A LEU* 1.3 57.2 + - - +
60A LYS 3.0 4.9 - - - -
61A GLY* 2.9 18.7 + - - -
62A PHE* 3.9 10.8 - - + -
359A LEU* 5.2 0.9 - - - +
58B THR* 3.1 32.5 + - + +
62B PHE* 3.5 36.3 - - + -
364B ILE* 3.6 19.5 - - + +
365B GLY 3.0 11.8 + - - -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 2.8 51.5 + - + +
56A GLY* 3.3 7.2 + - - +
58A THR* 1.3 72.8 - - - +
60A LYS* 1.3 55.3 + - - +
61A GLY 3.1 1.1 - - - -
62B PHE* 4.7 4.0 - - + -
362B LEU* 4.6 17.5 - - + -
363B LYS 3.6 23.8 - - - +
365B GLY* 3.2 12.3 - - - +
366B SER* 3.8 7.9 - - - +
367B LEU* 2.8 60.1 + - + +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 3.0 19.5 + - - +
57A THR 3.5 6.1 - - - +
58A THR 3.0 1.0 - - - -
59A LEU* 1.3 76.4 - - - +
61A GLY* 1.3 62.6 + - - +
62A PHE 3.2 0.9 - - - -
63A ARG* 3.3 26.7 - - + +
64A ARG 3.6 19.5 - - - +
65A ALA 3.0 22.1 + - - +
66A THR* 4.7 2.4 - - - +
68A THR* 2.7 31.9 + - + +
106A LEU 5.7 0.4 + - - -
107A LYS* 4.7 13.1 + - - +
367B LEU* 3.7 38.8 - - + +
368B VAL* 3.6 14.0 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il