Contacts of the helix formed by residues 37 - 60 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.6 33.2 - - + -
37A PHE* 3.9 23.6 - + - -
40A LEU* 3.5 22.0 - - + -
34B SER* 3.7 4.0 + - - -
36B VAL* 1.3 112.4 - - + +
38B GLY* 1.3 67.8 + - - +
39B GLY 3.2 2.9 + - - -
40B LEU* 3.3 6.3 + - + +
41B LYS* 3.0 52.1 + - + +
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER* 2.8 35.3 + - - -
36B VAL 3.7 1.2 - - - -
37B PHE* 1.3 76.4 - - - +
39B GLY* 1.3 56.4 + - - +
41B LYS* 4.6 0.7 - - - -
42B LEU* 3.0 30.0 + - - +
337B LYS 3.3 18.4 - - - +
338B SER* 3.6 8.6 - - - -
339B PRO* 3.7 3.7 - - - +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 5.2 1.2 + - - -
37B PHE 3.3 0.6 - - - -
38B GLY* 1.3 74.9 - - - +
40B LEU* 1.3 61.7 + - - +
42B LEU* 3.2 8.8 + - - +
43B LYS* 3.1 20.4 + - - +
337B LYS 3.6 6.6 + - - -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.6 46.0 - - + +
40A LEU* 4.2 20.3 - - + +
41A LYS* 4.2 23.1 - - + -
44A LEU* 3.9 26.7 - - + +
36B VAL 5.7 1.0 + - - +
37B PHE* 3.3 7.3 + - - +
39B GLY* 1.3 71.5 - - - +
41B LYS* 1.3 61.3 + - - +
43B LYS* 3.1 9.7 + - + +
44B LEU* 2.9 27.9 + - - +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.8 26.7 - - + -
34B SER* 5.4 6.1 + - - +
37B PHE* 3.0 45.7 + - + +
38B GLY* 3.9 3.8 - - - +
40B LEU* 1.3 73.5 - - - +
42B LEU* 1.3 60.5 + - - +
44B LEU* 3.2 12.0 + - + +
45B LYS* 2.9 35.4 + - + +
339B PRO* 3.9 21.1 - - + -
340B GLU* 5.6 2.9 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.0 18.5 + - - +
39B GLY* 3.5 7.2 - - - +
41B LYS* 1.3 76.1 - - - +
43B LYS* 1.3 58.9 + - - +
45B LYS* 3.2 4.1 + - + +
46B LYS* 2.9 44.9 + - - +
336B ALA* 3.9 27.8 - - + +
337B LYS 4.7 1.1 - - - -
338B SER 4.2 17.5 - - - +
339B PRO* 3.8 11.4 - - + +
344B SER* 4.3 16.2 - - - +
347B GLU* 3.5 23.3 - - + +
348B LEU* 4.4 14.4 - - + -
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.8 27.6 - - + -
39B GLY 3.1 12.6 + - - +
40B LEU* 3.3 15.7 - - + +
42B LEU* 1.3 77.1 - - - +
44B LEU* 1.3 60.9 + - - +
46B LYS* 3.2 18.4 + - + +
47B GLU* 2.7 55.7 + - + +
50B LYS* 4.7 3.2 - - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.3 24.0 - - + +
43A LYS* 3.8 23.6 - - + +
44A LEU* 3.7 38.4 - - + +
47A GLU* 4.0 11.7 - - + +
40B LEU 2.9 13.5 + - - +
41B LYS* 3.2 13.7 + - + +
43B LYS* 1.3 77.4 - - - +
45B LYS* 1.3 70.8 + - + +
47B GLU* 3.1 2.1 + - - -
48B LYS* 2.8 32.3 + - + +
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Residues in contact with LYS 45 (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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41B LYS* 2.9 21.1 + - - +
42B LEU* 3.6 8.3 - - + +
44B LEU* 1.3 87.1 - - + +
46B LYS* 1.3 62.2 + - - +
48B LYS* 4.2 11.8 - - + +
49B PHE* 2.9 38.1 + - + -
147B SER* 3.4 25.4 - - - +
151B GLU* 2.7 30.9 + - - +
339B PRO* 3.7 22.4 - - + -
348B LEU* 4.0 11.9 - - + -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 2.9 31.4 + - - +
43B LYS* 3.2 22.0 + - + +
45B LYS* 1.3 77.5 - - - +
47B GLU* 1.3 65.0 + - - +
49B PHE* 4.1 1.5 - - - +
50B LYS* 3.0 32.1 + - + +
347B GLU* 2.7 48.2 + - - +
348B LEU* 3.7 18.2 - - + -
351B ALA* 4.1 21.5 - - + +
352B VAL* 4.9 2.1 - - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.0 15.9 - - + +
47A GLU* 3.6 20.2 - - + -
48A LYS* 3.6 26.7 - - + +
51A THR* 4.0 2.9 + - - -
43B LYS* 2.7 55.4 + - + +
44B LEU* 3.7 6.3 - - - +
46B LYS* 1.3 74.0 - - - +
48B LYS* 1.3 64.3 + - - +
50B LYS* 3.0 32.5 + - - +
51B THR* 2.8 29.1 + - - -
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.7 26.2 - - + +
44B LEU* 2.8 24.5 + - + +
45B LYS* 3.7 16.4 - - + +
47B GLU* 1.3 72.6 - - - +
49B PHE* 1.3 67.3 + - + +
51B THR* 3.0 6.4 + - - -
52B LEU* 2.9 50.9 + - + +
151B GLU* 2.7 40.2 + - - +
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Residues in contact with PHE 49 (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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45B LYS* 2.9 38.1 + - + +
46B LYS* 4.3 1.1 - - - +
48B LYS* 1.3 79.7 - - + +
50B LYS* 1.3 61.0 + - - +
52B LEU* 3.8 19.1 - - + -
53B PHE* 2.9 51.1 + + + +
147B SER* 3.7 19.3 - - - -
150B LEU* 3.5 30.1 - - + -
151B GLU* 3.8 26.0 - - + -
154B VAL* 3.8 21.1 - - + -
348B LEU* 4.2 12.3 - - + -
352B VAL* 3.9 19.1 - - + -
999B HEM 4.2 5.8 - - + -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.9 9.0 - - - +
43B LYS* 4.7 2.6 - - - +
46B LYS* 3.0 22.0 + - + +
47B GLU* 3.0 39.5 + - - +
48B LYS 3.2 0.2 - - - -
49B PHE* 1.3 76.2 - - - +
51B THR* 1.3 54.5 + - - +
53B PHE* 3.5 2.5 + - - +
54B THR* 2.6 39.1 + - - -
351B ALA* 3.9 27.2 - - + +
352B VAL* 4.2 12.5 - - + +
355B TRP* 3.9 38.9 - - + +
356B VAL* 5.9 0.2 - - - -
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Residues in contact with THR 51 (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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47A GLU* 3.0 27.8 + - - +
50A LYS* 4.0 15.9 - - + +
51A THR* 2.7 24.2 + - - +
54A THR* 5.6 0.7 - - - +
355A TRP* 3.7 34.2 + - + +
47B GLU 2.8 15.2 + - - -
48B LYS 3.0 8.9 + - - -
50B LYS* 1.3 78.2 - - - +
52B LEU* 1.3 64.1 + - + +
54B THR* 3.2 4.4 + - - -
55B LEU* 3.2 22.5 + - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TRP* 4.3 21.1 - - + -
48B LYS* 2.9 36.7 + - + +
49B PHE* 3.7 35.0 - - + +
51B THR* 1.3 80.3 - - + +
53B PHE* 1.3 65.2 + - + +
55B LEU* 3.4 8.3 + - - +
56B GLY* 3.1 20.3 + - - -
154B VAL* 4.5 21.1 - - + -
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 2.9 52.0 + + - +
50B LYS 3.8 0.7 - - - +
52B LEU* 1.3 77.4 - - + +
54B THR* 1.3 60.9 + - - +
55B LEU 3.2 0.4 - - - -
56B GLY* 3.6 3.5 - - - +
57B THR* 2.9 34.0 + - - -
65B ALA* 3.9 12.4 - - + +
66B THR* 3.9 22.2 - - + -
150B LEU* 5.9 2.2 - - + -
154B VAL* 5.3 9.6 - - + -
352B VAL* 4.0 21.3 - - + -
356B VAL* 3.8 9.8 - - + +
999B HEM 3.6 48.5 - + + -
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.6 18.5 - - - +
54A THR* 3.9 21.8 - - + -
55A LEU* 4.6 5.4 - - + +
50B LYS 2.6 24.6 + - - -
51B THR* 3.2 5.8 + - - -
53B PHE* 1.3 76.3 - - - +
55B LEU* 1.3 63.2 + - - +
57B THR* 3.4 5.6 + - - -
58B THR* 2.9 32.7 + - - +
355B TRP* 2.7 30.3 + - - +
356B VAL* 4.4 3.6 - - - +
359B LEU* 4.9 15.3 - - + -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.5 5.3 - - + +
355A TRP* 3.7 34.3 - - + +
358A HIS* 5.0 12.8 - - + +
359A LEU* 2.9 35.2 - - + -
362A LEU* 4.9 2.5 - - + -
51B THR 3.2 9.1 + - - +
52B LEU* 3.5 9.6 - - - +
54B THR* 1.3 80.6 - - - +
56B GLY* 1.3 58.7 + - - +
58B THR* 3.2 4.9 + - - -
59B LEU* 2.8 56.8 + - + +
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Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 3.1 11.1 + - - -
53B PHE* 3.5 4.4 + - - -
54B THR 3.3 0.2 - - - -
55B LEU* 1.3 82.5 - - - +
57B THR* 1.3 59.9 + - - +
59B LEU* 3.5 6.9 + - - +
60B LYS* 3.0 31.6 + - - +
65B ALA* 4.1 13.9 - - - -
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Residues in contact with THR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE 2.9 24.4 + - - -
54B THR* 3.8 4.9 - - - -
56B GLY* 1.3 75.1 - - - +
58B THR* 1.3 60.9 + - - +
60B LYS* 3.2 7.4 + - - +
62B PHE* 2.8 46.4 + - + -
63B ARG 3.4 21.1 - - - +
65B ALA* 3.7 15.3 + - - +
356B VAL* 3.7 21.4 - - - +
359B LEU* 4.6 7.9 - - + -
360B ARG* 4.0 16.4 - - + -
999B HEM 5.0 0.7 + - - -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.4 5.9 - - + +
55A LEU* 5.6 0.5 - - - -
58A THR* 3.1 31.2 + - + +
62A PHE* 3.4 29.5 - - + -
359A LEU* 4.3 12.6 - - + -
363A LYS* 4.8 1.9 + - - -
54B THR* 2.9 27.0 + - - +
55B LEU* 3.4 8.3 - - - -
57B THR* 1.3 76.7 - - - +
59B LEU* 1.3 59.1 + - - +
61B GLY* 3.0 20.6 + - - -
62B PHE* 3.8 17.6 - - - -
364B ILE* 4.1 5.2 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.3 10.5 - - + -
362A LEU* 4.1 28.5 - - + -
363A LYS* 4.1 32.5 + - - +
55B LEU* 2.8 51.8 + - + +
56B GLY* 3.9 7.2 - - - +
58B THR* 1.3 73.4 - - - +
60B LYS* 1.3 62.7 + - + +
61B GLY 3.2 3.1 + - - -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY* 3.0 25.4 + - - +
57B THR 3.7 4.9 - - - +
58B THR 3.0 1.4 - - - -
59B LEU* 1.3 81.5 - - - +
61B GLY* 1.3 62.5 + - - +
62B PHE 3.3 0.7 - - - -
63B ARG* 3.3 36.0 - - + +
64B ARG 3.8 11.4 - - - +
65B ALA* 3.4 16.3 + - - -
68B THR* 2.9 31.7 + - + +
107B LYS 5.1 8.7 + - - -
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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) + - + + + + + -
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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