Contacts of the helix formed by residues 29 - 55 (chain U) in PDB entry 3EXG
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 ARG 29 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1U PHE* 2.6 39.1 - - - -
2U ALA 4.0 7.4 - - - +
3U ASN* 2.8 29.0 + - - +
27U LEU* 5.1 1.1 - - - -
28U THR* 1.3 70.3 - - - +
30U GLU* 1.3 69.4 + - - +
32U GLY* 3.6 1.1 + - - +
33U LEU* 3.3 40.0 + - + +
295U MET* 5.2 0.5 - - - +
300U LEU* 2.7 55.3 + - + +
305U GLU* 2.8 29.1 + - - -
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Residues in contact with GLU 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U ASN 4.8 0.4 + - - -
28U THR* 3.2 7.7 + - - +
29U ARG* 1.3 87.3 - - - +
31U ASP* 1.3 72.7 + - - +
33U LEU* 3.5 16.2 - - - +
34U LYS* 3.5 6.9 + - - +
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Residues in contact with ASP 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U LEU* 4.7 2.0 - - + -
28U THR* 3.0 38.1 + - + +
30U GLU* 1.3 80.1 + - - +
32U GLY* 1.3 56.7 + - - +
33U LEU 3.0 1.6 - - - -
34U LYS* 2.6 60.2 + - - +
35U TYR* 3.2 26.1 + - + -
234U ARG* 5.1 4.1 + - - +
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Residues in contact with GLY 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U LEU* 3.6 32.7 - - - +
28U THR 2.8 14.1 + - - -
29U ARG 4.1 1.1 - - - -
31U ASP* 1.3 71.8 - - - +
33U LEU* 1.3 55.1 + - - +
35U TYR* 3.4 9.0 + - - +
36U TYR* 2.8 24.4 + - - +
291U LEU* 3.9 3.8 - - - +
295U MET* 3.1 18.0 - - - +
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Residues in contact with LEU 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U ARG* 3.3 33.1 + - - +
30U GLU* 3.5 13.2 - - - +
31U ASP 2.9 0.6 + - - -
32U GLY* 1.3 74.7 - - - +
34U LYS* 1.3 61.5 + - - +
36U TYR* 3.9 2.8 - - - +
37U ARG* 3.4 22.3 + - - +
295U MET* 3.5 20.4 - - + -
300U LEU 4.7 0.7 - - - +
301U ALA* 3.9 21.8 - - + -
305U GLU* 4.1 18.2 - - - +
306U LEU* 4.4 4.5 - - + -
309U ILE* 4.3 22.2 - - + +
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Residues in contact with LYS 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U GLU 3.5 6.5 + - - +
31U ASP* 2.6 36.0 + - - +
33U LEU* 1.3 75.0 - - - +
35U TYR* 1.3 80.3 + - - +
37U ARG* 3.7 4.7 + - - +
38U MET* 3.1 50.8 + - + +
77U ALA* 5.7 4.0 - - - +
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Residues in contact with TYR 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U LEU* 4.2 11.2 - - + -
31U ASP* 3.2 20.3 + - + -
32U GLY* 3.6 16.8 - - - +
34U LYS* 1.3 106.9 + - - +
36U TYR* 1.3 66.5 + - - +
38U MET* 3.1 4.5 + - + +
39U MET* 2.9 29.5 + - - +
73U VAL* 4.2 14.4 - - + -
77U ALA* 3.5 24.4 + - + +
230U ILE* 3.6 30.1 - - + -
231U LEU* 5.1 2.9 - - + -
234U ARG* 3.1 46.0 + - - -
238U ARG* 4.9 1.6 + - - -
291U LEU* 4.3 6.1 - - + -
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Residues in contact with TYR 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32U GLY 2.8 17.8 + - - +
33U LEU* 4.2 3.8 - - - +
34U LYS 3.4 0.2 - - - -
35U TYR* 1.3 78.9 - - - +
37U ARG* 1.3 67.7 + - - +
38U MET 3.0 1.2 + - - -
39U MET* 3.1 3.9 + - + +
40U GLN* 3.1 30.6 + - + +
288U ILE* 3.6 33.7 - - + +
291U LEU* 3.7 20.6 - - + +
292U LYS* 4.3 17.9 - - + +
295U MET* 3.8 9.0 - - + -
306U LEU* 3.7 50.1 + - + +
309U ILE* 4.2 12.8 - - + -
310U ASP* 2.9 31.9 + - - -
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Residues in contact with ARG 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U LEU 3.4 17.0 + - - +
34U LYS* 4.0 4.5 - - - +
36U TYR* 1.3 79.1 - - - +
38U MET* 1.3 59.9 + - + +
40U GLN* 4.1 3.6 - - - +
41U THR* 2.8 34.4 + - - +
309U ILE* 3.6 36.9 - - + +
312U GLU* 3.2 49.6 + - - +
313U VAL* 4.0 18.6 - - + +
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Residues in contact with MET 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U LYS* 3.1 59.2 + - + +
35U TYR* 3.6 10.3 - - + +
36U TYR 3.0 1.6 + - - -
37U ARG* 1.3 79.6 - - + +
39U MET* 1.3 62.2 + - - +
41U THR* 3.5 3.9 + - - -
42U VAL* 3.3 24.9 + - - +
73U VAL* 4.0 24.4 - - + +
76U GLU* 5.5 9.0 - - + -
96U PHE* 4.1 19.6 - - + -
97U THR* 5.0 18.6 - - - +
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Residues in contact with MET 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35U TYR 2.9 12.7 + - - +
36U TYR* 3.8 3.6 - - - +
38U MET* 1.3 76.2 - - - +
40U GLN* 1.3 57.7 + - - +
42U VAL* 3.2 5.4 + - - +
43U ARG* 2.8 27.0 + - - +
69U GLU* 3.9 20.5 - - + +
70U ALA* 4.2 15.5 - - - -
73U VAL* 3.7 22.4 - - + -
230U ILE* 4.3 16.6 - - + -
287U PRO* 3.8 16.4 - - - +
288U ILE* 3.7 27.0 - - + +
291U LEU* 3.4 44.6 - - + -
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Residues in contact with GLN 40 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U TYR* 3.1 29.7 + - + +
37U ARG* 4.2 4.7 - - - +
39U MET* 1.3 72.8 - - - +
41U THR* 1.3 61.2 + - - +
43U ARG* 3.6 13.4 - - - +
44U ARG* 2.9 56.4 + - - +
288U ILE* 3.5 31.1 - - + +
309U ILE* 5.7 0.7 - - + -
310U ASP* 3.0 37.0 - - - +
313U VAL* 3.9 14.5 - - + +
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Residues in contact with THR 41 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U ARG* 2.8 25.6 + - - +
38U MET 3.8 3.8 - - - -
40U GLN* 1.3 77.2 - - - +
42U VAL* 1.3 59.9 + - - +
44U ARG* 3.3 1.4 + - - +
45U MET* 2.8 33.8 + - + +
96U PHE* 3.8 22.4 - - + -
102U VAL* 3.7 30.3 - - + -
313U VAL* 3.7 23.0 - - + +
316U GLU* 5.9 5.6 - - + -
317U ILE* 4.2 7.1 - - + +
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Residues in contact with VAL 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U MET 3.3 12.4 + - - +
39U MET 3.2 7.3 + - - +
41U THR* 1.3 78.3 - - - +
43U ARG* 1.3 67.0 + - - +
45U MET* 3.8 8.4 - - - +
46U GLU* 3.0 22.2 + - + +
65U CYS* 3.8 25.4 - - - -
69U GLU* 3.1 28.9 - - + +
72U CYS* 4.7 4.3 - - - -
73U VAL* 5.0 1.3 - - + -
93U GLY* 4.0 20.0 - - - +
96U PHE* 3.8 23.1 - - + -
97U THR* 4.5 7.4 - - + -
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Residues in contact with ARG 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39U MET 2.8 6.9 + - - -
40U GLN* 3.1 17.3 + - - +
41U THR 3.1 0.4 - - - -
42U VAL* 1.3 79.2 - - - +
44U ARG* 1.3 66.8 + - - +
46U GLU* 3.2 2.8 + - - +
47U LEU* 3.1 39.9 + - + +
66U ASP* 3.7 18.7 - - - +
67U GLY 3.7 7.3 - - - +
69U GLU* 2.5 42.4 + - - +
260U TYR* 3.9 14.3 - - - -
282U ARG* 4.5 9.2 - - - +
286U ASP* 2.7 34.1 + - - -
287U PRO* 3.9 5.3 - - - +
288U ILE* 3.6 26.4 - - + +
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Residues in contact with ARG 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2866 ASN 5.3 0.4 + - - -
2896 ASP* 4.6 5.9 + - - -
40U GLN* 2.9 43.3 + - - +
41U THR 4.0 0.4 - - - +
43U ARG* 1.3 75.6 - - - +
45U MET* 1.3 64.3 + - - +
47U LEU* 3.2 34.1 + - - +
48U LYS* 2.9 25.1 + - - +
310U ASP 5.6 0.4 - - - +
313U VAL* 3.6 17.0 - - + -
314U ARG* 3.2 59.5 - - + +
317U ILE* 3.5 23.5 - - + +
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Residues in contact with MET 45 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41U THR* 2.8 20.1 + - + +
42U VAL* 3.8 8.3 - - - +
44U ARG* 1.3 78.9 - - - +
46U GLU* 1.3 64.7 + - - +
48U LYS* 3.2 5.1 + - - +
49U ALA* 3.0 21.0 + - + +
92U HIS* 4.5 17.5 - - - +
93U GLY* 5.8 0.4 - - - -
96U PHE* 4.7 7.4 - - + -
102U VAL* 3.3 48.2 - - + +
105U ILE* 3.4 42.0 - - + -
106U LEU* 4.3 13.5 - - + +
109U LEU* 6.3 1.3 - - + -
317U ILE* 3.8 15.4 - - + +
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Residues in contact with GLU 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42U VAL* 3.0 18.6 + - + +
43U ARG 3.6 7.2 - - - +
45U MET* 1.3 77.8 - - - +
47U LEU* 1.3 67.4 + - - +
49U ALA* 3.2 5.3 + - - +
50U ASP* 2.9 22.7 + - - +
63U HIS 3.9 0.5 - - - +
64U LEU* 3.2 28.8 - - + +
65U CYS* 2.6 51.4 + - - +
66U ASP* 3.9 24.7 - - + +
92U HIS* 3.4 27.3 + - - +
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Residues in contact with LEU 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43U ARG* 3.1 33.5 + - + +
44U ARG* 3.2 42.1 + - - +
46U GLU* 1.3 75.5 - - - +
48U LYS* 1.3 58.3 + - - +
50U ASP* 3.0 9.1 + - + +
51U GLN* 2.9 28.1 + - - +
66U ASP* 4.2 18.8 - - - +
261U HIS* 4.3 13.5 - - + +
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Residues in contact with LYS 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2866 ASN* 3.2 10.1 - - - +
44U ARG 2.9 16.2 + - - +
45U MET* 3.7 4.5 - - - +
46U GLU 3.2 0.2 - - - -
47U LEU* 1.3 78.4 - - - +
49U ALA* 1.3 55.6 + - - +
51U GLN* 3.0 33.0 + - - +
52U LEU* 2.8 45.7 + - + +
106U LEU* 4.0 5.8 - - + -
317U ILE* 3.7 17.0 - - + -
318U GLU* 2.8 41.1 + - - -
321U ALA* 3.6 30.2 - - + +
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Residues in contact with ALA 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U MET* 3.0 13.2 + - + +
46U GLU* 3.4 11.0 - - - +
48U LYS* 1.3 75.3 - - - +
50U ASP* 1.3 54.4 + - - +
52U LEU* 2.9 4.6 + - - +
53U TYR* 2.7 38.8 + - - +
58U ILE* 3.7 11.4 - - + +
62U CYS* 4.5 3.1 - - - -
64U LEU* 3.9 16.8 - - + -
106U LEU* 4.5 4.2 - - + +
109U LEU* 4.1 24.5 - - + -
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Residues in contact with ASP 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U GLU 2.9 8.6 + - - +
47U LEU* 3.5 12.7 - - + +
49U ALA* 1.3 76.2 - - - +
51U GLN* 1.3 58.2 + - - +
53U TYR* 3.7 12.5 - - - +
54U LYS* 2.8 53.4 + - - +
62U CYS* 5.3 0.4 - - - -
64U LEU* 3.4 24.2 - - + +
261U HIS* 3.3 27.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN 51 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2894 ASP 5.6 0.4 - - - +
2866 ASN* 3.6 25.9 + - - +
47U LEU 2.9 15.2 + - - +
48U LYS* 3.0 38.8 + - - +
50U ASP* 1.3 74.7 - - - +
52U LEU* 1.3 70.9 + - - +
53U TYR 3.1 0.7 + - - -
54U LYS* 3.4 11.8 + - + +
55U GLN* 3.3 41.5 + - - +
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Residues in contact with LEU 52 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48U LYS* 2.8 44.1 + - + +
49U ALA* 2.9 5.4 + - - +
51U GLN* 1.3 79.2 - - + +
53U TYR* 1.3 60.4 + - - +
55U GLN* 3.4 15.0 + - - +
56U LYS 3.3 3.3 + - - -
57U ILE* 3.2 40.4 + - + +
58U ILE* 3.7 16.7 + - + -
106U LEU* 4.4 16.4 - - + -
110U THR* 4.6 13.7 - - + -
321U ALA* 4.5 8.5 - - + -
324U ALA* 5.6 0.7 - - + -
325U THR* 3.7 26.9 - - + -
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Residues in contact with TYR 53 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49U ALA 2.7 16.8 + - - +
50U ASP* 3.7 11.7 - - - +
52U LEU* 1.3 76.5 - - - +
54U LYS* 1.3 69.6 + - + +
55U GLN 3.0 1.1 - - - -
56U LYS* 2.8 21.7 + - + +
58U ILE* 3.2 37.0 - - + -
59U ARG* 4.5 0.9 - - - -
60U GLY 3.1 25.6 + - - -
61U PHE* 4.3 2.4 - - - -
62U CYS* 3.4 38.8 + - + -
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Residues in contact with LYS 54 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2584 HIS* 5.8 1.4 + - - -
2894 ASP* 3.3 43.7 - - + +
50U ASP* 2.8 49.7 + - - +
51U GLN* 3.7 11.1 - - + +
53U TYR* 1.3 77.9 - - + +
55U GLN* 1.3 60.1 + - + +
56U LYS* 3.5 9.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 55 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2584 HIS* 5.4 7.4 - - - +
2894 ASP* 3.1 30.8 - - + +
2904 ALA* 4.7 9.3 - - + -
2914 PRO* 5.5 2.4 - - - +
3274 LEU 4.6 5.4 - - - +
3284 ASN* 4.5 21.3 + - + +
51U GLN* 3.3 37.8 + - - +
52U LEU* 3.4 15.8 + - - +
53U TYR 3.0 1.4 - - - -
54U LYS* 1.3 76.8 - - + +
56U LYS* 1.3 73.7 + - - +
57U ILE* 3.3 23.6 + - + +
----------------------------------------------------------
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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