Contacts of the helix formed by residues 29 - 55 (chain G) in PDB entry 3EXE
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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G PHE* 3.5 26.3 - - - +
2G ALA 3.7 24.2 - - - +
3G ASN* 2.9 21.8 + - - +
4G ASP* 4.3 1.0 - - - +
27G LEU 3.9 0.2 + - - -
28G THR* 1.3 70.8 - - - +
30G GLU* 1.3 64.2 + - - +
32G GLY* 3.4 1.4 + - - -
33G LEU* 3.1 43.4 + - + +
295G MET* 5.0 0.7 - - - +
300G LEU* 2.7 50.4 + - + +
301G ALA* 3.6 2.6 - - - +
305G GLU* 2.8 41.2 + - - -
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Residues in contact with GLU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G THR* 3.3 8.2 + - - +
29G ARG* 1.3 81.2 - - - +
31G ASP* 1.3 82.9 + - - +
33G LEU* 3.4 8.5 + - - +
34G LYS* 3.0 29.8 + - + +
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Residues in contact with ASP 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 3.7 15.3 - - + -
28G THR* 2.9 25.5 + - - +
30G GLU* 1.3 93.6 - - - +
32G GLY* 1.3 60.4 + - - +
34G LYS* 3.2 12.8 + - - +
35G TYR* 2.9 57.2 + - + -
234G ARG* 3.8 8.3 + - - -
238G ARG* 5.2 2.9 + - - -
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Residues in contact with GLY 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 3.4 15.3 - - - +
28G THR 2.8 19.3 + - - -
29G ARG 3.8 0.4 - - - -
31G ASP* 1.3 72.3 - - - +
33G LEU* 1.3 55.3 + - - +
35G TYR* 3.3 5.6 + - - +
36G TYR* 2.8 32.2 + - - +
291G LEU* 3.8 1.7 - - - +
295G MET* 3.4 28.3 - - - +
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ARG* 3.1 56.0 + - + +
30G GLU* 3.9 7.0 - - - +
32G GLY* 1.3 75.7 - - - +
34G LYS* 1.3 61.4 + - - +
36G TYR* 3.8 3.9 - - - +
37G ARG* 3.1 25.6 + - - +
295G MET* 5.1 1.8 - - - -
300G LEU 5.1 0.2 - - - +
301G ALA* 4.0 25.8 - - + -
305G GLU* 4.5 9.4 - - + +
306G LEU* 4.1 7.0 - - + -
309G ILE* 3.8 26.9 - - + +
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Residues in contact with LYS 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G GLU* 3.0 23.4 + - + +
31G ASP* 3.4 13.4 + - - +
33G LEU* 1.3 75.3 - - - +
35G TYR* 1.3 79.6 + - + +
37G ARG* 3.4 5.6 + - - +
38G MET* 3.0 51.1 + - + +
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Residues in contact with TYR 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 3.7 19.3 - - + -
31G ASP* 2.9 40.2 + - + +
32G GLY* 3.8 4.3 - - - +
34G LYS* 1.3 87.1 - - + +
36G TYR* 1.3 67.4 - - - +
38G MET* 3.2 4.6 + - - +
39G MET* 2.9 29.7 + - + +
73G VAL* 4.1 13.0 - - + +
77G ALA* 3.5 25.4 + - + +
230G ILE* 3.6 32.3 - - + -
231G LEU* 4.4 5.4 - - + -
234G ARG* 2.9 40.8 + - - -
238G ARG* 4.4 4.2 + - - -
291G LEU* 3.9 12.3 - - + -
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Residues in contact with TYR 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLY 2.8 17.9 + - - +
33G LEU* 3.8 6.1 - - - +
35G TYR* 1.3 76.6 - - - +
37G ARG* 1.3 64.9 + - - +
39G MET* 3.9 2.9 - - - +
40G GLN* 2.9 33.4 + - + +
288G ILE* 3.6 33.3 - - + +
291G LEU* 3.5 10.9 - - + +
292G LYS* 3.9 27.8 - - + +
295G MET* 3.8 15.7 - - + -
306G LEU* 3.7 40.1 + - + +
309G ILE* 3.9 17.0 - - + -
310G ASP* 2.5 37.4 + - - -
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Residues in contact with ARG 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU 3.1 15.7 + - - +
34G LYS* 3.9 4.9 - - - +
36G TYR* 1.3 80.6 - - - +
38G MET* 1.3 59.1 + - + +
40G GLN* 3.9 1.8 - - - +
41G THR* 2.8 38.8 + - - +
309G ILE* 3.7 45.2 - - + +
312G GLU* 3.0 39.6 + - - +
313G VAL* 4.0 12.6 - - + +
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Residues in contact with MET 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LYS* 3.0 49.6 + - + +
35G TYR* 3.2 7.4 + - - +
37G ARG* 1.3 78.5 - - + +
39G MET* 1.3 63.3 + - - +
41G THR* 3.3 3.5 + - - -
42G VAL* 3.1 27.2 + - - +
73G VAL* 3.9 24.0 - - + +
76G GLU* 4.6 15.0 - - + -
96G PHE* 3.9 19.6 - - + -
97G THR* 3.7 35.2 - - + +
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Residues in contact with MET 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TYR 2.9 14.1 + - - +
36G TYR* 4.0 3.4 - - + +
38G MET* 1.3 76.9 - - - +
40G GLN* 1.3 57.6 + - - +
42G VAL 3.3 1.6 + - - -
43G ARG* 2.9 28.2 + - - +
69G GLU* 3.5 27.4 - - + +
70G ALA 4.0 1.3 - - - -
73G VAL* 3.5 25.1 - - + +
230G ILE* 4.0 21.5 - - + -
287G PRO* 3.9 41.1 - - - +
288G ILE* 3.7 16.6 - - + -
291G LEU* 3.3 36.3 - - + -
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Residues in contact with GLN 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TYR* 2.9 26.5 + - + +
37G ARG* 3.9 3.6 - - - +
39G MET* 1.3 78.5 - - - +
41G THR* 1.3 56.1 + - - +
43G ARG* 3.3 7.8 + - - +
44G ARG* 2.9 59.4 + - + +
288G ILE* 3.6 33.9 - - + +
310G ASP* 3.7 31.7 + - - +
313G VAL* 3.8 23.1 - - + -
314G ARG* 5.4 1.8 + - - +
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Residues in contact with THR 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ARG* 2.8 27.3 + - - +
38G MET 3.3 5.1 + - - -
40G GLN* 1.3 74.9 - - - +
42G VAL* 1.3 58.3 + - - +
44G ARG* 3.8 1.0 - - - +
45G MET* 2.8 33.9 + - + +
96G PHE* 3.6 26.1 - - + -
102G VAL* 3.6 29.6 - - + -
313G VAL* 3.4 22.6 - - - +
316G GLU* 3.8 15.2 + - - +
317G ILE* 4.1 3.4 - - + +
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Residues in contact with VAL 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G MET 3.1 19.5 + - - +
39G MET 3.7 6.7 - - - +
41G THR* 1.3 76.4 - - - +
43G ARG* 1.3 62.3 + - - +
45G MET* 3.3 9.0 + - + +
46G GLU* 3.0 26.1 + - + +
65G CYS* 3.6 31.9 - - - -
69G GLU* 3.8 13.7 - - + +
72G CYS* 4.2 12.6 - - - -
73G VAL* 4.7 1.6 - - + -
93G GLY* 3.7 22.7 - - - +
96G PHE* 3.7 23.1 - - + -
97G THR* 4.6 2.5 - - + -
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Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G MET 2.9 15.8 + - - +
40G GLN* 3.5 14.8 - - - +
42G VAL* 1.3 75.9 - - - +
44G ARG* 1.3 58.7 + - - +
46G GLU* 3.4 3.5 + - - +
47G LEU* 3.0 53.0 + - + +
66G ASP* 3.6 15.9 - - - +
67G GLY 3.7 0.6 - - - +
69G GLU* 2.9 44.6 + - - +
260G TYR* 3.6 14.4 - - - -
282G ARG* 3.8 18.7 - - - +
286G ASP* 2.8 35.4 + - - -
287G PRO* 3.8 7.5 - - - +
288G ILE* 3.5 22.0 - - + +
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Residues in contact with ARG 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLN* 2.9 43.5 + - - +
41G THR 4.1 1.3 - - - +
43G ARG* 1.3 73.6 - - - +
45G MET* 1.3 60.4 + - - +
47G LEU* 3.4 36.6 + - - +
48G LYS* 2.9 31.0 + - - +
313G VAL* 3.8 14.8 - - + -
314G ARG* 3.2 62.3 - - + +
317G ILE* 3.8 23.1 - - + +
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Residues in contact with MET 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G THR 2.8 20.7 + - - +
42G VAL* 4.2 17.7 - - + +
44G ARG* 1.3 77.9 - - - +
46G GLU* 1.3 60.4 + - - +
48G LYS* 3.4 5.7 + - - +
49G ALA* 3.0 25.9 + - + +
92G HIS* 3.4 38.4 - - + +
93G GLY* 4.2 2.2 - - - +
96G PHE* 4.2 12.6 - - + -
102G VAL* 4.3 19.1 - - + -
105G ILE* 3.7 34.8 - - + -
106G LEU* 3.9 18.9 - - + +
109G LEU* 5.9 1.1 - - + -
317G ILE* 3.7 14.5 - - + +
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL* 3.0 20.1 + - + +
43G ARG 3.8 3.6 - - - +
44G ARG 3.3 0.2 - - - -
45G MET* 1.3 79.9 - - + +
47G LEU* 1.3 60.3 + - - +
49G ALA* 3.2 4.9 + - - +
50G ASP 3.0 23.6 + - - -
63G HIS 3.9 0.7 - - - +
64G LEU* 3.2 25.3 - - + +
65G CYS* 2.8 47.1 + - - +
66G ASP* 4.2 22.2 - - + +
92G HIS* 2.6 42.7 + - - +
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ARG* 3.0 38.2 + - + +
44G ARG* 3.4 44.6 - - - +
46G GLU* 1.3 75.7 - - - +
48G LYS* 1.3 60.3 + - - +
50G ASP* 3.5 7.4 + - + +
51G GLN* 3.3 19.8 + - - +
66G ASP* 3.9 22.0 - - - +
261G HIS* 4.0 14.1 - - + -
282G ARG* 6.3 0.7 - - - +
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Residues in contact with LYS 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ARG 2.9 18.2 + - - +
45G MET* 3.6 5.2 - - - +
47G LEU* 1.3 74.5 - - - +
49G ALA* 1.3 59.7 + - - +
51G GLN* 2.8 34.3 + - - +
52G LEU* 2.9 36.4 + - + +
106G LEU* 4.0 10.8 - - + -
317G ILE* 3.4 20.4 - - + -
318G GLU* 2.8 36.1 + - - -
321G ALA* 3.4 34.6 - - + +
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G MET 3.0 14.8 + - - +
46G GLU* 3.6 10.8 - - - +
48G LYS* 1.3 72.9 - - - +
50G ASP* 1.3 67.8 + - - +
52G LEU* 4.3 2.9 - - - +
53G TYR* 2.9 26.3 + - - +
58G ILE* 3.6 24.0 - - + +
62G CYS* 4.3 5.3 - - - -
64G LEU* 4.0 16.4 - - + -
106G LEU* 4.6 2.2 - - + -
109G LEU* 4.2 15.0 - - + -
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Residues in contact with ASP 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLU 3.0 13.3 + - - +
47G LEU* 3.5 12.1 - - + +
49G ALA* 1.3 76.6 - - - +
51G GLN* 1.3 63.8 + - - +
53G TYR* 3.3 2.1 + - - +
54G LYS* 2.7 59.2 + - - +
64G LEU* 3.8 9.3 - - + +
261G HIS* 2.6 33.8 + - + +
265G MET* 3.6 21.2 - - - +
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Residues in contact with GLN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G LEU 3.3 10.0 + - - +
48G LYS* 2.8 44.7 + - - +
50G ASP* 1.3 83.2 + - - +
52G LEU* 1.3 63.9 + - - +
54G LYS* 3.4 7.2 + - - +
55G GLN* 3.1 46.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G LYS* 2.9 46.3 + - + +
51G GLN* 1.3 74.5 - - - +
53G TYR* 1.3 60.9 + - - +
55G GLN* 3.2 12.3 + - - +
56G LYS 3.1 4.3 + - - -
57G ILE* 2.9 46.5 + - + +
58G ILE* 3.6 28.9 - - + -
106G LEU* 4.3 20.4 - - + -
110G THR* 4.0 14.1 - - + -
321G ALA* 4.5 7.2 - - + -
324G ALA* 5.2 0.2 - - + -
325G THR* 3.7 23.1 - - - +
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Residues in contact with TYR 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA 2.9 18.4 + - - +
50G ASP 3.6 4.0 - - - +
52G LEU* 1.3 76.6 - - - +
54G LYS* 1.3 60.4 + - + +
56G LYS* 2.9 22.5 + - - +
58G ILE* 3.3 34.4 - - + +
59G ARG* 3.7 11.8 - - - -
60G GLY* 2.8 33.7 + - - -
62G CYS* 3.7 23.8 - - + -
265G MET* 3.4 42.9 - - + +
266G SER* 5.4 4.2 + - - -
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Residues in contact with LYS 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ASP* 2.7 44.4 + - - +
51G GLN* 3.8 7.2 - - - +
53G TYR* 1.3 80.0 - - + +
55G GLN* 1.3 62.1 + - + +
56G LYS* 3.2 9.8 + - - +
265G MET* 4.0 13.9 - - + -
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Residues in contact with GLN 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G GLN* 3.1 45.0 + - + +
52G LEU* 3.7 11.5 - - - +
53G TYR 3.1 0.6 - - - -
54G LYS* 1.3 77.2 - - + +
56G LYS* 1.3 68.4 + - - +
57G ILE* 3.1 32.0 + - + +
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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