Contacts of the helix formed by residues 28 - 55 (chain S) 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 THR 28 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S ASN 4.0 6.0 + - - +
4S ASP* 3.7 11.9 - - - +
26S VAL* 3.7 6.8 + - - +
27S LEU* 1.3 75.3 - - - +
29S ARG* 1.3 66.4 - - - +
30S GLU* 2.3 49.5 + - + +
31S ASP* 2.7 27.3 + - - +
32S GLY 3.0 7.4 + - - -
234S ARG* 5.2 0.2 - - - +
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Residues in contact with ARG 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S PHE* 3.2 30.8 - - - -
2S ALA 3.2 23.3 - - - +
3S ASN* 3.0 12.7 + - - +
28S THR* 1.3 71.5 - - - +
30S GLU* 1.3 61.9 + - - +
32S GLY* 3.3 1.5 + - - -
33S LEU* 3.0 44.5 + - + +
295S MET* 4.1 3.1 - - - +
300S LEU* 2.8 69.2 + - + +
301S ALA* 4.1 3.2 - - + +
305S GLU* 3.3 27.9 + - - -
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Residues in contact with GLU 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S ASN 4.2 0.4 + - - +
28S THR* 2.3 38.5 + - + +
29S ARG* 1.3 75.0 - - - +
31S ASP* 1.3 66.4 + - - +
33S LEU* 3.2 23.4 - - - +
34S LYS* 3.2 7.8 + - - +
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Residues in contact with ASP 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S LEU* 3.9 7.4 - - + -
28S THR* 2.7 21.2 + - - +
30S GLU* 1.3 83.8 - - - +
32S GLY* 1.3 58.8 + - - +
34S LYS* 3.1 22.1 + - - +
35S TYR* 2.8 60.8 + - + +
234S ARG* 4.6 4.8 + - - +
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Residues in contact with GLY 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S LEU* 3.4 30.0 - - - +
28S THR 3.0 9.5 + - - -
29S ARG 3.8 1.1 - - - -
31S ASP* 1.3 79.2 - - - +
33S LEU* 1.3 62.4 + - - +
35S TYR* 3.7 8.2 - - - +
36S TYR* 3.0 21.3 + - - +
291S LEU* 3.9 3.3 - - - +
295S MET* 3.2 18.1 - - - +
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Residues in contact with LEU 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S ARG* 3.0 40.8 + - - +
30S GLU* 3.2 15.9 - - - +
32S GLY* 1.3 78.9 - - - +
34S LYS* 1.3 61.4 + - - +
36S TYR* 3.6 3.1 + - - +
37S ARG* 3.3 20.6 + - - +
295S MET* 3.3 5.3 - - + +
301S ALA* 4.2 24.9 - - + -
305S GLU* 5.0 7.4 - - + +
306S LEU* 4.4 7.4 - - + -
309S ILE* 4.2 27.2 - - + +
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Residues in contact with LYS 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S GLU* 3.2 9.0 + - - +
31S ASP* 3.1 23.8 + - - +
33S LEU* 1.3 82.3 - - - +
35S TYR* 1.3 88.4 + - - +
37S ARG* 3.3 11.5 + - + +
38S MET* 3.2 48.1 + - + +
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Residues in contact with TYR 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S LEU* 4.3 6.7 - - + -
31S ASP* 2.8 42.4 + - + +
32S GLY* 3.2 9.8 + - - +
34S LYS* 1.3 95.9 + - - +
36S TYR* 1.3 68.0 + - - +
37S ARG 3.3 0.2 + - - -
38S MET* 3.3 4.6 + - + +
39S MET* 2.7 29.1 + - + +
73S VAL* 4.1 20.6 - - + -
77S ALA* 3.7 21.7 + - + +
230S ILE* 4.2 22.2 - - + -
231S LEU* 5.0 2.9 - - + -
234S ARG* 3.4 42.6 + - - -
238S ARG* 5.2 1.0 + - - -
291S LEU* 4.1 10.5 - - + -
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Residues in contact with TYR 36 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32S GLY 3.0 14.1 + - - +
33S LEU* 3.9 4.7 - - - +
35S TYR* 1.3 79.4 - - - +
37S ARG* 1.3 69.9 + - - +
39S MET* 3.2 4.7 + - + +
40S GLN* 2.8 35.7 + - + +
288S ILE* 3.6 35.2 - - + +
291S LEU* 3.6 19.6 - - + +
292S LYS* 4.5 13.6 - - + +
295S MET* 5.1 2.0 - - + -
306S LEU* 3.7 51.9 + - + +
309S ILE* 4.4 15.7 - - + -
310S ASP* 2.2 39.8 + - - -
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Residues in contact with ARG 37 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU 3.3 10.5 + - - +
34S LYS* 3.3 14.5 + - - +
35S TYR 3.2 0.8 - - - -
36S TYR* 1.3 80.1 - - - +
38S MET* 1.3 65.6 + - + +
40S GLN* 3.0 3.2 + - - +
41S THR* 2.7 28.3 + - - +
309S ILE* 2.9 45.7 - - + +
312S GLU* 2.8 44.2 + - - +
313S VAL* 3.9 18.0 - - + +
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Residues in contact with MET 38 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S LYS* 3.2 59.7 + - + +
35S TYR* 3.5 9.2 - - + +
37S ARG* 1.3 77.3 - - + +
39S MET* 1.3 68.8 + - - +
41S THR* 2.8 12.4 + - - -
42S VAL* 3.0 14.5 + - - +
73S VAL* 3.9 26.2 - - + -
76S GLU* 5.7 7.4 - - - -
96S PHE* 3.7 29.4 - - + -
97S THR* 4.9 15.7 - - + +
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Residues in contact with MET 39 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S TYR* 2.7 24.3 + - + +
36S TYR* 3.7 3.6 - - - +
38S MET* 1.3 74.8 - - - +
40S GLN* 1.3 62.7 + - - +
42S VAL* 3.4 1.3 + - - -
43S ARG* 3.1 16.6 + - - +
69S GLU* 3.6 33.0 - - + +
70S ALA* 4.1 10.1 - - - -
73S VAL* 3.6 24.2 - - + -
230S ILE* 4.4 13.5 - - + -
287S PRO* 3.4 27.1 - - - +
288S ILE* 3.5 32.7 - - + +
291S LEU* 3.7 28.0 - - + -
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Residues in contact with GLN 40 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S TYR* 2.8 48.5 + - + +
37S ARG* 3.7 3.1 - - - +
38S MET 2.8 0.4 + - - -
39S MET* 1.3 72.7 - - - +
41S THR* 1.3 62.0 + - - +
43S ARG* 3.2 9.0 + - - +
44S ARG* 3.0 70.4 + - - +
288S ILE* 3.8 26.4 - - + +
309S ILE 5.7 0.4 - - - +
310S ASP* 3.9 27.7 - - - +
313S VAL* 4.3 10.9 - - + +
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Residues in contact with THR 41 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 2.7 21.6 + - - +
38S MET* 2.8 7.2 + - - -
40S GLN* 1.3 77.6 - - - +
42S VAL* 1.3 62.7 + - - +
44S ARG* 3.4 0.7 + - - -
45S MET* 3.1 21.7 + - - +
96S PHE* 3.5 32.8 - - + -
102S VAL* 3.7 22.4 - - + -
313S VAL* 3.2 26.0 - - + +
316S GLU* 5.8 5.8 - - + -
317S ILE* 4.1 8.1 - - + +
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Residues in contact with VAL 42 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S MET 3.0 12.0 + - - +
39S MET* 3.9 6.3 - - - +
41S THR* 1.3 75.1 - - - +
43S ARG* 1.3 62.8 + - - +
45S MET* 3.4 8.7 + - - +
46S GLU* 2.9 25.5 + - + +
65S CYS* 3.8 26.9 - - - -
69S GLU* 3.8 19.1 - - + -
72S CYS* 4.2 10.3 - - - -
73S VAL* 5.1 2.0 - - + -
92S HIS 5.1 0.7 - - - +
93S GLY* 3.9 23.6 - - - +
96S PHE* 3.6 30.1 - - + -
97S THR* 4.5 4.3 - - + -
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Residues in contact with ARG 43 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S MET 3.1 12.6 + - - +
40S GLN* 3.2 15.9 + - - +
42S VAL* 1.3 78.6 - - - +
44S ARG* 1.3 69.3 + - - +
46S GLU* 3.5 3.8 - - - +
47S LEU* 2.8 52.9 + - + +
66S ASP* 3.9 13.4 - - - +
69S GLU* 2.4 45.8 + - - +
260S TYR* 4.0 14.6 - - - -
282S ARG* 4.5 11.7 - - - +
286S ASP* 2.8 39.0 + - - -
287S PRO* 3.9 5.5 - - - +
288S ILE* 3.8 14.3 - - + +
----------------------------------------------------------
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Residues in contact with ARG 44 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S GLN* 3.0 47.5 + - - +
41S THR 4.2 0.2 - - - +
43S ARG* 1.3 77.9 - - - +
45S MET* 1.3 60.9 + - - +
47S LEU* 3.9 30.6 - - - +
48S LYS* 3.1 26.5 + - - +
310S ASP 5.9 0.2 - - - +
313S VAL* 3.5 18.2 - - + -
314S ARG* 4.0 41.1 - - - +
317S ILE* 3.5 25.4 - - + +
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Residues in contact with MET 45 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S THR 3.1 17.7 + - - +
42S VAL* 3.7 9.4 - - - +
44S ARG* 1.3 76.6 - - - +
46S GLU* 1.3 61.5 + - - +
48S LYS* 3.0 6.3 + - - +
49S ALA* 2.8 29.2 + - + +
92S HIS* 4.5 20.0 - - - +
96S PHE* 4.5 6.5 - - + -
102S VAL* 3.4 43.5 - - + +
105S ILE* 3.2 47.8 - - + -
106S LEU* 4.5 13.2 - - + +
317S ILE* 3.9 13.0 - - + +
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Residues in contact with GLU 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S VAL* 2.9 24.4 + - + +
43S ARG 3.5 4.0 - - - +
45S MET* 1.3 79.7 - - + +
47S LEU* 1.3 61.5 + - - +
49S ALA* 3.4 5.9 + - - +
50S ASP* 3.1 23.2 + - - +
63S HIS 3.6 0.3 - - - +
64S LEU* 3.3 20.8 - - + +
65S CYS* 2.8 49.9 + - - +
66S ASP* 4.0 19.1 - - + +
92S HIS* 3.0 41.7 + - + +
261S HIS* 6.0 0.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S ARG* 2.8 41.1 + - + +
44S ARG* 4.1 34.8 - - - +
46S GLU* 1.3 71.2 - - - +
48S LYS* 1.3 62.8 + - - +
50S ASP* 3.5 9.6 + - - +
51S GLN* 3.3 21.1 + - - +
66S ASP* 4.1 11.7 - - - +
261S HIS* 4.0 26.2 - - + -
282S ARG* 5.8 8.7 - - - +
----------------------------------------------------------
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Residues in contact with LYS 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S ARG 3.1 19.8 + - - +
45S MET* 3.0 7.0 + - - +
47S LEU* 1.3 72.5 - - - +
49S ALA* 1.3 67.4 + - - +
51S GLN* 3.2 28.7 + - - +
52S LEU* 3.0 32.6 + - + +
106S LEU* 4.0 13.5 - - + -
314S ARG* 6.0 2.9 - - - +
317S ILE* 3.7 19.1 - - + -
318S GLU* 3.2 33.0 + - - -
321S ALA* 3.7 27.0 - - + +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S MET* 2.8 16.7 + - + +
46S GLU* 3.7 14.6 - - - +
48S LYS* 1.3 76.3 - - - +
50S ASP* 1.3 62.3 + - - +
52S LEU* 2.9 3.9 + - - -
53S TYR* 2.8 25.0 + - - +
58S ILE* 3.4 11.6 - - + +
62S CYS* 4.5 2.5 - - - -
64S LEU* 4.3 7.0 - - + -
106S LEU* 4.3 8.5 - - + +
109S LEU* 3.9 27.1 - - + -
----------------------------------------------------------
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Residues in contact with ASP 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S GLU 3.1 9.6 + - - +
47S LEU* 3.7 11.4 - - - +
48S LYS 3.3 0.2 - - - -
49S ALA* 1.3 78.9 - - - +
51S GLN* 1.3 60.6 + - - +
53S TYR* 3.4 11.4 + - - +
54S LYS* 2.9 53.6 + - - +
62S CYS* 5.3 0.2 - - - -
64S LEU* 3.3 27.3 - - + +
261S HIS* 3.7 26.8 + - + +
----------------------------------------------------------
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Residues in contact with GLN 51 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S LEU 3.3 9.8 + - - +
48S LYS* 3.2 32.6 + - - +
49S ALA 3.1 1.0 - - - -
50S ASP* 1.3 81.1 - - - +
52S LEU* 1.3 71.7 + - - +
54S LYS* 3.4 9.7 + - + +
55S GLN* 2.8 49.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S LYS* 3.0 30.2 + - + +
49S ALA 2.9 7.7 + - - +
51S GLN* 1.3 79.0 - - - +
53S TYR* 1.3 58.2 + - - +
55S GLN* 3.4 10.9 + - - +
56S LYS 3.2 5.4 + - - -
57S ILE* 3.0 46.4 + - + +
58S ILE* 3.5 14.6 + - + -
106S LEU* 4.8 23.1 - - + -
110S THR* 3.6 27.8 - - + -
321S ALA* 5.2 5.8 - - + +
324S ALA* 5.2 2.7 - - + -
325S THR* 4.3 16.2 - - + -
----------------------------------------------------------
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Residues in contact with TYR 53 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S ALA 2.8 15.8 + - - +
50S ASP* 3.5 13.2 - - - +
52S LEU* 1.3 75.4 - - - +
54S LYS* 1.3 66.3 + - + +
55S GLN 3.2 1.3 - - - -
56S LYS* 3.1 26.3 + - - +
58S ILE* 3.7 36.3 - - + +
59S ARG* 4.5 1.3 - - - -
60S GLY 3.1 27.7 + - - -
61S PHE 4.4 0.2 - - - -
62S CYS* 3.3 37.3 + - + -
64S LEU* 6.5 0.9 - - + -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S ASP* 2.9 42.3 + - - +
51S GLN* 3.4 10.5 + - + +
53S TYR* 1.3 81.8 - - + +
55S GLN* 1.3 60.1 + - + +
56S LYS* 3.6 9.5 + - - +
261S HIS* 5.5 3.6 + - - -
----------------------------------------------------------
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Residues in contact with GLN 55 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S GLN* 2.8 50.8 + - + +
52S LEU* 3.7 11.8 - - - +
53S TYR 3.2 0.2 - - - -
54S LYS* 1.3 76.9 - - + +
56S LYS* 1.3 71.4 + - - +
57S ILE* 3.6 27.2 + - + +
----------------------------------------------------------
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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