Contacts of the helix formed by residues 3 - 27 (chain B) in PDB entry 3Q02
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 HIS 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.0 27.6 + + - -
212A GLU* 3.7 5.9 + - - +
222A ASP* 4.1 0.9 - - - -
241A TYR* 5.7 1.0 - - - -
271A ARG* 3.8 24.0 + - - +
350A GLU* 3.2 28.0 + - + +
351A GLU 5.2 1.4 + - - -
352A ILE* 4.1 16.7 - - + +
1B VAL 3.3 3.5 + - - +
2B HIS* 1.3 108.1 + + - +
4B PRO* 1.3 65.5 - - + +
5B PRO* 3.4 9.4 - - + -
6B SER* 2.8 35.0 + - - +
7B TYR* 3.7 2.3 + - - +
381B ZN 3.0 21.0 - - - -
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Residues in contact with PRO 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 5.9 0.2 - - - +
350A GLU* 3.4 30.5 - - + +
3B HIS* 1.3 90.7 - - + +
5B PRO* 1.4 69.7 - - + +
7B TYR* 3.2 17.4 + - + +
8B VAL* 3.3 14.1 + - - +
74B ALA* 4.4 9.4 - - + +
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Residues in contact with PRO 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 5.9 3.8 - - + -
271A ARG* 6.3 0.4 - - - +
3B HIS* 3.4 10.8 - - + -
4B PRO* 1.4 99.2 - - + +
6B SER* 1.3 51.0 + - - +
8B VAL* 3.2 11.5 - - + +
9B ALA* 2.7 36.6 + - - +
74B ALA* 4.2 12.5 - - + +
77B HIS* 4.0 27.1 - - + +
78B LEU* 4.1 20.2 - - + +
81B GLU* 5.0 8.3 - - - +
367B THR* 5.1 7.0 - - + -
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Residues in contact with SER 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 4.4 2.4 + - - -
1B VAL* 3.4 46.5 + - - +
3B HIS* 2.8 18.4 + - - +
5B PRO* 1.3 76.6 - - - +
7B TYR* 1.3 57.5 + - - -
9B ALA* 3.3 8.0 + - - +
10B HIS* 2.9 27.5 + - - +
366B PRO 4.3 0.2 + - - -
367B THR* 3.9 18.2 - - - +
381B ZN 4.2 2.4 - - - -
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Residues in contact with TYR 7 (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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3B HIS 3.7 3.0 + - - +
4B PRO* 3.2 12.7 + - + +
6B SER* 1.3 76.8 - - - +
8B VAL* 1.3 61.9 + - + +
10B HIS* 3.2 13.0 + - + +
11B LEU* 3.0 61.0 + - + +
63B GLY 5.3 1.4 + - - -
71B MET* 5.8 7.9 - - + -
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO 3.3 12.8 + - - +
5B PRO* 3.2 20.4 - - + +
7B TYR* 1.3 80.1 - - + +
9B ALA* 1.3 60.0 + - - +
11B LEU* 4.2 8.1 - - + -
12B ALA* 2.8 28.9 + - + +
64B PHE* 4.9 13.2 - - + -
71B MET* 5.0 17.0 - - - +
74B ALA* 3.5 30.3 - - + +
75B LEU* 3.6 32.3 - - + -
78B LEU* 4.8 2.2 - - + -
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO 2.7 23.6 + - - +
6B SER* 3.5 6.7 - - - +
7B TYR 3.3 0.2 - - - -
8B VAL* 1.3 73.3 - - - +
10B HIS* 1.3 58.0 + - - +
12B ALA* 3.7 1.8 - - - +
13B SER* 2.8 36.3 + - - -
78B LEU* 3.6 18.8 - - + -
367B THR* 3.9 12.6 - - - +
368B GLY 5.8 0.7 - - - -
369B THR* 3.3 26.6 - - - +
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Residues in contact with HIS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER 2.9 13.9 + - - +
7B TYR* 3.3 16.0 + - + +
8B VAL 3.2 0.2 - - - -
9B ALA* 1.3 78.4 - - - +
11B LEU* 1.3 70.8 + - + +
13B SER* 3.9 2.9 - - - -
14B ASP* 2.9 47.8 + - + +
256B ALA* 3.9 22.6 - - + +
257B GLN* 4.4 24.6 + - + +
260B SER* 5.9 1.6 - - - -
367B THR 5.1 0.8 + - - +
368B GLY 6.0 1.8 - - - -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.0 57.1 + - + +
8B VAL* 3.2 11.6 + - + +
10B HIS* 1.3 92.3 - - + +
12B ALA* 1.3 63.5 + - - +
14B ASP* 3.7 4.7 - - + +
15B PHE* 3.1 23.9 + - - +
18B ARG* 4.8 0.7 + - - -
62B MET 4.1 12.4 - - - +
63B GLY* 4.1 17.9 - - - +
64B PHE* 4.0 28.9 - - + -
71B MET* 5.5 2.2 - - - -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL 2.8 20.5 + - - +
9B ALA* 3.9 4.9 - - - +
11B LEU* 1.3 74.7 - - - +
13B SER* 1.3 61.4 + - - +
15B PHE* 3.5 1.8 + - - +
16B GLY 3.1 17.0 + - - -
36B PRO 3.8 3.0 - - - +
37B TYR* 4.9 15.0 - - + -
40B ALA* 3.3 32.0 - - + +
64B PHE* 4.6 10.0 - - + -
75B LEU* 5.0 13.2 - - + -
78B LEU* 5.1 0.4 - - + -
369B THR* 6.5 0.2 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 2.8 23.9 + - - -
10B HIS* 3.9 3.8 - - - -
12B ALA* 1.3 70.5 - - - +
14B ASP* 1.3 60.7 + - - +
16B GLY* 3.3 0.7 + - - -
17B VAL* 2.8 36.6 + - - +
36B PRO* 4.0 6.2 - - - +
37B TYR* 5.4 1.4 - - - +
256B ALA* 4.1 8.1 - - - -
368B GLY 4.7 2.7 - - - -
369B THR* 3.5 10.9 - - - +
370B VAL* 2.9 46.2 + - - +
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B HIS* 2.9 33.9 + - + +
11B LEU* 3.7 7.6 - - + +
13B SER* 1.3 78.3 - - - +
15B PHE* 1.3 62.2 + - - +
17B VAL* 3.6 2.0 + - - +
18B ARG* 3.2 51.7 + - - +
255B SER* 4.3 10.0 - - - -
256B ALA* 3.9 26.0 + - + +
257B GLN 5.3 0.2 + - - -
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Residues in contact with PHE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 3.1 17.2 + - - +
12B ALA* 3.7 4.3 - - - +
14B ASP* 1.3 76.8 - - - +
16B GLY* 1.3 60.7 + - - +
18B ARG* 3.1 23.9 + - - +
19B VAL* 3.0 46.7 + - + +
39B VAL* 4.2 1.3 - - + -
40B ALA* 3.7 30.1 - - + -
43B LEU* 3.2 36.8 - - + -
61B ALA* 3.3 25.6 - - + -
62B MET* 3.9 26.7 - - + +
293B LEU* 4.3 3.8 - - + -
295B MET* 3.8 22.7 - - + -
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Residues in contact with GLY 16 (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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12B ALA 3.1 8.1 + - - -
15B PHE* 1.3 76.0 - - - +
17B VAL* 1.3 60.5 + - - +
19B VAL* 3.1 4.3 + - - +
20B PHE* 2.8 24.4 + - - +
34B PHE* 3.6 7.6 - - - -
36B PRO* 3.4 34.8 - - - -
39B VAL* 3.6 12.3 - - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER 2.8 26.4 + - - +
14B ASP 4.0 4.5 - - - +
16B GLY* 1.3 72.9 - - - +
18B ARG* 1.3 57.7 + - + +
20B PHE* 3.1 8.3 + - - +
21B GLN* 2.9 31.9 + - + +
36B PRO* 4.2 6.1 - - + -
254B LEU* 4.0 17.5 - - + +
255B SER* 3.9 29.8 - - - +
256B ALA 4.3 11.2 - - - +
259B ILE* 5.6 0.2 - - + -
370B VAL* 4.4 7.9 - - + -
373B MET* 3.4 33.4 - - + -
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Residues in contact with ARG 18 (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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11B LEU 4.8 1.0 + - - -
14B ASP* 3.2 34.6 + - - +
15B PHE* 3.1 36.5 + - - +
17B VAL* 1.3 80.4 - - + +
19B VAL* 1.3 63.2 + - - +
21B GLN* 3.3 19.1 + - - +
22B GLN* 3.3 24.9 + - - +
60B ALA 5.4 0.4 + - - -
61B ALA* 2.8 34.3 + - - +
62B MET 4.6 6.1 + - - -
63B GLY* 5.8 0.4 - - - -
293B LEU* 4.1 22.9 - - + +
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Residues in contact with VAL 19 (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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15B PHE* 3.0 42.6 + - + +
16B GLY 3.1 6.5 + - - +
18B ARG* 1.3 74.6 - - - +
20B PHE* 1.3 64.3 + - - +
22B GLN* 3.1 7.8 + - - +
23B VAL* 3.1 19.1 + - + +
34B PHE* 3.5 26.2 - - + -
39B VAL* 4.2 8.3 - - + -
286B LEU* 4.3 10.5 - - + -
289B PRO* 4.0 18.4 - - + -
290B LEU* 4.3 9.6 - - + -
293B LEU* 3.6 21.3 - - + -
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Residues in contact with PHE 20 (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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16B GLY 2.8 16.5 + - - +
17B VAL* 3.1 9.2 + - - +
19B VAL* 1.3 74.6 - - - +
21B GLN* 1.3 62.2 + - + +
23B VAL* 2.9 6.8 + - + +
24B ALA* 2.8 48.1 + - + -
32B VAL* 4.1 20.9 - - + -
34B PHE* 3.7 33.4 - + + -
251B THR* 4.2 11.2 - - + -
254B LEU* 4.4 11.7 - - + -
359B LEU* 4.4 6.5 - - + -
373B MET* 3.6 31.9 - - + -
374B GLY* 4.0 35.7 - - - -
375B GLN* 4.4 5.6 - - + -
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Residues in contact with GLN 21 (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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17B VAL* 2.9 20.1 + - + +
18B ARG* 3.6 23.0 - - - +
19B VAL 3.3 0.2 - - - -
20B PHE* 1.3 81.2 - - + +
22B GLN* 1.3 60.0 + - - +
24B ALA* 3.9 3.9 - - - +
25B GLN* 2.9 49.7 + - - +
251B THR* 2.9 33.8 + - + +
252B ASN* 3.0 24.9 + - - +
254B LEU* 3.5 28.1 + - + +
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Residues in contact with GLN 22 (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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18B ARG 3.6 12.9 + - - +
19B VAL 3.1 9.0 + - - +
21B GLN* 1.3 79.5 - - - +
23B VAL* 1.3 62.7 + - - +
25B GLN* 3.7 24.4 + - - +
26B ALA* 3.5 19.1 + - - +
289B PRO* 3.7 36.2 - - + +
292B ASN* 3.2 34.3 + - - +
293B LEU* 3.9 19.1 - - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.1 15.9 + - + +
20B PHE* 2.9 11.0 + - + +
22B GLN* 1.3 75.4 - - - +
24B ALA* 1.3 64.6 + - - +
26B ALA* 3.2 5.3 + - - +
27B SER* 3.1 27.5 + - - +
32B VAL* 3.9 30.7 - - + -
34B PHE* 4.3 10.8 - - + -
284B VAL* 3.7 36.3 - - + -
289B PRO* 3.7 18.2 - - + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 2.8 32.0 + - + +
21B GLN 4.0 1.6 - - - +
23B VAL* 1.3 74.4 - - - +
25B GLN* 1.3 62.3 + - - +
27B SER* 3.4 1.9 - - - +
28B LYS* 3.2 27.2 + - - +
32B VAL* 5.2 1.3 - - - -
251B THR* 3.7 25.6 - - + -
375B GLN* 3.6 27.5 + - - +
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN* 2.9 41.9 + - + +
22B GLN* 4.0 25.9 + - - +
23B VAL 3.2 0.2 - - - -
24B ALA* 1.3 79.1 - - + +
26B ALA* 1.3 60.1 + - - +
28B LYS* 4.0 17.7 - - - +
251B THR* 5.5 2.7 - - + -
252B ASN* 3.4 30.7 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN 3.5 13.3 + - - +
23B VAL* 3.2 4.8 + - - +
24B ALA 3.2 0.2 - - - -
25B GLN* 1.3 79.0 - - - +
27B SER* 1.3 62.5 + - - +
28B LYS* 3.3 4.4 + - - -
30B ARG* 3.0 14.4 + - - -
288B LYS* 6.5 0.9 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.1 20.7 + - - +
24B ALA 3.4 3.1 - - - -
26B ALA* 1.3 79.6 - - - +
28B LYS* 1.3 63.3 + - - +
29B ASP 3.1 4.6 + - - -
30B ARG* 3.1 31.8 + - - +
32B VAL* 4.1 17.8 - - - +
375B GLN* 3.1 16.1 + - - -
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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