Contacts of the helix formed by residues 7 - 36 (chain B) in PDB entry 3ITX
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 ALA 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.7 3.3 + - - -
5B ARG 4.2 1.2 + - - -
6B ILE* 1.3 74.8 - - - +
8B GLN* 1.3 65.0 + - - +
9B ASP* 3.3 24.0 - - - +
10B VAL* 3.0 30.2 + - + +
11B VAL* 3.3 6.9 + - - +
409B SER* 5.5 0.6 - - - -
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.2 58.4 - - + +
6B ILE 3.2 2.6 + - - +
7B ALA* 1.3 71.8 - - - +
9B ASP* 1.3 57.6 + - - +
11B VAL* 3.2 10.9 + - - +
12B ALA* 2.9 28.5 + - - +
90B GLN* 4.8 2.9 - - - +
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Residues in contact with ASP 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA* 3.3 20.8 - - - +
8B GLN* 1.3 79.3 - - - +
10B VAL* 1.3 81.8 + - - +
12B ALA* 3.7 6.9 - - - +
13B ARG* 2.8 48.6 + - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.5 2.9 - - + -
7B ALA* 3.0 21.7 + - + +
9B ASP* 1.3 90.6 + - - +
11B VAL* 1.3 61.0 + - - +
13B ARG* 3.4 13.7 + - - +
14B GLU* 2.9 39.7 + - + +
405B THR* 4.3 10.5 - - + +
408B ALA* 4.6 4.9 - - + +
409B SER* 4.1 37.0 - - - +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.1 10.5 - - + -
7B ALA 3.8 11.4 - - - +
8B GLN* 3.2 8.9 + - - +
10B VAL* 1.3 77.2 - - - +
12B ALA* 1.3 57.9 + - - +
14B GLU* 3.8 0.3 - - - +
15B ASN* 2.9 56.1 + - - +
90B GLN* 4.1 13.2 - - + +
91B LEU* 4.1 23.3 - - + -
397B GLY 4.6 7.2 - - - +
398B GLY 3.8 18.2 - - - +
399B ALA* 4.3 4.7 - - + -
405B THR* 4.1 7.9 - - + -
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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 GLN 2.9 17.6 + - - +
9B ASP* 3.7 8.5 - - - +
11B VAL* 1.3 78.5 - - - +
13B ARG* 1.3 56.9 + - - +
15B ASN* 3.7 5.0 - - - +
16B ASP* 2.9 44.8 + - - +
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 2.8 44.0 + - - +
10B VAL* 3.6 12.9 - - - +
12B ALA* 1.3 77.2 - - - +
14B GLU* 1.3 76.0 + - - +
16B ASP* 3.9 5.0 - - - +
17B ARG* 3.1 42.9 + - + +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 2.9 23.8 + - + +
11B VAL 4.0 2.0 - - - +
13B ARG* 1.3 87.2 - - - +
15B ASN* 1.3 64.5 + - - +
17B ARG* 2.8 30.0 + - - +
18B ARG* 2.9 61.2 + - - +
404B ALA 4.9 1.9 - - - +
405B THR* 3.4 36.3 + - + +
408B ALA* 3.6 25.0 - - + +
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Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 2.9 25.9 + - - +
12B ALA* 3.7 5.7 - - - +
14B GLU* 1.3 75.3 - - - +
16B ASP* 1.3 63.7 + - - +
18B ARG* 3.0 5.7 + - - +
19B ALA* 2.8 27.8 + - - -
394B ARG* 4.4 16.2 + - + +
398B GLY 3.1 24.0 + - - -
399B ALA* 3.4 7.0 - - - +
400B VAL* 2.8 43.8 + - + +
405B THR* 4.7 1.6 + - - -
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 2.9 35.7 + - - +
13B ARG* 3.9 4.9 - - - +
15B ASN* 1.3 74.9 - - - +
17B ARG* 1.3 63.5 + - + +
18B ARG 3.2 0.7 + - - -
19B ALA* 3.3 22.9 + - - +
20B SER* 4.7 1.2 + - - -
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.1 26.5 + - + +
14B GLU* 2.8 52.3 + - - +
15B ASN 3.3 0.2 - - - -
16B ASP* 1.3 77.2 - - + +
18B ARG* 1.3 78.0 + - + +
20B SER* 5.0 3.6 + - - -
21B ALA* 5.5 1.2 + - - +
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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
----------------------------------------------------------
14B GLU* 2.9 50.9 + - - +
15B ASN 3.0 7.6 + - - +
17B ARG* 1.3 96.1 - - + +
19B ALA* 1.3 63.4 + - - +
20B SER 3.4 2.9 - - - -
21B ALA* 3.2 11.8 + - + +
22B LEU* 2.9 23.6 + - - +
400B VAL* 4.3 21.1 - - + -
401B ASP* 3.7 28.0 + - - +
404B ALA* 3.5 27.9 - - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN 2.8 12.4 + - - +
16B ASP* 3.3 23.1 + - + +
18B ARG* 1.3 76.1 - - - +
20B SER* 1.3 59.6 + - - +
22B LEU* 3.3 8.0 + - - +
23B LYS* 2.9 30.9 + - - +
394B ARG* 5.8 9.0 - - - +
400B VAL* 5.8 0.4 - - - -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 4.7 1.3 + - - -
17B ARG 5.0 3.5 + - - -
18B ARG 3.4 0.6 - - - -
19B ALA* 1.3 79.1 - - - +
21B ALA* 1.3 64.7 + - - +
23B LYS* 3.4 9.1 + - - +
24B GLU* 3.1 24.5 + - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG 5.5 0.8 + - - +
18B ARG* 3.2 16.1 + - + +
20B SER* 1.3 77.5 - - - +
22B LEU* 1.3 63.3 + - - +
24B GLU* 3.1 11.4 + - - +
25B ASP* 3.0 26.6 + - - +
35C ARG* 3.7 23.9 + - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG 2.9 16.5 + - - +
19B ALA* 3.7 4.9 - - - +
21B ALA* 1.3 72.0 - - - +
23B LYS* 1.3 62.3 + - - +
25B ASP* 3.1 7.6 + - + +
26B TYR* 2.8 35.0 + - + +
387B PRO* 3.7 24.7 - - + +
390B ALA* 3.7 21.1 - - + -
391B GLU* 3.6 35.4 - - + +
394B ARG* 4.2 8.7 - - - -
400B VAL* 3.9 35.2 - - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 2.9 17.6 + - - +
20B SER* 3.6 8.7 - - - +
22B LEU* 1.3 77.6 - - - +
24B GLU* 1.3 57.4 + - - +
26B TYR* 3.8 5.2 - - - +
27B GLU* 2.9 71.3 + - + +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER 3.1 14.7 + - - +
21B ALA* 3.3 12.9 - - - +
23B LYS* 1.3 77.3 - - - +
25B ASP* 1.3 62.1 + - - +
27B GLU* 4.0 7.8 - - - +
28B ALA* 3.1 24.3 + - - +
31C ALA* 4.5 14.4 - - - +
35C ARG* 4.1 30.4 + - - +
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 3.0 11.9 + - - +
22B LEU* 3.7 9.5 - - + +
24B GLU* 1.3 73.7 - - - +
26B TYR* 1.3 61.4 + - - +
28B ALA* 3.3 5.8 + - - +
29B LEU* 3.0 31.0 + - - +
387B PRO* 3.8 24.0 - - + +
32C ASN* 3.4 18.3 + - - +
35C ARG* 2.7 44.7 + - - -
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Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 2.8 26.2 + - + +
23B LYS* 3.8 6.1 - - - +
25B ASP* 1.3 73.3 - - - +
27B GLU* 1.3 63.4 + - + +
29B LEU* 3.5 2.5 + - + +
30B GLY* 2.9 25.1 + - - -
40B ILE* 3.0 36.6 - - + +
41B GLU* 2.7 29.6 + - - -
44B THR* 2.8 23.6 + - - -
387B PRO* 3.7 29.3 - - + +
388B ILE* 4.2 3.8 - - + -
391B GLU* 3.6 22.7 - - + +
395B ARG* 3.5 17.3 + - - -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 2.9 64.0 + - + +
24B GLU* 4.0 6.4 - - - +
26B TYR* 1.3 80.4 - - + +
28B ALA* 1.3 60.6 + - - +
30B GLY* 3.4 1.4 + - - +
31B ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.1 19.1 + - + +
25B ASP* 3.7 7.2 - - - +
26B TYR 3.3 0.2 - - - -
27B GLU* 1.3 78.1 - - - +
29B LEU* 1.3 61.7 + - - +
31B ALA* 3.4 6.6 + - - +
32B ASN* 3.2 21.1 + - - +
35B ARG* 5.0 1.7 + - - -
28C ALA* 4.5 23.4 - - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP 3.0 16.8 + - - +
26B TYR* 3.9 4.3 - - + +
28B ALA* 1.3 75.1 - - - +
30B GLY* 1.3 60.6 + - - +
32B ASN* 3.2 11.9 + - + +
33B LEU* 2.8 45.7 + - + +
40B ILE* 4.9 2.0 - - + -
383B THR* 3.8 25.8 - - + -
384B ASP 3.5 22.0 - - - +
385B VAL* 4.2 2.0 - - - -
387B PRO* 4.1 16.8 - - + -
388B ILE* 3.8 31.9 - - + -
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR 2.9 17.7 + - - -
27B GLU* 3.8 2.7 - - - -
28B ALA 3.3 0.2 - - - -
29B LEU* 1.3 77.7 - - - +
31B ALA* 1.3 55.2 + - - +
33B LEU* 3.3 2.5 + - - +
34B ALA* 2.8 30.7 + - - +
38B VAL 4.8 0.7 - - - +
40B ILE* 4.0 28.1 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU 3.0 16.6 + - - +
28B ALA* 3.7 7.4 - - - +
29B LEU 3.3 0.2 - - - -
30B GLY* 1.3 75.0 - - - +
32B ASN* 1.3 62.6 + - - +
34B ALA* 3.4 7.8 + - - +
35B ARG* 3.1 43.8 + - - +
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.2 12.2 + - - +
29B LEU* 3.2 16.4 + - + +
31B ALA* 1.3 77.1 - - - +
33B LEU* 1.3 66.9 + - - +
35B ARG* 3.2 27.5 + - - +
36B ARG* 2.8 49.3 + - - +
383B THR* 5.3 0.2 - - - +
25C ASP* 2.8 30.8 + - - +
384C ASP* 5.9 0.6 + - - -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.8 34.8 + - + +
30B GLY* 3.8 4.3 - - - +
32B ASN* 1.3 73.6 - - - +
34B ALA* 1.3 60.8 + - - +
36B ARG* 2.9 38.7 + - - +
37B GLY 3.1 0.2 + - - -
38B VAL* 2.8 45.9 + - + +
40B ILE* 3.6 36.1 - - + +
43B VAL* 5.1 0.4 - - + -
355B LEU* 4.0 31.0 - - + -
388B ILE* 4.2 11.7 - - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY 2.8 18.4 + - - +
31B ALA* 3.5 10.1 - - - +
32B ASN 3.2 0.2 - - - -
33B LEU* 1.3 78.3 - - - +
35B ARG* 1.3 58.3 + - + +
37B GLY* 3.0 17.8 + - - -
38B VAL 3.5 9.8 + - - +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 5.0 1.6 + - - -
31B ALA* 3.1 31.5 + - - +
32B ASN* 3.2 23.2 + - - +
34B ALA* 1.3 76.1 - - + +
36B ARG* 1.3 62.4 + - + +
37B GLY 3.2 1.5 + - - -
21C ALA* 4.5 24.6 - - + +
24C GLU* 3.8 32.7 + - - +
25C ASP* 2.8 32.1 + - - +
----------------------------------------------------------
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 2.8 41.4 + - - +
33B LEU* 2.9 20.5 + - - +
35B ARG* 1.3 79.9 - - + +
37B GLY* 1.3 62.3 + - - +
38B VAL* 3.3 15.5 + - + +
355B LEU* 4.4 13.5 + - - +
357B ASP* 5.8 0.2 - - - +
379B ARG* 3.1 24.1 + - - +
380B ALA* 4.2 4.8 - - - +
383B THR* 3.0 37.6 + - - +
384C ASP* 5.8 2.0 + - - -
----------------------------------------------------------
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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