Contacts of the helix formed by residues 6 - 31 (chain M) in PDB entry 2AXT
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 LEU 6 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B BCR 4.0 20.2 - - + -
530B MGE 3.5 42.4 - - - +
4M ASN* 3.2 5.1 + - - +
5M GLN* 1.3 80.3 - - + +
7M GLY* 1.3 58.1 + - - +
8M LEU 3.3 1.3 - - - -
9M ILE* 3.2 9.8 + - + +
10M ALA* 2.8 30.9 + - - +
5216M LMT 3.6 44.0 - - + +
5008m LEU* 4.3 19.1 - - + -
5001t MET* 4.2 20.6 - - + -
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Residues in contact with GLY 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L PHE 3.9 18.6 - - - -
36L PHE* 3.6 17.3 - - - -
4M ASN* 3.0 16.3 + - - -
6M LEU* 1.3 80.2 - - - +
8M LEU* 1.3 63.0 + - - +
10M ALA* 4.3 4.0 - - - -
11M THR* 2.9 31.0 + - - -
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Residues in contact with LEU 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L PHE* 3.4 18.8 - - + -
4M ASN 4.6 0.2 + - - -
5M GLN 4.2 4.1 + - - +
6M LEU 3.3 0.8 - - - -
7M GLY* 1.3 75.2 - - - +
9M ILE* 1.3 65.6 + - + +
11M THR* 4.5 1.0 - - - -
12M ALA* 3.2 24.5 + - - +
1T MET* 4.2 26.0 - - + +
5T THR* 3.1 29.8 - - + +
5527b BCR 5.7 1.1 - - + -
216m LMT 4.1 35.8 - - + +
5006m LEU* 4.3 15.7 - - + -
5009m ILE* 4.3 22.5 - - + +
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Residues in contact with ILE 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B BCR 4.0 22.0 - - + -
5M GLN 3.5 24.2 - - - +
6M LEU* 3.8 10.5 - - + +
7M GLY 3.1 0.2 - - - -
8M LEU* 1.3 78.0 - - + +
10M ALA* 1.3 67.5 + - - +
11M THR 2.9 2.1 + - - -
12M ALA* 4.1 4.3 - - + -
13M LEU* 2.8 46.3 + - + +
5216M LMT 6.0 2.0 - - + -
5005m GLN 5.5 0.2 - - - +
5008m LEU* 4.3 28.7 - - + +
5009m ILE* 3.3 41.3 - - + +
5012m ALA* 5.3 6.5 - - + -
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Residues in contact with ALA 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B BCR 3.7 22.6 - - + +
530B MGE 4.0 22.7 - - + +
35L PHE* 3.7 28.3 - - + -
6M LEU 2.8 22.6 + - - +
7M GLY* 3.9 3.4 - - - +
9M ILE* 1.3 75.1 - - - +
11M THR* 1.3 56.8 + - - +
13M LEU* 5.3 0.2 - - - -
14M PHE* 3.0 26.7 + - - +
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Residues in contact with THR 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L ALA* 4.8 3.1 - - + +
32L SER* 3.5 35.8 + - - -
35L PHE* 4.0 7.4 - - - +
36L PHE* 4.5 2.6 - - - -
7M GLY 2.9 19.0 + - - -
8M LEU 4.5 2.2 - - - -
10M ALA* 1.3 78.3 - - - +
12M ALA* 1.3 64.7 + - - +
14M PHE* 3.4 5.3 + - + +
15M VAL* 3.1 33.9 + - + +
5T THR* 3.8 27.6 - - + -
9T ILE* 4.0 14.4 - - + -
216m LMT 5.7 2.7 - - + -
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Residues in contact with ALA 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M LEU 3.2 20.0 + - - +
9M ILE* 3.0 7.4 + - + +
11M THR* 1.3 79.4 - - - +
13M LEU* 1.3 65.1 + - + +
15M VAL* 3.2 5.1 + - - +
16M LEU* 3.0 38.5 + - + +
216m LMT 4.1 23.7 - - + +
5009m ILE* 5.3 7.9 - - + -
5013m LEU* 5.0 9.2 - - + -
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Residues in contact with LEU 13 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B BCR 3.9 28.0 - - + -
530B MGE 4.0 42.6 - - + -
9M ILE* 2.8 29.3 + - + +
12M ALA* 1.3 72.0 - - + +
14M PHE* 1.3 60.0 + - - +
15M VAL 2.8 11.1 + - - -
16M LEU* 4.5 4.3 - - + +
17M VAL* 3.1 38.3 + - + +
5216M LMT 5.8 5.4 - - + -
5012m ALA* 5.0 8.7 - - + -
5013m LEU* 5.6 1.3 - - + -
5016m LEU* 3.4 33.4 - - + -
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Residues in contact with PHE 14 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B CLA 3.3 37.2 - - + -
523B CLA 3.8 17.5 - - + -
530B MGE 4.2 21.6 - - + +
24L ILE* 3.8 9.0 - - + +
27L LEU* 3.7 38.8 - - + -
28L ALA* 3.8 25.4 - - + -
31L PHE* 5.1 7.0 - + + -
35L PHE* 4.6 13.0 - + + -
10M ALA 3.0 22.5 + - - +
11M THR* 3.7 6.3 - - - +
12M ALA 3.4 0.4 - - - -
13M LEU* 1.3 77.4 - - - +
15M VAL* 1.3 56.1 + - - +
18M PRO* 3.5 20.3 - - + +
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Residues in contact with VAL 15 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ILE* 3.8 6.4 - - + +
25L LEU* 3.9 26.0 - - + -
28L ALA* 3.6 29.2 - - + -
11M THR* 3.1 20.6 + - + +
12M ALA* 3.6 6.7 - - - +
13M LEU 2.8 1.8 + - - -
14M PHE* 1.3 78.5 - - - +
16M LEU* 1.3 67.3 + - + +
18M PRO* 3.5 3.1 - - - +
19M SER* 2.7 39.1 + - - +
8T PHE* 5.7 9.4 - - + -
9T ILE* 5.0 6.5 - - + -
216m LMT 6.4 1.3 - - + -
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Residues in contact with LEU 16 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ALA* 3.0 21.4 + - + +
13M LEU* 4.3 2.2 - - + +
15M VAL* 1.3 84.3 - - + +
17M VAL* 1.3 57.6 + - + +
19M SER* 2.8 7.0 + - - -
20M VAL* 2.6 48.3 + - + +
8T PHE* 6.3 3.6 - - + -
5530b MGE 5.1 16.2 - - + -
216m LMT 6.5 2.2 - - + -
5013m LEU* 3.4 33.2 - - + -
5016m LEU* 4.5 17.9 - - + -
5017m VAL* 5.1 10.8 - - + -
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Residues in contact with VAL 17 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B CLA 5.3 0.7 - - + -
530B MGE 4.2 35.2 - - + -
210L MGE 3.8 28.5 - - + -
13M LEU* 3.1 30.7 + - + +
16M LEU* 1.3 77.3 - - + +
18M PRO* 1.3 74.6 - - + +
20M VAL* 3.1 6.1 + - - +
21M PHE* 3.1 17.8 + - - +
5476c UNK 5.0 20.4 - - + +
5016m LEU* 5.1 8.7 - - + -
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Residues in contact with PRO 18 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B CLA 4.8 8.1 - - + -
530B MGE 6.4 0.2 - - + -
24L ILE* 3.5 31.0 - - + -
210L MGE 3.8 28.7 - - + +
13M LEU 3.6 7.6 - - - +
14M PHE* 3.5 17.0 - - + +
15M VAL 3.5 4.9 - - - +
17M VAL* 1.3 99.8 - - + +
19M SER* 1.3 64.3 + - - +
21M PHE* 3.0 20.9 + - + +
22M LEU* 3.1 16.5 + - - +
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Residues in contact with SER 19 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C UNK 6.0 1.4 - - - +
21L LEU* 3.4 23.1 - - - +
24L ILE* 4.3 16.6 - - - +
25L LEU* 5.7 2.6 - - - +
15M VAL* 2.7 31.8 + - - +
16M LEU* 2.8 7.1 + - - -
18M PRO* 1.3 78.3 - - - +
20M VAL* 1.3 60.4 + - - +
22M LEU* 3.5 5.9 + - - +
23M ILE* 3.2 30.5 + - - +
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Residues in contact with VAL 20 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C UNK 5.7 5.2 - - + -
16M LEU* 2.6 32.3 + - + +
17M VAL* 3.6 4.9 - - - +
19M SER* 1.3 69.2 - - - +
21M PHE* 1.3 68.3 + - - +
22M LEU 3.0 2.0 - - - -
23M ILE* 2.9 16.4 + - + +
24M ILE* 2.8 38.3 + - + +
5476c UNK 5.2 7.9 - - + -
5020m VAL* 3.4 48.7 - - + -
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Residues in contact with PHE 21 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 4.2 14.4 - + + -
521B CLA 3.7 20.2 - - + -
524B CLA 3.7 48.0 - - + -
210L MGE 4.0 29.4 - - + -
17M VAL* 3.1 11.4 + - + +
18M PRO* 3.0 12.3 + - + +
20M VAL* 1.3 78.9 - - - +
22M LEU* 1.3 85.0 + - + +
24M ILE* 3.5 6.5 + - - +
25M LEU* 3.3 45.1 + - + +
5476c UNK 4.6 23.6 - - + -
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Residues in contact with LEU 22 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 5.6 0.2 - - + -
12L LEU* 3.9 24.9 - - + +
16L SER 4.6 2.5 - - - +
17L LEU* 4.2 18.7 - - + +
20L GLY* 3.2 40.6 - - - -
21L LEU* 3.9 7.6 - - + +
24L ILE* 4.9 4.9 - - + -
210L MGE 3.8 28.0 - - + -
18M PRO 3.1 11.3 + - - +
19M SER* 3.7 6.5 - - - +
20M VAL 3.0 0.6 - - - -
21M PHE* 1.3 97.2 - - + +
23M ILE* 1.3 65.8 + - - +
24M ILE 3.2 0.2 + - - -
25M LEU* 3.2 2.6 + - - +
26M TYR* 3.0 24.3 + - - +
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Residues in contact with ILE 23 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C UNK 3.4 54.1 - - + -
476C UNK 4.7 8.7 - - + -
17L LEU* 4.3 17.7 - - + -
21L LEU* 5.1 6.3 - - + -
19M SER* 3.2 22.0 + - - +
20M VAL* 2.9 18.0 + - + +
22M LEU* 1.3 75.7 - - - +
24M ILE* 1.3 65.6 + - - +
26M TYR* 3.5 2.3 + - + +
27M VAL* 3.1 28.9 + - + +
5024m ILE* 3.5 25.4 - - + -
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Residues in contact with ILE 24 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M VAL* 2.8 26.6 + - + +
21M PHE 3.7 7.2 - - - +
23M ILE* 1.3 77.7 - - - +
25M LEU* 1.3 69.5 + - + +
27M VAL* 3.8 2.2 - - - +
28M GLN* 2.9 22.4 + - + +
5476c UNK 3.6 45.5 - - + -
5023m ILE* 3.5 31.4 - - + -
5024m ILE* 4.0 26.4 - - + +
5027m VAL* 4.1 26.5 - - + -
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Residues in contact with LEU 25 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TRP* 3.6 15.9 - - + -
524B CLA 3.9 24.7 - - + -
10L VAL* 4.7 14.6 - - + -
11L GLU 5.0 1.1 - - - +
12L LEU* 3.3 35.9 - - + +
21M PHE* 3.3 37.4 + - + +
22M LEU 3.2 3.0 + - - +
24M ILE* 1.3 83.4 - - + +
26M TYR* 1.3 65.0 + - - +
28M GLN* 2.9 17.2 - - + +
29M THR* 2.9 24.5 + - - -
5476c UNK 4.5 13.0 - - + -
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Residues in contact with TYR 26 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C UNK 4.5 21.1 - - + +
12L LEU* 3.6 25.6 - - + +
13L ASN 4.0 1.1 - - - -
14L ARG* 3.0 65.7 + - + -
17L LEU* 4.1 29.4 - - + -
5213L SQD 3.9 11.2 + - + +
22M LEU 3.0 19.4 + - - +
23M ILE* 3.8 3.6 - - + +
25M LEU* 1.3 71.1 - - - +
27M VAL* 1.3 84.8 + - + +
29M THR* 2.8 26.0 + - - -
30M GLU* 3.1 37.4 + - + +
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Residues in contact with VAL 27 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C UNK 3.8 34.8 - - + -
476C UNK 4.3 8.5 - - + -
23M ILE* 3.1 20.6 + - + +
24M ILE 4.0 1.6 - - - +
26M TYR* 1.3 89.0 - - + +
28M GLN* 1.3 62.8 + - - +
29M THR 2.9 1.4 + - - -
30M GLU* 3.0 15.3 + - + +
31M SER* 3.2 12.0 + - - -
36M SER* 4.3 16.6 - - - +
5024m ILE* 4.1 13.9 - - + -
5028m GLN* 3.4 28.9 - - + +
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Residues in contact with GLN 28 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L VAL* 2.9 32.3 + - - +
11L GLU* 4.3 0.4 - - - +
24M ILE 2.9 17.1 + - - +
25M LEU* 2.9 26.2 + - + +
27M VAL* 1.3 73.4 - - - +
29M THR* 1.3 82.2 + - - +
31M SER* 3.2 9.9 + - - -
32M GLN* 3.3 4.8 + - - +
5476c UNK 5.9 0.7 - - + -
5027m VAL* 3.4 29.8 - - + -
5028m GLN* 3.8 6.5 - - + +
5031m SER* 2.8 28.9 + - - +
5035m SER 4.3 0.2 - - - +
5036m SER* 2.2 37.2 + - - +
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Residues in contact with THR 29 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L GLU* 3.5 11.6 - - + -
12L LEU 3.0 37.5 + - - +
13L ASN* 5.1 3.1 - - - +
25M LEU 2.9 7.0 + - - -
26M TYR 2.8 13.4 + - - -
28M GLN* 1.3 93.6 + - - +
30M GLU* 1.3 75.3 - - - +
32M GLN* 2.9 33.2 + - - +
33M GLN* 5.6 0.2 - - - +
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Residues in contact with GLU 30 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C UNK 5.8 4.0 - - + -
13L ASN* 5.9 1.4 - - - -
14L ARG* 4.2 10.1 + - - +
26M TYR* 3.1 50.0 + - + +
27M VAL* 3.0 8.7 + - + +
29M THR* 1.3 91.8 - - - +
31M SER* 1.3 57.7 + - - +
32M GLN 3.1 4.7 + - - -
33M GLN* 3.2 14.2 + - - +
35M SER* 3.2 41.1 + - - +
36M SER* 5.1 3.4 - - - -
----------------------------------------------------------
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Residues in contact with SER 31 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M VAL 3.2 8.5 + - - -
28M GLN 3.2 4.9 + - - -
30M GLU* 1.3 72.2 - - - +
32M GLN* 1.3 55.1 + - - +
33M GLN 2.8 6.3 - - - -
34M LYS 3.0 14.0 + - - -
35M SER 3.0 13.3 + - - +
36M SER* 3.3 19.5 - - - -
5028m GLN* 2.7 24.8 + - - -
5031m SER* 2.7 27.3 + - - -
5032m GLN* 3.2 22.6 - - - +
----------------------------------------------------------
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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