Contacts of the helix formed by residues 4 - 35 (chain A) in PDB entry 1A3N
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 PRO 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 4.6 0.4 - - - +
3A SER* 1.4 90.2 - - - +
5A ALA* 1.3 62.1 + - - +
7A LYS* 3.3 10.8 + - + +
8A THR* 3.0 27.6 + - - -
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Residues in contact with ALA 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.2 8.0 + - - +
4A PRO* 1.3 79.4 - - - +
6A ASP* 1.3 64.3 + - - +
8A THR* 3.3 7.2 + - - -
9A ASN* 2.9 34.9 + - - +
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.6 14.7 - - + -
3A SER* 2.9 33.6 + - - +
5A ALA* 1.3 79.1 - - - +
7A LYS* 1.4 58.0 + - - +
9A ASN* 3.2 1.2 + - - +
10A VAL* 2.9 34.6 + - - +
123A ALA* 4.9 0.5 - - - +
124A SER* 2.8 37.9 + - - +
127A LYS* 2.7 43.4 + - - +
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 6.0 1.4 - - - +
2A LEU* 3.4 36.9 + - + -
3A SER 2.8 21.4 + - - +
4A PRO* 3.8 8.6 - - + +
6A ASP* 1.4 72.6 - - - +
8A THR* 1.3 57.0 + - - +
10A VAL* 3.4 6.5 + - - +
11A LYS* 2.9 39.1 + - + +
73A VAL* 4.0 34.5 - - + +
74A ASP* 2.8 32.8 + - - +
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO 3.0 15.1 + - - -
5A ALA* 3.3 11.7 + - - -
7A LYS* 1.3 74.8 - - - +
9A ASN* 1.3 61.5 + - - +
11A LYS* 3.4 7.3 + - - +
12A ALA* 2.9 32.0 + - + +
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Residues in contact with ASN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ALA* 2.9 24.5 + - - +
6A ASP 3.6 1.1 - - - +
8A THR* 1.3 77.8 - - - +
10A VAL* 1.3 61.1 - - - +
12A ALA* 3.4 5.8 + - - +
13A ALA* 2.9 31.2 + - - +
120A ALA* 3.6 22.9 + - - +
121A VAL* 3.7 27.1 - - + +
124A SER* 2.9 32.0 + - - +
125A LEU* 5.6 0.2 - - - -
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 5.7 1.8 - - + -
6A ASP* 2.9 23.6 + - + +
7A LYS* 3.8 5.8 - - - +
9A ASN* 1.3 77.6 - - - +
11A LYS* 1.4 59.2 + - + +
13A ALA* 3.3 0.9 + - - +
14A TRP* 2.9 30.5 + - + +
70A VAL* 3.9 26.2 - - + -
73A VAL* 5.4 4.5 - - + -
124A SER 3.8 15.7 - - - +
125A LEU* 4.4 15.1 - - + +
128A PHE* 3.6 48.9 - - + -
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 2.9 25.4 + - - +
8A THR* 4.0 5.2 - - - +
10A VAL* 1.4 76.9 - - + +
12A ALA* 1.3 58.1 + - - +
15A GLY* 2.8 28.6 + - - -
70A VAL* 3.6 39.9 - - + +
71A ALA* 5.6 3.3 + - - +
73A VAL* 4.1 17.6 - - + +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 2.9 21.3 + - + +
9A ASN* 3.8 6.1 - - - +
11A LYS* 1.3 79.4 - - - +
13A ALA* 1.3 62.9 + - - +
15A GLY* 3.8 0.9 - - - -
16A LYS* 3.0 23.0 + - - +
116A GLU* 5.1 5.6 - - + +
121A VAL* 6.3 1.3 - - + -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN 2.9 19.1 + - - +
10A VAL 3.3 2.4 + - - +
12A ALA* 1.3 77.5 - - - +
14A TRP* 1.3 61.1 + - - +
16A LYS* 3.2 8.5 + - - +
17A VAL* 3.1 24.2 + - - +
109A LEU* 6.0 0.7 - - + -
113A LEU* 4.1 15.8 - - + +
116A GLU* 4.9 7.4 - - + -
121A VAL* 4.0 21.5 - - + -
125A LEU* 4.2 19.1 - - + -
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Residues in contact with TRP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 2.9 22.4 + - + +
11A LYS 4.4 1.1 - - - +
13A ALA* 1.3 70.0 - - - +
15A GLY* 1.3 65.1 + - - +
17A VAL* 3.2 17.4 + - + +
18A GLY* 3.1 18.7 + - - -
21A ALA* 3.9 24.4 - - + +
24A TYR* 5.8 2.9 - - + -
25A GLY* 6.0 1.3 - - - -
63A ALA* 3.6 26.2 - - + -
66A LEU* 3.8 28.5 - - + -
67A THR* 2.7 36.9 + - + +
70A VAL* 4.0 30.7 - - + -
105A LEU* 5.4 7.0 - - + -
109A LEU* 3.9 31.6 - - + -
125A LEU* 5.4 5.3 - - + +
128A PHE* 6.0 4.0 - + - -
129A LEU* 6.4 0.9 - - + -
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS 2.8 20.2 + - - -
12A ALA* 3.8 1.6 - - - -
14A TRP* 1.3 78.0 - - - +
16A LYS* 1.4 58.4 + - - +
18A GLY* 3.2 14.5 + - - -
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 3.0 12.9 + - - +
13A ALA 3.2 6.9 + - - +
15A GLY* 1.4 74.0 - - - +
17A VAL* 1.3 66.2 + - - +
18A GLY* 3.2 1.6 + - - -
20A HIS* 4.9 4.7 - - - -
112A HIS 5.7 0.7 - - - +
113A LEU* 3.3 28.7 - - + -
116A GLU* 3.5 32.3 + - + +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.1 15.2 + - - +
14A TRP* 3.2 25.3 + - + +
16A LYS* 1.3 76.7 - - - +
18A GLY* 1.3 64.4 + - - +
19A ALA 3.2 0.5 + - - -
20A HIS* 3.0 27.1 + - - -
21A ALA* 3.4 36.1 - - + +
24A TYR* 3.6 24.9 - - + -
109A LEU* 3.6 30.1 - - + -
113A LEU* 4.5 8.5 - - + -
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.1 9.7 + - - +
15A GLY* 3.2 12.8 + - - -
16A LYS 3.1 3.2 - - - -
17A VAL* 1.3 77.9 - - - +
19A ALA* 1.3 61.7 + - - -
20A HIS 3.3 1.2 + - - -
21A ALA* 3.4 18.7 + - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL 3.2 1.0 + - - -
18A GLY* 1.3 70.6 - - - -
20A HIS* 1.3 62.8 + - + +
21A ALA* 3.2 2.9 + - - -
22A GLY 4.6 2.9 + - - -
23A GLU 5.4 0.3 + - - -
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 4.9 4.3 - - - -
17A VAL* 3.0 21.1 + - - +
19A ALA* 1.3 80.0 - - + +
21A ALA* 1.3 65.2 + - - +
22A GLY 3.3 2.0 - - - -
23A GLU* 3.1 25.2 + - - +
24A TYR* 2.9 57.1 + - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.9 23.2 - - + +
17A VAL* 3.4 20.6 - - + +
18A GLY 3.4 15.4 + - - +
19A ALA* 3.2 2.5 - - - -
20A HIS* 1.3 77.7 - - - +
22A GLY* 1.3 56.7 + - - +
24A TYR* 3.2 4.2 + - - +
25A GLY 2.8 25.1 + - - -
63A ALA* 3.1 14.0 - - + +
64A ASP* 5.6 2.9 - - - +
67A THR* 4.5 8.1 - - - +
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 4.6 3.0 + - - -
20A HIS 3.3 0.6 - - - -
21A ALA* 1.3 76.3 - - - +
23A GLU* 1.3 62.2 + - - +
25A GLY* 3.4 1.2 + - - -
26A ALA* 3.1 22.2 + - - +
56A LYS 4.7 1.0 - - - +
59A GLY 3.9 5.4 - - - -
60A LYS* 3.9 28.4 + - - -
63A ALA* 3.7 11.1 - - - +
64A ASP* 5.6 2.1 + - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 5.4 0.4 + - - -
20A HIS* 3.1 30.8 + - - +
22A GLY* 1.3 74.7 - - - +
24A TYR* 1.3 77.5 + - + +
26A ALA* 3.3 7.3 + - - +
27A GLU* 3.0 30.4 + - + +
112A HIS* 4.0 12.8 + - - -
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 5.8 3.4 - - + -
17A VAL* 3.6 39.3 - - + -
20A HIS* 2.9 48.0 + + + +
21A ALA* 3.6 5.2 - - - +
23A GLU* 1.3 87.6 - - + +
25A GLY* 1.3 61.5 + - - +
27A GLU* 4.2 1.6 - - - -
28A ALA* 2.8 29.6 + - - +
105A LEU* 4.8 2.6 - - + +
108A THR* 3.6 19.6 - - + +
109A LEU* 4.4 12.1 - - + -
112A HIS* 3.2 63.6 + + + +
113A LEU* 5.5 2.1 - - + +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 6.0 1.1 - - - -
21A ALA 2.8 14.3 + - - -
22A GLY 3.4 0.4 + - - -
24A TYR* 1.3 78.3 - - - +
26A ALA* 1.3 61.4 + - - +
28A ALA* 3.3 7.1 + - - +
29A LEU* 3.1 26.3 + - - +
59A GLY* 3.7 21.5 - - - -
62A VAL* 5.2 4.7 - - - +
63A ALA* 4.4 6.5 - - - -
101A LEU* 5.5 0.2 - - - +
105A LEU* 4.6 10.3 - - - +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 3.1 13.9 + - - +
23A GLU* 3.6 9.6 - - - +
25A GLY* 1.3 75.8 - - - +
27A GLU* 1.3 61.7 + - - +
29A LEU* 3.3 4.6 + - - +
30A GLU* 3.0 23.6 + - - +
55A VAL* 3.8 10.9 - - + +
56A LYS* 3.7 38.4 - - + +
59A GLY* 3.5 9.5 - - - -
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.0 21.5 + - + +
24A TYR* 3.7 7.3 - - - +
25A GLY 3.3 0.2 - - - -
26A ALA* 1.3 74.8 - - - +
28A ALA* 1.3 58.2 + - - +
30A GLU* 3.2 11.2 + - - +
31A ARG* 2.8 73.5 + - + +
108A THR* 3.6 13.3 - - + +
111A ALA* 4.6 1.4 - - - +
112A HIS* 2.7 34.9 + - - -
124B PRO* 4.6 8.3 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 2.8 13.1 + - - +
25A GLY 3.3 3.6 + - - +
27A GLU* 1.3 77.6 - - - +
29A LEU* 1.3 56.9 + - - +
31A ARG* 3.3 2.5 + - - -
32A MET* 2.9 25.8 + - - +
101A LEU* 4.1 6.7 - - + -
104A CYS* 3.5 18.5 - - - +
105A LEU* 3.5 38.1 - - + +
108A THR* 3.3 18.5 + - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 3.1 12.5 + - - +
26A ALA* 3.7 5.8 - - - +
27A GLU 3.3 0.2 - - - -
28A ALA* 1.3 76.2 - - - +
30A GLU* 1.3 56.0 + - - +
32A MET* 3.1 25.9 + - + +
33A PHE* 2.8 51.3 + - + -
43A PHE* 4.8 2.5 - - + -
55A VAL* 3.8 11.9 - - + +
58A HIS* 3.5 32.8 - - + +
59A GLY* 3.5 38.8 - - - +
62A VAL* 4.5 6.3 - - + -
101A LEU* 4.2 20.0 - - + -
142A HEM 6.1 1.1 - - + -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.0 14.0 + - - +
27A GLU* 3.6 13.7 - - - +
29A LEU* 1.3 75.8 - - - +
31A ARG* 1.3 63.4 + - - +
33A PHE* 3.3 9.8 + - - +
34A LEU* 3.1 35.0 + - + +
48A LEU 5.9 2.5 - - - +
50A HIS* 2.5 53.9 + - - +
51A GLY 5.2 1.2 + - - -
55A VAL* 4.6 6.8 - - + +
124B PRO* 4.0 26.4 - - + +
125B PRO* 5.6 1.4 - - - +
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 2.8 43.1 + - - +
28A ALA 3.5 7.4 - - - +
30A GLU* 1.3 74.4 - - - +
32A MET* 1.3 58.4 + - - +
34A LEU* 3.9 1.7 - - - +
35A SER* 2.9 35.0 + - - -
104A CYS* 3.8 12.1 - - + -
107A VAL* 3.9 20.0 - - - +
108A THR* 3.3 23.8 + - - +
111A ALA* 4.3 10.5 - - - +
119B GLY 5.3 0.6 + - - -
120B LYS* 5.3 2.6 + - - +
122B PHE* 3.0 30.9 + - - -
123B THR* 3.5 12.9 + - - +
124B PRO* 3.7 29.8 - - + +
127B GLN* 3.0 36.5 + - - +
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 2.9 13.5 + - - +
29A LEU* 3.1 21.7 + - + +
31A ARG* 1.3 77.6 - - - +
33A PHE* 1.3 90.1 + - + +
36A PHE* 2.8 45.2 + - + +
39A THR* 3.5 27.8 - - + +
43A PHE* 4.8 1.1 - - + -
97A ASN 4.6 0.9 - - - +
100A LEU* 4.4 3.6 - - + -
101A LEU* 3.5 34.1 - - + +
104A CYS* 3.5 15.6 - - + -
142A HEM 3.8 21.1 - - + -
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.8 43.2 + - + +
30A GLU* 3.3 8.7 + - - +
32A MET* 1.3 96.0 - - + +
34A LEU* 1.3 62.4 + - + +
37A PRO* 3.6 21.1 - - - +
39A THR* 3.5 17.0 - - - -
40A LYS* 3.7 34.7 + - + +
43A PHE* 3.5 46.2 - + - -
46A PHE* 5.6 0.4 - + - -
48A LEU* 3.7 31.0 - - + +
55A VAL* 4.2 12.8 - - + -
58A HIS* 5.6 0.4 - + - -
----------------------------------------------------------
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.1 25.1 + - + +
31A ARG 4.0 2.2 - - - +
33A PHE* 1.3 79.6 - - + +
35A SER* 1.3 61.9 + - - +
37A PRO* 4.0 9.7 - - - +
124B PRO* 3.5 31.6 - - + +
125B PRO* 3.7 22.4 - - + -
128B ALA* 3.6 20.2 - - + +
132B LYS* 6.2 0.2 - - - -
----------------------------------------------------------
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG 2.9 19.2 + - - -
34A LEU* 1.3 77.8 - - - +
36A PHE* 1.3 89.7 - - - +
37A PRO* 3.5 6.6 - - - +
124B PRO 4.8 0.2 + - - -
127B GLN* 3.6 13.3 + - - +
128B ALA* 3.5 20.2 + - - +
131B GLN* 3.4 28.2 - - - +
132B LYS* 5.9 2.8 - - - +
----------------------------------------------------------
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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).
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