Contacts of the helix formed by residues 8 - 37 (chain A) in PDB entry 1FQY
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 LYS 8 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 1.3 70.2 + - - +
10A PHE* 3.3 5.2 - - - +
11A TRP* 3.2 38.0 + - + +
12A ARG* 3.5 29.4 + - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 1.3 78.4 - - - +
10A PHE* 1.3 57.4 + - - +
11A TRP 2.8 5.9 + - - -
12A ARG* 3.2 21.5 + - + +
13A ALA* 2.8 36.0 + - + +
70A ILE* 6.5 0.7 - - + -
71A SER* 5.6 11.4 - - - +
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Residues in contact with PHE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS 3.3 2.5 - - - +
9A LEU* 1.3 77.6 - - - +
11A TRP* 1.3 100.3 + + + +
13A ALA* 3.2 19.8 - - - +
14A VAL* 3.2 20.6 - - + +
91A ILE* 5.3 9.0 - - + -
93A ARG* 3.6 47.8 - - - +
94A ALA* 5.5 0.2 - - - -
96A MET* 4.1 17.3 - - + -
97A TYR* 3.9 27.1 - + - -
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Residues in contact with TRP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.5 36.1 - - + +
9A LEU 2.8 2.0 + - - -
10A PHE* 1.3 111.4 - + + +
12A ARG* 1.3 68.3 + - - +
13A ALA 2.8 1.6 + - - -
14A VAL* 3.0 17.4 + - + +
15A VAL* 3.0 16.2 + - - +
93A ARG* 4.5 14.1 - - - -
96A MET* 5.5 9.6 - - + -
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.5 27.0 + - - +
9A LEU* 3.2 19.5 + - + +
11A TRP* 1.3 77.2 - - - +
13A ALA* 1.3 52.1 - - - +
15A VAL* 2.8 14.7 - - + +
16A ALA* 2.4 43.0 + - + +
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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 LEU* 2.8 22.7 + - + +
10A PHE* 3.2 14.8 - - - +
12A ARG* 1.3 80.3 - - - +
14A VAL* 1.3 64.4 + - - +
16A ALA* 2.9 19.1 + - - +
17A GLU* 3.0 11.9 + - - +
68A GLY* 6.4 1.1 - - - -
71A SER* 4.1 12.6 - - - +
72A GLY* 5.1 4.4 - - - +
97A TYR* 3.6 21.1 - - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.2 37.9 + - + +
11A TRP* 3.0 12.4 + - + +
13A ALA* 1.3 77.2 - - - +
15A VAL* 1.3 53.7 + - + +
17A GLU* 2.9 11.5 + - - +
18A PHE* 2.5 34.2 + - + -
96A MET* 4.5 20.2 - - + +
97A TYR* 4.8 11.0 + - + -
99A ILE* 6.1 0.4 - - + -
100A ALA* 3.3 28.5 - - + -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP 3.0 7.3 + - - +
12A ARG* 2.8 41.3 - - + +
14A VAL* 1.3 78.1 - - + +
16A ALA* 1.3 54.1 + - - +
18A PHE* 2.6 34.5 + - + -
19A LEU* 2.7 28.0 + - + +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.4 34.4 + - + +
13A ALA* 3.0 14.6 - - - +
15A VAL* 1.3 67.5 - - - +
17A GLU* 1.3 57.2 + - - +
19A LEU* 4.1 5.1 - - - +
20A ALA* 3.0 26.5 + - - +
67A VAL* 3.8 17.4 - - + +
68A GLY* 4.8 11.9 - - - +
72A GLY 4.8 5.2 - - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.0 8.7 + - - +
14A VAL* 2.9 7.4 + - - +
16A ALA* 1.3 78.2 - - - +
18A PHE* 1.3 66.3 + - - +
19A LEU 3.1 1.8 - - - -
20A ALA* 4.2 4.9 - - - -
21A THR* 3.0 32.9 + - - +
67A VAL* 6.0 0.9 - - + -
72A GLY* 2.9 21.7 - - - +
73A ALA 4.4 1.8 - - - +
74A HIS* 2.9 44.7 + - - +
75A LEU* 5.4 0.2 - - + -
97A TYR* 2.1 53.4 - - - +
100A ALA* 5.4 3.1 - - + +
101A GLN* 4.6 10.4 + - + -
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 2.5 19.9 + - + +
15A VAL* 2.6 23.7 + - + +
17A GLU* 1.3 71.5 - - - +
19A LEU* 1.3 64.8 + - + +
21A THR* 4.3 0.7 - - - -
22A THR* 2.6 31.7 + - - -
100A ALA* 4.0 18.1 - - + +
103A VAL* 3.2 41.1 - - + -
104A GLY* 3.7 16.3 - - - -
107A VAL* 4.2 19.7 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 2.7 24.3 + - + +
16A ALA* 4.1 4.7 - - - +
18A PHE* 1.3 80.3 - - + +
20A ALA* 1.3 57.9 + - - +
22A THR* 2.6 39.7 + - - -
23A LEU* 3.1 19.6 + - + +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 3.0 19.4 + - - +
17A GLU* 3.5 4.9 + - + +
19A LEU* 1.3 78.3 - - - +
21A THR* 1.3 54.7 + - - +
23A LEU* 2.7 18.7 + - - +
24A PHE* 2.7 34.2 + - - +
63A LEU* 4.4 14.2 - - + +
67A VAL* 3.9 18.8 - - + -
75A LEU* 4.4 12.1 - - + -
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.0 19.5 + - - +
18A PHE 4.3 3.1 - - - +
20A ALA* 1.3 75.1 - - - +
22A THR* 1.3 60.4 + - - +
24A PHE* 3.1 11.4 + - + +
25A VAL* 2.8 48.4 + - + +
74A HIS 4.6 0.5 + - - -
75A LEU* 3.2 37.6 + - - +
101A GLN* 4.0 31.0 - - - +
104A GLY* 5.0 0.2 - - - -
105A ALA 4.6 7.2 - - - +
194A ALA* 4.8 5.6 - - + -
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 2.6 24.1 + - - -
19A LEU* 2.6 21.6 + - - -
21A THR* 1.3 75.6 - - - +
23A LEU* 1.3 65.2 + - + +
25A VAL 3.3 0.5 + - - -
26A PHE* 3.0 24.1 + - + +
104A GLY* 3.2 28.9 - - - +
107A VAL* 4.3 11.6 - - + +
108A ALA* 3.6 25.6 - - + +
111A ILE* 6.1 0.9 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.1 22.7 + - + +
20A ALA* 2.7 19.0 + - - +
22A THR* 1.3 79.3 - - + +
24A PHE* 1.3 62.6 + - - +
26A PHE* 3.2 9.1 + - + +
27A ILE* 3.0 32.8 + - + +
63A LEU* 4.4 20.2 - - + -
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 2.7 12.1 + - - +
21A THR* 3.1 14.1 - - + +
23A LEU* 1.3 73.5 - - - +
25A VAL* 1.3 91.4 + - + +
26A PHE 3.0 1.6 + - - -
27A ILE* 3.2 5.5 + - - +
28A SER* 3.0 34.8 + - - -
56A PHE* 4.1 18.6 - + + -
59A SER* 4.1 10.5 + - - -
60A ILE* 3.7 36.3 - - + -
63A LEU* 3.5 23.7 - - + +
75A LEU* 3.9 21.3 - - + -
180A HIS* 5.7 1.8 - - - -
192A ASN* 4.7 21.1 - - + -
194A ALA* 6.5 0.4 - - + -
195A ARG* 5.4 7.0 - - + -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 2.8 32.1 + - + +
22A THR* 4.1 4.0 - - - +
24A PHE* 1.3 92.4 - - + +
26A PHE* 1.3 61.7 + - - +
28A SER* 2.7 22.8 + - - +
29A ILE* 3.0 23.7 + - + +
105A ALA* 4.9 9.2 - - + +
108A ALA* 4.3 14.4 - - + -
109A THR* 5.7 4.0 - - - +
128A ASP* 5.8 2.0 - - - +
194A ALA* 5.6 1.1 - - + -
195A ARG* 4.5 27.1 - - + +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.0 18.7 + - + +
23A LEU* 3.6 9.0 - - + +
24A PHE 3.0 0.4 + - - -
25A VAL* 1.3 76.3 - - - +
27A ILE* 1.3 60.6 + - + +
29A ILE* 3.0 10.6 - - + +
30A GLY* 2.6 36.2 + - - -
108A ALA* 4.1 19.9 - - - +
111A ILE* 4.7 13.2 - - + -
112A LEU* 3.2 39.3 - - + -
115A ILE* 3.1 28.0 - - + -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.0 24.0 - - + +
24A PHE* 3.6 7.0 - - - +
26A PHE* 1.3 80.7 - - + +
28A SER* 1.3 58.4 - - - +
30A GLY* 2.5 21.9 + - - -
31A SER* 2.8 19.8 + - - +
55A ALA* 4.9 9.4 - - + -
59A SER* 3.5 26.2 - - - +
63A LEU* 4.4 10.3 - - + -
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.0 16.0 + - - -
25A VAL* 2.7 40.6 + - - +
27A ILE* 1.3 83.0 - - - +
29A ILE* 1.3 59.8 + - - +
30A GLY 3.1 0.2 + - - -
31A SER* 3.3 15.9 + - - -
32A ALA* 3.4 13.7 + - - +
55A ALA* 4.6 6.7 - - - -
56A PHE* 3.3 44.5 - - - +
59A SER* 5.0 0.4 + - - -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.0 20.1 + - + +
26A PHE* 3.0 28.0 - - + +
28A SER* 1.3 79.0 + - - +
30A GLY* 1.3 66.2 + - - +
32A ALA* 4.3 5.4 - - + -
33A LEU* 3.2 35.2 + - + +
56A PHE* 4.9 1.8 - - - -
108A ALA 5.1 3.4 - - - +
109A THR* 4.7 20.2 - - + +
112A LEU* 3.6 32.4 - - + +
125A GLY 4.8 12.6 - - - +
128A ASP* 5.1 20.0 - - + +
199A SER* 5.3 7.6 - - - -
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 2.6 17.4 + - - -
27A ILE* 2.5 16.9 + - - -
29A ILE* 1.3 74.7 - - - +
31A SER* 1.3 50.3 + - - -
33A LEU* 3.4 1.8 - - - +
34A GLY* 2.5 35.1 + - - -
112A LEU* 4.9 8.1 - - - -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 2.8 12.7 + - - +
28A SER 3.3 7.1 + - - -
30A GLY* 1.3 70.4 - - - +
32A ALA* 1.3 57.8 + - - +
34A GLY* 2.6 20.8 + - - +
35A PHE* 2.8 35.7 + - - -
51A LYS* 5.3 1.8 - - - -
52A VAL* 4.8 6.0 + - - -
55A ALA* 2.8 35.1 - - - +
56A PHE* 5.2 0.2 - - - -
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 3.4 13.2 + - - +
29A ILE* 4.4 5.8 - - + +
30A GLY 3.2 0.6 + - - -
31A SER* 1.3 81.2 + - - +
33A LEU* 1.3 69.1 + - + +
35A PHE* 2.9 14.6 + - - +
36A LYS* 3.7 4.9 + - - +
47A GLN* 3.9 21.0 + - - +
52A VAL* 3.9 27.2 - - + +
56A PHE* 4.6 6.7 - - + -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.2 22.0 + - + +
30A GLY* 3.2 3.0 + - - +
32A ALA* 1.3 80.5 - - + +
34A GLY* 1.3 69.3 + - - +
35A PHE 3.1 0.9 + - - -
36A LYS* 3.4 19.1 + - + +
37A TYR* 3.4 14.8 + - - +
112A LEU* 3.5 33.7 - - + -
116A THR* 4.5 5.2 - - + -
119A LEU* 3.9 26.2 - - + +
125A GLY* 3.5 36.3 - - - +
126A ARG 5.0 0.2 - - - +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY 2.5 20.8 + - - -
31A SER* 2.6 12.3 + - - -
33A LEU* 1.3 72.1 - - - +
35A PHE* 1.3 60.8 + - - -
37A TYR* 2.8 35.5 + - - -
38A PRO* 5.1 1.4 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 2.8 44.1 + - - -
32A ALA 2.9 6.2 + - - +
34A GLY* 1.3 75.4 - - - +
36A LYS* 1.3 62.0 + - - +
37A TYR 3.2 4.5 + - - -
38A PRO* 5.4 1.4 - - - +
43A GLN* 4.6 16.4 - - - -
44A THR* 2.8 28.2 + - - +
47A GLN* 3.9 6.5 - - + -
48A ASP* 3.9 11.9 - - - -
51A LYS* 3.1 52.0 - - + +
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA 3.7 6.1 + - - +
33A LEU* 3.4 14.5 + - + +
35A PHE* 1.3 76.4 - - - +
37A TYR* 1.3 70.0 + - + +
38A PRO 4.0 4.0 - - - +
40A GLY* 5.1 6.2 - - - +
44A THR* 3.2 30.7 - - + +
45A ALA 5.8 1.3 - - - +
47A GLN* 5.1 4.0 - - + +
119A LEU* 5.4 15.1 + - + +
121A GLY* 5.1 15.6 - - - +
122A ASN 5.3 5.5 + - - +
123A SER* 5.4 5.7 - - - +
124A LEU 5.5 2.6 - - - +
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.4 10.5 - - - +
34A GLY* 2.8 35.6 + - - -
35A PHE 3.2 6.3 + - - -
36A LYS* 1.3 83.9 - - + +
38A PRO* 1.4 104.1 - - + +
39A VAL* 3.3 1.6 + - - -
40A GLY 4.6 1.2 + - - -
116A THR* 6.3 1.6 - - + -
118A SER* 5.8 2.9 - - - -
119A LEU* 3.2 37.9 - - + -
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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