Contacts of the helix formed by residues 10 - 36 (chain A) in PDB entry 1IER
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 THR 10 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.3 8.3 - - - +
8A TYR 3.8 0.2 + - - -
9A SER* 1.3 74.4 - - - +
11A GLU* 1.3 70.7 + - - +
13A GLU* 3.7 19.1 - - - +
14A ALA* 2.9 30.1 + - - +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.3 21.9 - - - +
10A THR* 1.3 83.9 + - - +
12A VAL* 1.3 61.7 + - - +
14A ALA* 3.6 4.9 + - - +
15A ALA* 2.9 28.6 + - - +
116A LEU* 3.6 23.2 - - + +
120A GLN* 3.3 19.5 + - - +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.5 29.4 - - + +
9A SER* 3.4 21.8 + - - +
10A THR 3.4 0.2 - - - -
11A GLU* 1.3 72.3 - - - +
13A GLU* 1.3 56.2 + - - +
15A ALA* 2.9 4.4 + - - +
16A VAL* 2.8 42.4 + - + +
113A LEU* 4.7 1.1 - - + -
116A LEU* 3.8 26.7 - - + -
117A GLY* 4.4 4.3 - - - -
120A GLN* 4.0 10.1 - - + -
122A ASP* 4.2 7.2 - - - +
125A LEU* 3.8 30.7 - - + -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 2.7 32.9 + - - -
8A TYR* 3.7 20.4 + - + -
9A SER 3.1 15.8 + - - +
10A THR* 3.7 14.8 - - - +
11A GLU 3.4 0.2 - - - -
12A VAL* 1.3 74.5 - - - +
14A ALA* 1.3 63.1 + - - +
16A VAL 3.4 0.2 + - - -
17A ASN* 3.1 12.2 + - - +
69A GLN* 3.0 36.3 + - - +
74A GLY* 3.9 1.3 - - - -
75A ARG* 2.7 36.2 + - - +
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR 2.9 18.3 + - - +
11A GLU* 3.8 5.4 - - - +
13A GLU* 1.3 79.6 - - - +
15A ALA* 1.3 62.6 + - - +
17A ASN* 3.3 9.4 + - - +
18A ARG* 3.1 21.3 + - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU 2.9 20.0 + - - +
12A VAL 2.9 1.9 + - - +
14A ALA* 1.3 74.6 - - - +
16A VAL* 1.4 55.0 + - - +
18A ARG* 3.3 12.7 + - - +
19A LEU* 2.9 31.5 + - - +
113A LEU* 3.4 29.0 - - + +
116A LEU* 3.7 10.1 - - + -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.5 15.0 - - - +
12A VAL* 2.8 29.9 + - + +
13A GLU 3.7 4.5 - - - +
15A ALA* 1.4 69.1 - - - +
17A ASN* 1.3 58.7 + - - +
19A LEU* 3.1 8.4 + - - +
20A VAL* 3.0 28.6 + - + +
65A LEU* 4.0 31.8 - - + +
68A MET* 3.9 22.4 - - + -
69A GLN* 3.9 19.7 - - + +
113A LEU* 4.2 17.0 - - + -
125A LEU* 4.4 0.9 - - + -
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.1 14.1 + - - +
14A ALA* 3.7 10.7 - - - +
15A ALA 3.2 0.2 - - - -
16A VAL* 1.3 77.0 - - - +
18A ARG* 1.3 61.5 + - - +
20A VAL* 3.3 8.1 + - - +
21A ASN* 3.2 21.0 + - - +
66A LEU* 5.1 5.7 - - - +
69A GLN* 3.0 23.0 + - - +
75A ARG 3.0 16.6 - - - +
76A ALA* 3.3 10.5 - - - +
77A LEU* 3.3 49.6 + - + +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.1 13.0 + - - +
15A ALA* 3.5 14.1 + - - +
17A ASN* 1.3 75.6 - - - +
19A LEU* 1.3 65.0 + - - +
21A ASN* 3.2 10.3 + - + +
22A LEU* 3.0 43.1 + - - +
109A ALA* 4.3 27.1 + - - +
112A ASP* 4.6 12.5 + - - +
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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 ALA 2.9 12.9 + - - +
16A VAL* 3.1 8.5 + - - +
18A ARG* 1.3 75.7 - - - +
20A VAL* 1.3 65.4 + - - +
22A LEU* 3.1 9.5 + - + +
23A TYR* 3.0 48.9 + - + -
65A LEU* 3.9 22.9 - - + -
106A LEU* 4.7 1.8 - - + +
109A ALA* 3.7 30.7 - - + +
110A LEU* 3.8 23.1 - - + -
113A LEU* 3.4 34.5 - - + -
129A LEU* 5.1 0.2 - - + -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.0 20.5 + - + +
17A ASN* 3.6 13.5 - - - +
18A ARG 3.3 0.2 - - - -
19A LEU* 1.3 75.7 - - - +
21A ASN* 1.3 66.0 + - - +
23A TYR* 3.3 2.3 + - - +
24A LEU* 3.0 42.5 + - + +
62A ALA* 3.9 13.6 - - + +
65A LEU* 3.7 31.2 - - + -
66A LEU* 4.0 31.6 - - + +
77A LEU 5.9 1.1 - - - +
78A PHE* 4.1 10.8 - - + -
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Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN 3.2 9.5 + - - +
18A ARG* 3.4 11.7 - - + +
20A VAL* 1.3 81.8 - - - +
22A LEU* 1.3 65.8 + - - +
24A LEU* 3.8 7.0 - - - +
25A ARG* 2.9 31.9 + - - +
79A GLN* 3.9 22.8 + - + +
80A ASP 3.3 24.2 + - - +
81A LEU* 3.5 14.5 - - - +
82A GLN* 5.8 1.2 - - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.0 41.7 + - - +
19A LEU* 3.1 11.2 + - + +
21A ASN* 1.3 87.3 - - - +
23A TYR* 1.3 57.7 + - - +
25A ARG* 3.4 8.3 + - + +
26A ALA* 2.8 28.2 + - - +
105A SER* 4.9 6.5 - - - +
106A LEU* 3.8 21.6 - - + +
109A ALA* 3.9 28.3 - - + -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.0 46.2 + - + +
20A VAL 3.3 0.2 + - - -
22A LEU* 1.3 75.7 - - - +
24A LEU* 1.3 53.4 + - - +
26A ALA* 3.1 7.7 + - - +
27A SER* 2.7 34.8 + - - -
58A LYS* 3.5 51.6 - - + +
61A GLY* 3.9 11.7 - - - -
62A ALA* 3.9 16.4 - - + -
65A LEU* 4.1 8.5 - - + -
106A LEU* 4.1 17.8 - - + +
110A LEU* 3.6 21.2 - - + +
133A PHE* 3.3 31.7 - + - -
136A GLU* 6.0 1.8 - - - -
137A GLU* 4.1 9.3 + - - -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.0 36.6 + - + +
21A ASN* 3.8 4.0 - - - +
23A TYR* 1.3 72.6 - - - +
25A ARG* 1.3 64.5 + - - +
27A SER* 3.3 7.3 + - - -
28A TYR* 3.0 22.9 + - - +
59A ARG* 4.6 18.6 - - + +
62A ALA* 3.6 21.1 - - + -
63A GLU* 6.1 1.6 - - + -
66A LEU* 5.5 3.1 - - + -
78A PHE* 4.7 15.5 - - + -
81A LEU* 3.9 30.8 - - + +
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.9 23.6 + - - +
22A LEU* 3.7 9.9 - - + +
24A LEU* 1.3 80.6 - - - +
26A ALA* 1.4 60.6 + - - +
28A TYR* 3.3 5.9 + - + +
29A THR* 3.0 32.7 + - - -
81A LEU* 4.3 7.1 - - + +
82A GLN* 3.4 47.2 + - + +
83A LYS 2.7 23.6 + - - -
84A PRO* 4.5 0.4 - - - -
85A SER* 3.4 27.5 - - - +
102A LEU* 6.2 2.9 - - - -
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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 LEU 2.8 15.7 + - - +
23A TYR* 3.1 9.4 + - - +
25A ARG* 1.4 74.8 - - - +
27A SER* 1.3 63.0 + - - +
29A THR* 3.3 3.5 + - - -
30A TYR* 3.1 29.4 + - - -
58A LYS* 4.1 8.3 - - + -
102A LEU* 4.2 26.4 - - + +
106A LEU* 3.8 27.4 - - + -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR 2.7 15.4 + - - -
24A LEU* 3.4 15.9 - - - -
26A ALA* 1.3 72.5 - - - +
28A TYR* 1.3 56.7 + - - +
30A TYR 3.2 1.6 + - - -
31A LEU* 2.9 26.4 + - - +
55A ALA* 2.9 36.0 + - - +
58A LYS* 3.8 12.2 - - - +
59A ARG* 3.7 15.5 - - - +
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.0 16.4 + - - +
25A ARG* 3.6 7.0 - - - +
26A ALA 3.3 0.2 - - - -
27A SER* 1.3 75.5 - - - +
29A THR* 1.3 61.0 + - - +
31A LEU* 3.3 27.0 + - + +
32A SER* 3.2 17.4 + - - -
81A LEU* 4.4 23.1 - - + -
82A GLN 3.7 18.2 - - - -
83A LYS* 3.8 23.0 - - + +
84A PRO* 3.7 18.8 - - + +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.0 23.1 + - - -
26A ALA* 3.5 8.5 - - - -
28A TYR* 1.3 75.3 - - - +
30A TYR* 1.3 56.4 + - - +
32A SER* 3.2 4.3 + - - -
33A LEU* 2.9 45.0 + - + +
84A PRO* 3.8 23.8 - - - +
85A SER* 4.9 2.3 + - - +
89A TRP* 4.0 17.6 - - + -
102A LEU* 3.9 25.1 - - + +
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.1 20.2 + - - -
27A SER 3.2 1.5 + - - +
29A THR* 1.3 71.8 - - - +
31A LEU* 1.3 59.8 - - - +
33A LEU* 3.6 10.9 - - + +
34A GLY* 2.8 25.8 + - - -
51A PHE* 3.4 55.9 - + - +
52A ARG* 4.8 0.2 - - - -
54A LEU* 3.7 25.6 - - + -
55A ALA* 3.6 14.1 - - + +
58A LYS* 3.9 20.4 - - + -
99A ALA* 3.7 13.4 + - + -
102A LEU* 3.6 20.5 - - + +
103A GLU* 2.6 39.9 + - - +
144A MET* 3.6 8.0 - - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 2.9 13.5 + - - +
28A TYR* 3.4 30.5 - - + +
29A THR 3.2 0.2 - - - -
30A TYR* 1.3 73.5 - - - +
32A SER* 1.3 64.1 + - - +
34A GLY* 3.3 2.0 + - - -
35A PHE* 3.0 58.1 + - + -
52A ARG* 5.2 7.2 - - + +
55A ALA* 3.9 12.2 - - + +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.2 10.2 + - - -
29A THR 3.3 8.5 - - - -
31A LEU* 1.3 81.4 - - - +
33A LEU* 1.3 62.1 + - - +
35A PHE* 3.9 3.4 - - - +
36A TYR* 3.1 24.3 + - - +
84A PRO* 3.8 17.5 - - - +
86A GLN 3.9 5.9 + - - -
87A ASP* 4.6 5.5 + - - -
89A TRP* 3.0 20.9 + - - -
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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 THR* 2.9 40.2 + - + +
30A TYR* 3.6 20.9 - - + +
32A SER* 1.3 77.5 + - - +
34A GLY* 1.3 61.1 + - - +
36A TYR* 3.5 5.4 + - - +
37A PHE* 3.2 27.0 - - + -
51A PHE* 3.8 24.9 - - + -
89A TRP* 3.4 43.0 - - + +
95A ALA* 3.5 33.2 - - + +
98A ALA* 5.3 1.6 - - + -
99A ALA* 5.3 5.4 - - + +
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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 TYR 2.8 20.2 + - - -
31A LEU 3.3 1.3 + - - -
33A LEU* 1.3 70.7 - - - +
35A PHE* 1.3 62.7 + - - +
37A PHE 3.2 10.0 + - - -
38A ASP 3.4 0.9 + - - -
48A CYS* 3.3 39.0 - - - +
51A PHE* 3.6 15.1 - - - +
52A ARG* 4.1 6.7 - - - -
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.0 50.5 + - + +
32A SER* 3.4 3.6 + - - +
34A GLY* 1.3 75.8 - - - +
36A TYR* 1.3 60.5 + - - +
38A ASP* 3.2 37.0 + - + +
39A ARG* 3.5 10.0 + - - +
48A CYS* 5.9 0.2 - - - -
52A ARG* 3.6 46.9 - - - -
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER 3.1 17.1 + - - +
33A LEU 3.6 3.6 - - - +
34A GLY 3.3 0.4 - - - -
35A PHE* 1.3 75.6 - - - +
37A PHE* 1.3 83.8 + + - +
39A ARG* 3.2 59.4 - - - +
42A VAL* 3.4 29.7 - - + +
87A ASP 4.4 4.7 - - - +
88A GLU* 3.8 14.1 + - + +
89A TRP* 3.5 35.9 - + + -
90A GLY* 2.7 42.6 + - - -
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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