Contacts of the helix formed by residues 11 - 40 (chain A) in PDB entry 1CD9
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 11 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 1.3 94.5 - - + +
12A GLN* 1.3 63.9 + - - +
13A SER* 4.3 10.3 - - - +
14A PHE* 4.1 13.5 - - + -
15A LEU* 3.3 20.5 + - - +
121A GLN* 3.7 23.6 - - - +
124A GLU* 5.9 1.1 - - - +
125A LEU* 4.3 3.1 - - + -
165D PHE* 3.6 37.2 - - + -
166D HIS* 4.2 2.9 - - - +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.8 0.5 + - - +
11A PRO* 1.3 70.7 - - - +
13A SER* 1.3 66.9 + - - +
14A PHE 3.1 0.2 - - - -
15A LEU* 3.2 8.9 + - - +
16A LEU* 3.0 41.5 + - + +
172A LEU 4.7 0.9 - - - +
173A ALA* 2.8 44.3 + - - +
174A GLN* 5.2 3.2 + - - -
175A PRO* 4.7 5.0 - - - +
166D HIS* 3.1 37.1 + - + +
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 4.3 8.9 - - - +
12A GLN* 1.3 77.9 - - - +
14A PHE* 1.3 65.7 + - - +
16A LEU* 3.3 3.9 + - - +
17A LYS* 3.1 37.9 + - - +
80B TYR* 5.6 2.7 + - - -
195B SER 5.9 0.2 - - - -
196B LEU* 3.9 18.4 - - - +
197B PRO* 6.3 0.2 - - - -
166D HIS* 5.6 0.2 - - - -
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.0 24.5 - - + -
11A PRO* 3.6 22.6 + - + +
12A GLN 3.1 0.4 - - - -
13A SER* 1.3 82.4 + - - +
15A LEU* 1.3 70.0 + - + +
17A LYS* 3.1 13.7 + - + +
18A CYS* 2.9 52.7 + - - -
76A LEU* 4.3 16.8 - - + -
117A THR* 4.4 17.7 - - + -
118A ILE* 4.6 9.4 - - + -
121A GLN* 3.4 53.4 - - + +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 5.1 2.7 - - - +
10A LEU* 3.9 35.9 - - + +
11A PRO 3.3 13.4 + - - +
12A GLN* 3.2 14.9 + - - +
14A PHE* 1.3 87.8 - - + +
16A LEU* 1.3 61.7 + - - +
18A CYS* 3.5 4.4 + - + +
19A LEU* 3.1 27.8 + - - +
169A LEU* 4.0 27.7 - - + +
172A LEU* 3.5 43.5 - - + +
173A ALA* 3.6 13.9 - - + +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 3.0 38.2 + - + +
13A SER* 3.9 4.5 - - - +
15A LEU* 1.3 73.7 - - - +
17A LYS* 1.3 65.3 + - - +
19A LEU* 3.3 22.4 + - + +
20A GLU* 3.1 22.0 + - - +
23A ARG* 5.6 0.2 + - - -
173A ALA* 4.6 13.2 - - + -
194B SER 5.0 0.2 - - - +
195B SER* 3.4 42.2 - - - +
196B LEU* 4.0 16.6 - - + +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.1 24.6 + - - +
14A PHE* 3.5 11.4 - - + +
16A LEU* 1.3 73.2 - - - +
18A CYS* 1.3 67.4 + - - +
20A GLU* 3.1 8.4 + - - +
21A GLN* 2.9 28.8 + - - +
117A THR* 6.2 1.6 - - + -
78B TYR* 3.7 33.8 + - + +
80B TYR* 3.9 29.7 + - - -
102B ASP* 2.9 29.2 + - - +
105B ASP* 4.2 15.0 + - - -
193B ARG* 5.3 1.3 - - - +
196B LEU* 4.1 21.5 - - + -
197B PRO* 5.7 0.4 - - - -
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Residues in contact with CYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 2.9 53.9 + - - -
15A LEU* 3.7 10.8 - - - +
16A LEU 3.2 0.2 - - - -
17A LYS* 1.3 77.1 - - - +
19A LEU* 1.3 56.7 + - - +
21A GLN* 3.0 5.2 + - - +
22A VAL* 2.8 31.4 + - - +
76A LEU* 6.1 0.4 - - - -
79A LEU* 5.8 0.2 - - - -
114A PHE* 3.8 24.1 - - + -
117A THR* 5.0 3.4 - - - -
118A ILE* 4.5 6.1 - - - -
169A LEU* 3.7 24.7 - - + -
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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 LEU 3.1 16.0 + - - +
16A LEU* 3.6 26.2 - - + +
17A LYS 3.2 0.2 - - - -
18A CYS* 1.3 77.7 - - - +
20A GLU* 1.3 61.1 + - - +
22A VAL* 3.6 5.4 + - - +
23A ARG* 3.2 44.3 + - - +
166A TYR* 3.9 28.8 - - + +
169A LEU* 3.3 29.8 - - + -
170A ARG* 3.6 25.6 - - + +
173A ALA* 4.3 10.3 - - + -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 3.1 12.3 + - - +
17A LYS* 3.1 9.6 + - - +
19A LEU* 1.3 75.6 - - - +
21A GLN* 1.3 62.0 + - - +
23A ARG* 3.3 15.3 + - - +
24A LYS* 3.0 27.2 + - - +
78B TYR* 2.7 24.1 + - - +
104B MET* 4.3 3.3 - - - +
143B TYR* 3.8 28.4 - - + +
144B MET* 3.8 14.9 - - - +
145B GLU 4.6 2.6 + - - -
193B ARG* 2.8 43.0 + - - +
196B LEU* 4.0 5.6 - - - +
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 2.9 16.4 + - - +
18A CYS* 3.5 7.4 - - - +
20A GLU* 1.3 72.7 - - - +
22A VAL* 1.3 67.1 + - - +
24A LYS* 3.2 8.2 + - + +
25A ILE* 3.0 32.1 + - + +
110A ASP 4.5 3.6 + - - -
113A ASP* 4.0 6.7 + - - +
114A PHE* 3.2 49.0 - - + +
117A THR* 3.2 28.8 + - - +
77B LEU 4.4 1.8 + - - -
78B TYR* 3.3 44.4 - - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A CYS 2.8 15.5 + - - +
19A LEU* 3.8 6.1 - - - +
21A GLN* 1.3 77.2 - - - +
23A ARG* 1.3 57.4 + - - +
25A ILE* 3.8 3.9 - - - +
26A GLN* 2.9 44.0 + - + +
114A PHE* 3.5 27.6 - - + -
162A LEU* 3.8 30.6 - - + +
165A SER* 4.6 7.9 - - - -
166A TYR* 3.7 25.4 - - + +
169A LEU* 4.0 15.3 - - + -
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 5.6 0.4 + - - -
19A LEU* 3.2 31.4 + - - +
20A GLU* 3.8 20.0 + - - +
22A VAL* 1.3 80.1 - - - +
24A LYS* 1.3 61.4 + - - +
26A GLN* 3.3 21.2 + - - +
27A GLY* 3.0 19.1 + - - -
166A TYR* 3.1 33.5 + - + -
142B GLU 5.5 1.1 - - - -
143B TYR* 3.3 39.9 + - + +
145B GLU* 3.8 45.0 + - - +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.0 17.1 + - - +
21A GLN* 3.2 6.3 + - + +
23A ARG* 1.3 74.7 - - - +
25A ILE* 1.3 59.7 + - + +
27A GLY* 3.0 4.9 + - - -
28A ASP* 2.9 37.5 + - - +
110A ASP* 3.0 31.9 + - + +
17B LEU* 5.7 2.4 - - - +
20B ASN* 5.2 9.1 - - - +
72B ARG* 5.1 0.9 - - - +
77B LEU* 4.5 18.3 - - - +
78B TYR* 4.3 14.6 - - + +
104B MET* 5.0 1.9 - - - +
143B TYR* 3.8 53.6 + - + +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.0 15.6 + - + +
22A VAL* 3.9 3.4 - - - +
24A LYS* 1.3 73.2 - - + +
26A GLN* 1.3 65.4 + - - +
28A ASP* 2.9 8.7 + - - +
29A GLY* 2.9 22.0 + - - -
83A LEU* 4.9 2.9 - - + -
107A LEU* 3.7 19.1 - - + -
110A ASP* 3.6 39.0 - - + +
111A VAL* 3.8 15.0 - - + -
114A PHE* 3.5 35.4 - - + -
158A LEU* 4.1 4.8 - - + +
159A GLN* 5.4 0.2 + - - -
162A LEU* 3.4 21.0 - - + +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 2.9 29.4 + - - +
23A ARG* 3.3 32.8 - - - +
24A LYS 3.3 0.2 - - - -
25A ILE* 1.3 76.5 - - - +
27A GLY* 1.3 61.5 + - - +
29A GLY 4.1 0.4 - - - -
30A ALA* 3.4 16.3 + - - +
159A GLN* 3.4 26.5 - - - +
162A LEU* 3.9 31.8 - - + +
163A GLU* 4.4 14.0 - - - +
166A TYR* 4.5 8.2 - - - +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG 3.0 12.4 + - - -
24A LYS* 3.0 5.5 + - - -
26A GLN* 1.3 77.8 - - - +
28A ASP* 1.3 65.4 + - - +
30A ALA* 3.6 6.7 + - - +
31A ALA* 3.3 20.3 + - - +
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 2.9 23.9 + - - +
25A ILE* 2.9 7.4 + - - +
27A GLY* 1.3 76.9 - - - +
29A GLY* 1.3 65.3 + - - +
31A ALA* 3.1 8.7 + - - +
32A LEU* 3.0 20.6 + - - +
103A THR* 4.7 3.2 - - - +
106A THR* 3.8 17.0 - - + +
107A LEU* 3.6 24.1 - - + +
110A ASP* 2.6 42.0 - - - +
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE 2.9 13.2 + - - -
28A ASP* 1.3 76.9 - - - +
30A ALA* 1.3 56.7 + - - +
32A LEU* 3.3 2.9 + - - +
33A GLN* 2.8 40.4 + - - +
107A LEU* 3.9 21.2 - - - +
155A ALA* 4.8 3.1 - - - +
158A LEU* 5.6 2.0 - - - -
159A GLN* 4.0 12.3 - - - -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN 3.4 19.9 + - - +
27A GLY* 3.7 8.3 - - - +
28A ASP 3.2 0.4 - - - -
29A GLY* 1.3 77.0 - - - +
31A ALA* 1.3 56.1 + - - +
33A GLN* 3.4 13.7 + - - +
34A GLU* 2.8 29.5 + - - +
159A GLN* 4.3 2.1 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.3 10.5 + - - +
28A ASP* 3.1 12.2 + - - +
30A ALA* 1.3 79.8 - - - +
32A LEU* 1.3 56.1 + - - +
34A GLU* 3.1 7.3 + - - +
35A LYS* 2.8 30.1 + - - +
103A THR* 4.0 13.2 - - + +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP 3.0 12.7 + - - +
29A GLY* 3.3 8.3 + - - +
31A ALA* 1.3 76.3 - - - +
33A GLN* 1.3 62.2 + - - +
35A LYS* 3.1 4.4 + - - +
36A LEU* 2.9 35.4 + - + +
90A LEU* 4.8 2.9 - - + -
93A LEU* 5.8 0.2 - - + -
96A ILE* 4.6 5.4 - - + -
100A LEU* 3.7 24.9 - - + -
103A THR* 3.6 20.8 - - + +
104A LEU* 3.7 30.1 - - + +
107A LEU* 3.7 26.0 - - + -
151A GLY* 4.7 4.7 - - - +
155A ALA* 4.3 17.5 - - + -
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 2.8 25.9 + - - +
30A ALA* 3.8 8.7 - - - +
32A LEU* 1.3 73.9 - - - +
34A GLU* 1.3 61.4 + - - +
36A LEU* 4.1 10.8 - - + +
37A CYS* 3.2 23.0 + - - +
42A LEU 5.0 0.9 - - - +
45A PRO* 5.4 5.7 - - - +
152A VAL* 4.4 9.2 - - + +
155A ALA* 3.6 21.6 - - + +
156A SER* 3.7 26.2 + - - -
159A GLN* 3.4 25.0 + - - +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 2.8 17.5 + - - +
31A ALA* 3.4 8.5 - - - +
33A GLN* 1.3 73.8 - - - +
35A LYS* 1.3 72.3 + - - +
37A CYS* 3.0 9.9 + - - +
38A ALA* 2.8 39.4 + - - +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA 2.8 14.0 + - - +
32A LEU* 3.4 11.0 - - - +
34A GLU* 1.3 81.4 + - - +
36A LEU* 1.3 54.1 + - - +
38A ALA* 3.0 3.6 + - + +
39A THR* 2.7 50.6 + - - +
99A GLU* 3.9 28.7 + - - -
100A LEU* 3.7 25.1 - - + -
103A THR* 4.4 16.2 - - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.9 32.3 + - + +
33A GLN* 4.1 8.7 - - + +
35A LYS* 1.3 75.5 - - - +
37A CYS* 1.3 58.2 + - - +
40A TYR* 3.0 50.2 + - + +
42A LEU* 3.6 6.7 + - + +
96A ILE* 4.0 12.1 - - + -
100A LEU* 3.4 26.5 - - + -
148A ARG* 3.9 16.8 - - + +
151A GLY* 3.9 8.1 - - - +
152A VAL* 3.7 39.7 - - + +
----------------------------------------------------------
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 3.2 15.0 + - - +
34A GLU* 3.0 11.2 + - - +
36A LEU* 1.3 79.4 - - - +
38A ALA* 1.3 60.7 + - - +
41A LYS* 3.0 28.9 + - - +
42A LEU 3.7 8.2 + - - +
43A CYS* 2.0 54.5 - - + +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 2.8 35.2 + - - +
35A LYS* 3.6 5.4 - - + +
37A CYS* 1.3 82.2 - - - +
39A THR* 1.3 63.7 + - - +
41A LYS* 4.4 6.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 2.7 43.4 + - - +
38A ALA* 1.3 77.0 - - - +
40A TYR* 1.3 92.8 + - + +
41A LYS* 3.8 0.7 - - - -
99A GLU* 4.5 18.2 - - + +
100A LEU* 4.3 9.9 - - + -
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.0 31.3 + - + +
39A THR* 1.3 105.3 - - + +
41A LYS* 1.3 58.2 + - - +
42A LEU* 2.6 35.4 + - + +
96A ILE* 4.6 4.0 - - + -
97A SER* 2.8 30.6 + - - -
99A GLU* 4.5 5.2 - - + +
100A LEU* 4.0 17.9 - - + +
148A ARG* 3.6 56.8 + - + +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il