Contacts of the helix formed by residues 11 - 41 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.8 34.7 - - + -
166B HIS* 3.8 8.1 - - + +
9C SER 4.3 0.2 - - - +
10C LEU* 1.3 90.6 - - + +
12C GLN* 1.3 67.4 + - - +
13C SER* 3.2 11.0 - - - +
14C PHE* 2.8 27.7 + - + +
15C LEU* 3.5 3.4 + - - +
121C GLN* 3.5 25.1 - - - +
124C GLU* 5.7 1.8 - - - +
125C LEU* 4.6 2.0 - - + -
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B HIS* 3.1 32.5 + - + +
10C LEU 3.6 2.8 + - - +
11C PRO* 1.3 69.2 - - - +
13C SER* 1.3 62.8 + - - +
15C LEU* 2.9 11.8 + - - +
16C LEU* 2.9 39.5 + - + +
172C LEU 4.7 0.9 - - - +
173C ALA* 3.2 42.7 + - - +
174C GLN 4.0 2.0 + - - -
175C PRO* 3.7 24.5 + - - +
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Residues in contact with SER 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO* 3.2 11.6 + - - +
12C GLN* 1.3 77.6 - - - +
14C PHE* 1.3 63.6 + - - +
16C LEU* 3.8 4.9 - - - +
17C LYS* 3.1 38.3 + - - +
196D LEU* 4.1 20.3 - - - +
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Residues in contact with PHE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.1 13.7 - - + -
11C PRO* 2.8 28.4 + - + +
13C SER* 1.3 73.8 + - - +
15C LEU* 1.3 74.6 + - + +
17C LYS* 3.2 9.3 + - + +
18C CYS* 2.9 59.1 + - - -
76C LEU* 4.0 29.4 - - + -
117C THR* 4.3 20.0 - - + -
118C ILE* 4.4 10.8 - - + -
121C GLN* 3.4 49.6 - - + +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C SER* 5.9 2.5 - - - +
10C LEU* 4.1 38.8 - - + +
11C PRO 3.5 2.4 + - - +
12C GLN* 2.9 17.1 + - - +
14C PHE* 1.3 86.8 - - + +
16C LEU* 1.3 62.5 + - - +
18C CYS* 3.3 5.6 + - - +
19C LEU* 3.1 28.8 + - - +
76C LEU* 5.6 0.2 - - + -
169C LEU* 3.9 29.6 - - + +
172C LEU* 3.7 19.1 - - + +
173C ALA* 3.7 39.5 - - + +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 2.9 37.0 + - + +
13C SER* 4.0 5.4 - - - +
15C LEU* 1.3 73.6 - - - +
17C LYS* 1.3 64.4 + - - +
19C LEU* 3.4 19.2 + - + +
20C GLU* 3.3 21.0 + - - +
23C ARG* 5.5 0.7 + - - -
173C ALA* 4.5 7.9 - - + -
175C PRO* 4.1 27.8 - - + -
194D SER 5.0 0.7 - - - +
195D SER* 3.5 37.0 - - - +
196D LEU* 4.0 18.8 - - + +
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 3.1 27.2 + - - +
14C PHE* 3.6 8.5 - - + +
16C LEU* 1.3 76.1 - - - +
18C CYS* 1.3 65.5 + - - +
20C GLU* 3.2 7.4 + - - +
21C GLN* 3.0 32.0 + - - +
117C THR* 5.8 4.0 - - + -
78D TYR* 4.2 29.7 + - + +
80D TYR* 4.3 21.8 + - - -
102D ASP* 4.5 14.3 + - - +
105D ASP* 5.2 8.5 + - - -
193D ARG* 4.8 4.3 - - - +
196D LEU* 4.1 25.8 - - + -
197D PRO* 5.8 2.0 - - - -
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Residues in contact with CYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 2.9 54.5 + - - +
15C LEU* 3.4 11.9 - - - +
17C LYS* 1.3 76.5 - - - +
19C LEU* 1.3 57.2 + - - +
21C GLN* 3.1 5.4 + - - +
22C VAL* 2.9 30.3 + - - +
76C LEU* 6.0 0.2 - - - -
114C PHE* 3.7 25.9 - - + -
117C THR* 5.1 2.7 - - - -
118C ILE* 4.6 4.0 - - - -
169C LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU 3.1 18.4 + - - +
16C LEU* 3.7 26.9 - - + +
17C LYS 3.3 0.2 - - - -
18C CYS* 1.3 76.4 - - - +
20C GLU* 1.3 60.3 + - - +
22C VAL* 3.6 3.3 + - - +
23C ARG* 3.2 45.4 + - - +
166C TYR* 3.5 32.3 - - + +
169C LEU* 3.5 28.3 - - + -
170C ARG* 3.7 26.7 - - + +
173C ALA* 4.5 9.2 - - + -
175C PRO* 5.4 3.6 - - + -
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU 3.3 10.6 + - - +
17C LYS* 3.2 9.4 + - - +
18C CYS 3.2 0.6 - - - -
19C LEU* 1.3 77.1 - - - +
21C GLN* 1.3 62.0 + - - +
23C ARG* 3.3 14.5 + - - +
24C LYS* 2.9 27.5 + - - +
78D TYR* 3.0 21.6 + - - +
104D MET* 4.7 2.4 - - - +
143D TYR* 3.8 28.2 - - + +
144D MET* 3.7 16.4 - - - +
145D GLU 4.5 2.8 + - - +
193D ARG* 2.8 46.2 + - - +
196D LEU* 4.5 5.4 - - + +
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LYS* 3.0 22.2 + - - +
18C CYS 3.1 6.0 + - - +
20C GLU* 1.3 71.9 - - - +
22C VAL* 1.3 66.9 + - - +
24C LYS* 3.6 6.7 - - - +
25C ILE* 2.8 33.0 + - + +
110C ASP 4.6 2.0 + - - -
113C ASP* 3.9 6.5 - - - +
114C PHE* 3.2 50.2 - - + +
117C THR* 3.1 29.4 + - - +
78D TYR* 3.5 43.3 - - + -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C CYS 2.9 17.6 + - - +
19C LEU* 3.7 9.2 - - - +
21C GLN* 1.3 78.0 - - - +
23C ARG* 1.3 58.2 + - - +
25C ILE* 3.2 6.0 + - - +
26C GLN* 2.8 50.5 + - - +
114C PHE* 3.7 22.9 - - + -
162C LEU* 3.8 30.7 - - + +
165C SER* 4.7 9.4 - - - -
166C TYR* 3.9 17.7 - - + +
169C LEU* 4.5 11.7 - - + -
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Residues in contact with ARG 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU 5.5 0.6 + - - -
19C LEU* 3.2 29.1 + - - +
20C GLU* 3.7 22.3 - - - +
21C GLN 3.2 0.2 - - - -
22C VAL* 1.3 75.8 - - - +
24C LYS* 1.3 66.2 + - - +
26C GLN* 3.0 21.2 + - - +
27C GLY* 2.9 19.9 + - - -
166C TYR* 3.0 34.9 + - + -
142D GLU 4.9 2.5 - - - -
143D TYR* 3.0 45.2 + - + +
144D MET 5.3 0.4 - - - -
145D GLU* 3.5 48.2 + - - +
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLU 2.9 20.0 + - - +
21C GLN* 3.2 6.9 + - - +
23C ARG* 1.3 70.4 - - - +
25C ILE* 1.3 60.4 + - + +
27C GLY* 3.1 4.2 + - - -
28C ASP* 3.0 40.0 + - - +
110C ASP* 3.4 26.9 + - + +
17D LEU* 4.3 10.3 - - - +
20D ASN* 4.7 8.7 - - - +
72D ARG* 5.3 0.4 - - - +
77D LEU* 3.9 13.9 - - - +
78D TYR* 3.7 23.6 - - + +
104D MET* 3.8 13.4 - - - +
143D TYR* 3.5 45.3 + - + +
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLN* 2.8 22.9 + - + +
22C VAL* 3.5 3.6 - - - +
24C LYS* 1.3 74.4 - - + +
26C GLN* 1.3 64.0 + - - +
27C GLY 3.1 2.0 - - - -
28C ASP* 3.2 7.0 + - - +
29C GLY* 3.0 19.6 + - - -
83C LEU* 5.1 3.1 - - + -
107C LEU* 3.6 20.1 - - + +
110C ASP* 3.5 40.6 - - + +
111C VAL* 4.0 13.7 - - + -
114C PHE* 3.7 28.7 - - + -
158C LEU* 4.1 4.6 - - + +
159C GLN* 5.0 0.5 + - - -
162C LEU* 3.4 22.3 - - + +
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Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 2.8 30.5 + - - +
23C ARG* 3.0 36.3 + - - +
25C ILE* 1.3 73.4 - - - +
27C GLY* 1.3 60.8 + - - +
29C GLY 4.0 0.7 - - - -
30C ALA* 3.4 18.4 + - - +
159C GLN* 3.3 29.4 - - + +
162C LEU* 3.9 22.6 - - + +
163C GLU* 4.2 20.3 - - - +
166C TYR* 5.1 5.6 - - - +
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Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG 2.9 12.6 + - - -
24C LYS* 3.6 4.7 - - - -
26C GLN* 1.3 77.1 - - - +
28C ASP* 1.3 61.8 + - - +
30C ALA* 3.5 6.8 + - - +
31C ALA* 3.1 25.5 + - - +
142D GLU* 5.5 7.4 - - - -
143D TYR* 6.1 1.3 - - - -
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LYS* 3.0 24.5 + - - +
25C ILE* 3.2 7.3 + - - +
27C GLY* 1.3 76.4 - - - +
29C GLY* 1.3 58.9 + - - +
31C ALA* 3.3 8.5 + - - +
32C LEU* 3.0 26.2 + - - +
103C THR* 4.6 3.6 - - - +
106C THR* 3.7 17.8 - - + +
107C LEU* 3.7 23.2 - - + +
110C ASP* 2.5 40.5 - - - +
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE 3.0 14.8 + - - -
26C GLN 3.8 0.2 + - - -
28C ASP* 1.3 73.6 - - - +
30C ALA* 1.3 60.1 + - - +
32C LEU* 3.2 5.5 + - - +
33C GLN* 2.8 38.1 + - - +
107C LEU* 4.1 19.2 - - - +
155C ALA* 4.8 4.4 - - - +
158C LEU* 5.8 1.3 - - - -
159C GLN* 4.0 13.0 - - - -
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN 3.4 17.7 + - - +
27C GLY* 3.7 7.9 - - - +
28C ASP 3.2 0.8 - - - -
29C GLY* 1.3 73.6 - - - +
31C ALA* 1.3 56.7 + - - +
33C GLN* 3.3 12.1 + - - +
34C GLU* 2.8 36.5 + - - +
159C GLN* 4.3 1.5 - - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 3.1 11.2 + - - +
28C ASP* 3.3 13.0 - - - +
30C ALA* 1.3 78.2 - - - +
32C LEU* 1.3 56.3 + - - +
34C GLU* 3.1 7.9 + - - +
35C LYS* 2.9 30.0 + - - +
103C THR* 3.9 13.6 - - + +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP 3.0 13.2 + - - +
29C GLY* 3.2 9.9 - - - +
31C ALA* 1.3 73.5 - - - +
33C GLN* 1.3 67.7 + - - +
35C LYS* 3.1 4.0 + - - +
36C LEU* 3.0 34.6 + - + +
90C LEU* 4.9 3.6 - - + -
96C ILE* 4.7 2.7 - - + -
100C LEU* 3.8 24.5 - - + -
103C THR* 3.7 19.0 - - + +
104C LEU* 3.8 31.9 - - + +
107C LEU* 3.8 24.0 - - + -
151C GLY* 4.6 9.4 - - - +
155C ALA* 4.2 17.0 - - + -
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY 2.8 25.6 + - - +
30C ALA* 3.8 8.9 - - - +
32C LEU* 1.3 75.2 - - - +
34C GLU* 1.3 61.3 + - - +
36C LEU* 4.0 10.6 - - + +
37C CYS* 3.1 23.4 + - - +
42C LEU 4.8 1.4 - - - +
45C PRO* 5.0 9.2 - - - +
152C VAL* 4.3 11.4 - - + +
155C ALA* 3.8 22.2 - - + +
156C SER* 4.1 22.9 + - - -
159C GLN* 3.9 22.2 - - - +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA 2.8 22.6 + - - +
31C ALA* 3.4 8.1 - - - +
33C GLN* 1.3 72.3 - - - +
35C LYS* 1.3 62.1 + - - +
37C CYS* 2.9 11.6 + - - +
38C ALA* 2.8 45.3 + - - +
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA 2.9 13.0 + - - +
32C LEU* 3.5 10.5 - - - +
34C GLU* 1.3 80.5 + - - +
36C LEU* 1.3 56.8 + - - +
38C ALA* 3.1 3.9 + - + -
39C THR* 2.7 48.8 + - - +
99C GLU* 3.8 26.6 + - - -
100C LEU* 3.8 24.5 - - + -
103C THR* 4.2 18.4 - - + +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.0 36.0 + - + +
33C GLN* 4.0 7.9 - - + +
35C LYS* 1.3 76.3 - - - +
37C CYS* 1.3 61.7 + - - +
40C TYR* 3.2 40.5 + - + +
42C LEU* 3.5 15.7 + - + +
96C ILE* 4.4 8.5 - - + -
100C LEU* 3.1 29.2 - - + -
148C ARG* 4.1 17.3 - - + +
151C GLY* 4.2 3.6 - - - -
152C VAL* 3.7 40.4 - - + +
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN 3.1 17.2 + - - +
34C GLU* 2.9 12.8 + - - +
36C LEU* 1.3 75.8 - - - +
38C ALA* 1.3 61.3 + - - +
41C LYS* 3.1 28.4 + - - +
42C LEU 3.4 11.6 + - - +
43C CYS* 2.1 49.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 2.8 34.8 + - - +
35C LYS* 3.6 6.7 - - + +
37C CYS* 1.3 81.9 - - - +
39C THR* 1.3 64.0 + - - +
40C TYR 3.8 0.2 + - - -
41C LYS* 4.5 5.4 + - - +
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LYS* 2.7 43.0 + - - +
38C ALA* 1.3 75.4 - - - +
40C TYR* 1.3 96.7 + - + +
41C LYS 3.8 0.2 - - - -
99C GLU* 4.3 18.1 + - + +
100C LEU* 4.2 9.2 - - + -
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Residues in contact with TYR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.2 30.8 + - + +
39C THR* 1.3 109.5 - - + +
41C LYS* 1.3 58.9 + - - +
42C LEU* 2.6 35.3 + - + +
96C ILE* 4.7 2.2 - - + -
97C SER* 2.6 33.1 + - - -
99C GLU* 4.3 5.9 - - + +
100C LEU* 3.9 18.4 - - + +
148C ARG* 3.6 58.5 + - + +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C CYS* 3.1 19.9 + - - +
38C ALA 5.1 5.2 - - - +
39C THR 3.8 0.6 - - - -
40C TYR* 1.3 74.9 - - - +
42C LEU* 1.3 57.4 + - - +
43C CYS* 3.4 20.1 + - - +
44C HIS* 5.6 0.5 + - - -
----------------------------------------------------------
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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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