Contacts of the helix formed by residues 143 - 174 (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 SER 143 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 1.3 79.1 - - - +
144A ALA* 1.3 66.9 + - - +
145A PHE* 3.2 9.6 + - - +
146A GLN* 2.9 30.8 + - - +
147A ARG* 2.9 32.1 + - - +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE 5.5 0.6 - - - +
143A SER* 1.3 75.9 - - - +
145A PHE* 1.3 65.3 + - - +
147A ARG* 3.1 27.9 + - - +
148A ARG* 2.9 51.5 + - - +
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.4 20.9 - - + -
48A LEU* 4.6 9.9 - - + -
51A LEU* 4.0 25.6 - - + -
143A SER* 3.2 8.6 + - - +
144A ALA* 1.3 81.1 - - - +
146A GLN* 1.3 65.6 + - + +
148A ARG* 3.0 14.2 + - + +
149A ALA* 2.8 41.2 + - + +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 6.5 0.4 - - + -
55A LEU* 3.3 34.8 - - + +
140A ALA* 5.4 1.0 - - - +
141A PHE* 3.8 16.8 + - - -
142A ALA* 2.5 42.5 + - - +
143A SER* 2.9 25.7 + - - +
145A PHE* 1.3 84.2 - - + +
147A ARG* 1.3 56.8 + - - +
149A ALA* 4.0 2.9 - - - +
150A GLY* 2.7 29.6 + - - -
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA 5.4 0.2 - - - +
93A LEU* 3.4 35.7 - - - +
94A GLU* 4.9 15.9 + - - +
96A ILE* 3.0 41.9 + - + +
97A SER* 5.0 1.4 - - - +
141A PHE* 3.9 24.1 + - + +
142A ALA 5.4 1.0 + - - -
143A SER* 2.9 18.3 + - - +
144A ALA* 3.4 34.3 - - - +
146A GLN* 1.3 77.9 - - - +
148A ARG* 1.3 56.4 + - - +
151A GLY* 2.9 24.8 + - - -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.9 5.8 - - - +
40A TYR* 3.6 59.6 + - + +
42A LEU* 3.5 20.2 - - + +
96A ILE* 4.2 14.8 + - + +
97A SER* 5.4 5.5 - - - -
144A ALA* 2.9 40.8 + - - +
145A PHE* 3.6 11.0 - - + +
147A ARG* 1.3 73.5 - - - +
149A ALA* 1.3 64.2 + - - +
151A GLY* 3.5 1.9 + - - -
152A VAL* 3.3 24.1 + - - +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.3 2.6 - - - +
48A LEU* 3.8 25.3 - - + +
51A LEU* 4.4 12.3 - - + -
55A LEU* 5.3 2.7 - - + -
145A PHE* 2.8 39.9 + - + +
146A GLN* 4.0 3.1 - - - +
148A ARG* 1.3 70.2 - - - +
150A GLY* 1.3 68.6 + - - +
152A VAL* 2.8 15.4 + - - +
153A LEU* 2.9 18.3 + - + +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.8 7.1 - - - +
57A ILE* 5.3 1.1 - - - -
93A LEU* 3.9 6.1 - - - -
141A PHE* 3.9 20.9 - - - -
146A GLN 2.7 23.0 + - - -
147A ARG 3.9 0.9 - - - -
149A ALA* 1.3 71.8 - - - +
151A GLY* 1.3 52.3 + - - +
153A LEU* 3.1 7.1 + - - +
154A VAL* 2.7 39.8 + - - +
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.7 4.5 - - - +
36A LEU* 3.9 6.9 - - - +
93A LEU* 3.6 22.8 - - - +
96A ILE* 4.1 10.3 - - - -
147A ARG 2.9 15.9 + - - -
148A ARG 3.9 2.2 - - - -
149A ALA 3.0 0.6 + - - -
150A GLY* 1.3 76.3 - - - +
152A VAL* 1.3 56.3 + - - +
154A VAL* 4.0 1.0 - - - +
155A ALA* 2.9 32.7 + - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 4.4 8.2 - - + +
36A LEU* 3.7 19.5 - - + -
42A LEU* 3.8 34.8 - - + +
43A CYS 5.6 0.4 - - - -
44A HIS 4.8 1.1 - - - -
45A PRO* 3.8 35.4 - - + -
48A LEU* 4.0 12.6 - - + -
148A ARG 3.3 14.2 + - - +
149A ALA 2.8 11.0 + - - +
151A GLY* 1.3 71.4 - - - +
153A LEU* 1.3 58.0 - - - +
155A ALA* 3.7 3.9 + - - +
156A SER* 3.1 25.6 + - - -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 4.1 15.7 - - + +
48A LEU* 3.8 40.4 - - + +
49A VAL* 4.6 5.6 - - + +
51A LEU* 4.1 11.4 - - + -
52A GLY* 3.9 24.2 - - - +
55A LEU* 5.0 2.7 - - + -
57A ILE* 4.6 13.0 - - + -
149A ALA* 2.9 16.8 + - + +
150A GLY* 3.5 10.1 - - - +
152A VAL* 1.3 74.8 - - - +
154A VAL* 1.3 61.2 + - - +
156A SER* 2.9 7.0 + - - -
157A HIS* 2.9 46.9 + - - +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 4.5 14.6 - - + +
86A TYR* 4.2 13.9 - - + -
89A LEU* 3.9 35.2 - - + -
90A LEU* 3.6 30.5 - - + +
93A LEU* 4.8 5.4 - - + -
141A PHE* 4.6 8.5 - - + -
150A GLY 2.7 27.7 + - - +
151A GLY* 4.0 3.8 - - - +
153A LEU* 1.3 69.8 - - - +
155A ALA* 1.3 58.4 + - - +
157A HIS* 3.1 7.8 + - - +
158A LEU* 2.8 29.7 + - + +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 4.8 4.7 - - - +
32A LEU* 4.3 19.1 - - + -
33A GLN* 3.6 29.8 - - + -
36A LEU* 5.4 0.2 - - + -
90A LEU* 5.3 0.8 - - - +
107A LEU* 5.6 2.2 - - - -
151A GLY 2.9 19.6 + - - +
152A VAL 3.8 1.8 - - - +
154A VAL* 1.3 78.2 - - - +
156A SER* 1.3 58.8 + - - +
158A LEU* 3.7 8.7 - - - +
159A GLN* 3.0 35.8 + - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.8 9.5 + - - -
45A PRO* 3.5 29.6 - - - +
46A GLU* 5.1 0.3 + - - -
152A VAL 3.1 19.6 + - - -
153A LEU* 2.9 9.4 + - - -
155A ALA* 1.3 77.4 - - - +
157A HIS* 1.3 64.3 + - - +
159A GLN* 3.4 5.7 - - - +
160A SER* 3.1 30.1 + - - -
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Residues in contact with HIS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 5.6 4.9 - - - -
57A ILE* 3.2 37.9 - - + +
58A PRO 3.7 10.8 + - - -
59A TRP* 5.1 6.0 - - + +
86A TYR* 3.5 24.5 + - + +
153A LEU* 2.9 29.8 + - + +
154A VAL* 3.7 4.7 - - - +
156A SER* 1.3 81.0 - - - +
158A LEU* 1.3 66.0 + - - +
159A GLN 3.1 0.2 - - - -
160A SER* 3.3 7.6 + - - +
161A PHE* 2.9 24.8 + - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.1 4.9 - - + +
29A GLY* 5.6 3.1 - - - -
83A LEU* 4.7 8.1 - - + -
86A TYR* 3.7 38.9 - - + -
90A LEU* 4.6 8.7 - - + -
107A LEU* 4.0 37.0 - - + -
111A VAL* 4.1 13.0 - - + -
154A VAL* 2.8 18.5 + - + +
155A ALA* 3.7 5.8 - - - +
157A HIS* 1.3 75.9 - - - +
159A GLN* 1.3 66.4 + - - +
161A PHE* 3.1 7.5 + - + +
162A LEU* 2.9 43.4 + - + +
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE 5.4 0.2 + - - -
26A GLN* 3.4 38.3 - - - +
29A GLY* 4.0 18.4 - - - -
30A ALA* 4.9 1.7 - - - +
33A GLN* 3.4 24.5 - - - +
155A ALA* 3.0 25.0 + - - +
156A SER* 3.4 9.2 - - - +
158A LEU* 1.3 81.0 - - - +
160A SER* 1.3 63.0 + - - +
162A LEU* 3.2 7.1 + - - +
163A GLU* 3.0 35.5 + - + +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER* 3.1 13.7 + - - -
157A HIS* 3.8 9.4 - - - -
159A GLN* 1.3 76.3 - - - +
161A PHE* 1.3 63.9 - - - +
163A GLU* 3.2 22.3 + - - +
164A VAL* 3.3 20.5 + - - +
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 3.8 35.0 - - + +
61A PRO 4.3 1.8 - - - -
62A LEU* 3.7 33.4 - - + +
78A GLN 4.7 0.4 - - - -
79A LEU* 3.7 14.1 - - + -
82A GLY* 3.7 17.5 - - - -
83A LEU* 3.9 29.4 - - + -
86A TYR* 3.8 19.3 - + + +
157A HIS 2.9 14.6 + - - +
158A LEU* 3.3 9.2 - - + +
160A SER* 1.3 77.7 - - - +
162A LEU* 1.3 68.9 + - + +
164A VAL* 3.5 6.1 + - - +
165A SER* 2.9 42.0 + - - -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.8 24.5 - - + +
25A ILE* 3.4 34.8 - - + -
26A GLN* 3.9 33.6 - - + +
83A LEU* 4.0 26.2 - - + -
114A PHE* 4.7 3.4 - - + -
158A LEU* 2.9 28.1 + - + +
159A GLN* 3.2 6.7 + - - +
161A PHE* 1.3 84.9 - - + +
163A GLU* 1.3 59.6 + - - +
165A SER* 3.7 4.6 - - - +
166A TYR* 2.9 29.8 + - - +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 4.4 12.1 - - - +
159A GLN* 3.0 27.8 + - + +
160A SER* 3.2 15.5 + - - +
162A LEU* 1.3 77.2 - - - +
164A VAL* 1.3 62.9 + - + +
166A TYR* 3.4 7.0 + - - +
167A ARG* 3.3 25.5 + - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.6 29.4 - - + -
160A SER 3.3 16.1 + - - +
161A PHE* 3.9 2.0 - - - +
162A LEU 3.3 0.2 - - - -
163A GLU* 1.3 74.8 - - + +
165A SER* 1.3 66.4 + - - +
167A ARG* 3.0 10.7 + - + +
168A VAL* 2.9 30.4 + - + +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.6 10.8 - - - -
62A LEU* 4.0 9.4 - - - +
79A LEU* 3.5 31.7 - - - +
161A PHE* 2.9 28.2 + - - -
162A LEU* 3.7 9.9 - - - -
164A VAL* 1.3 79.1 - - - +
166A TYR* 1.3 62.6 + - - +
168A VAL* 3.1 8.2 + - - +
169A LEU* 2.8 33.0 + - - +
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.9 30.1 - - + +
22A VAL* 3.7 22.8 - - + +
23A ARG* 3.1 44.5 + - + -
26A GLN* 4.5 8.7 - - - +
162A LEU 2.9 19.1 + - - +
163A GLU* 3.5 9.2 - - - +
165A SER* 1.3 76.8 - - - +
167A ARG* 1.3 67.0 + - - +
169A LEU* 3.8 0.4 - - - -
170A ARG* 2.8 78.9 + - + +
145B GLU* 4.6 2.4 + - - -
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU 3.3 14.1 + - - +
164A VAL* 3.0 10.3 + - + +
166A TYR* 1.3 88.6 - - - +
168A VAL* 1.3 62.6 + - + +
170A ARG* 3.2 44.8 - - - +
171A HIS* 3.1 24.1 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 5.6 3.4 - - + -
65A CYS* 3.4 46.9 - - + +
66A PRO* 5.2 2.9 - - + -
75A CYS* 3.8 13.9 - - - -
79A LEU* 6.0 2.5 - - + -
164A VAL* 2.9 31.3 + - + +
165A SER* 3.6 9.6 - - - +
167A ARG* 1.3 78.2 - - + +
169A LEU* 1.3 67.9 + - + +
171A HIS* 3.2 8.3 + - + +
172A LEU* 3.1 30.5 + - + +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 6.0 0.2 - - + -
15A LEU* 4.0 24.7 - - + +
18A CYS* 3.7 31.0 - - + -
19A LEU* 3.3 20.8 - - + +
22A VAL* 4.0 23.6 - - + -
75A CYS* 6.4 0.4 - - - -
76A LEU* 5.1 5.2 - - + -
79A LEU* 4.0 27.8 - - + -
114A PHE* 4.6 2.2 - - + -
165A SER* 2.8 23.9 + - - +
168A VAL* 1.3 73.7 - - + +
170A ARG* 1.3 64.7 + - - +
172A LEU* 3.0 15.7 + - + +
173A ALA* 2.9 23.0 + - - +
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.6 16.1 - - + +
166A TYR* 2.8 57.4 + - + +
167A ARG* 3.2 44.2 - - - +
169A LEU* 1.3 72.8 - - - +
171A HIS* 1.3 62.9 + - - +
173A ALA* 3.5 12.7 + - - +
174A GLN* 3.9 6.4 + - - +
145B GLU* 4.8 10.1 + - - -
----------------------------------------------------------
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Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A CYS 5.4 7.4 - - - -
66A PRO* 5.9 3.5 + - + -
68A GLN 5.5 4.2 + - - -
69A ALA* 5.6 6.1 - - - +
167A ARG 3.1 12.3 + - - +
168A VAL* 3.3 11.7 - - + +
170A ARG* 1.3 75.4 - - - +
172A LEU* 1.3 83.3 + - + +
174A GLN* 2.9 30.7 + - - +
175A PRO* 4.9 1.0 - - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 4.7 6.1 + - - +
10A LEU* 4.1 24.5 - - + -
12A GLN* 4.7 0.2 - - - +
15A LEU* 3.5 24.9 - - + +
65A CYS 5.7 1.1 - - - +
68A GLN 4.3 16.4 - - - +
69A ALA* 4.8 9.2 - - + +
72A LEU* 4.2 16.2 - - + -
75A CYS* 5.0 9.2 - - - -
76A LEU* 5.4 2.7 - - + -
168A VAL* 3.1 23.5 + - + +
169A LEU* 3.0 17.3 + - + +
171A HIS* 1.3 94.8 - - + +
173A ALA* 1.3 60.8 - - - +
174A GLN 3.0 1.6 + - - -
175A PRO* 3.1 22.7 - - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 2.8 37.1 + - - +
15A LEU* 3.6 15.9 - - + +
16A LEU* 4.6 9.2 - - + -
19A LEU* 4.3 17.5 - - + -
169A LEU 2.9 10.8 + - - +
170A ARG* 3.5 13.7 - - - +
171A HIS 3.1 0.6 + - - -
172A LEU* 1.3 75.4 - - - +
174A GLN* 1.3 62.0 + - - +
175A PRO* 3.5 3.4 - - - +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 5.2 3.8 - - - +
12A GLN* 5.2 2.4 + - - -
170A ARG 3.9 4.9 + - - +
171A HIS* 2.9 21.9 + - - +
173A ALA* 1.3 85.0 + - + +
175A PRO* 1.4 77.6 + - - +
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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