Contacts of the helix formed by residues 110 - 134 (chain P) in PDB entry 3L73
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 TYR 110 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P SER 2.8 15.9 + - - +
108P TYR 3.8 2.5 - - - -
109P LEU* 1.3 79.0 - - + +
111P LYS* 1.3 64.7 + - - +
112P GLU* 3.3 5.6 - - - -
113P THR* 2.8 27.5 + - - +
114P TRP 3.0 7.4 + - - -
201P LEU* 4.4 6.1 - - + -
204P SER* 3.4 33.4 + - - +
205P GLY 3.3 23.2 + - - -
206P SER 3.7 3.1 + - - -
207P ASN* 3.7 24.0 + - + -
314P ARG* 3.4 32.4 + - - -
502P HEM 4.2 19.5 - - + -
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Residues in contact with LYS 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P TYR 3.9 5.4 - - - +
109P LEU* 3.1 21.9 + - - +
110P TYR* 1.3 72.9 - - - +
112P GLU* 1.3 65.9 + - + +
114P TRP* 3.1 4.3 + - - +
115P ASN* 2.8 41.9 + - - +
306P PRO* 4.1 30.1 + - + +
307P PHE* 3.6 37.7 - - + -
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Residues in contact with GLU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C HIS* 5.2 5.9 + - + -
10C PRO* 4.9 6.6 - - - +
110P TYR* 3.0 2.7 + - - -
111P LYS* 1.3 78.2 + - + +
113P THR* 1.3 68.5 + - - +
115P ASN* 4.3 7.6 - - - +
116P THR* 3.0 29.7 + - + +
200P PHE* 3.2 49.2 - - + +
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Residues in contact with THR 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P TYR* 2.8 22.2 + - - +
112P GLU* 1.3 77.8 + - - +
114P TRP* 1.3 61.8 + - - +
116P THR* 2.9 19.3 + - - -
117P GLY 3.0 0.3 + - - -
197P HIS* 2.9 32.4 - - + +
200P PHE* 3.6 8.3 + - - +
201P LEU* 3.2 41.9 + - + +
204P SER* 5.3 0.3 + - - -
502P HEM 3.7 31.4 - - + -
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Residues in contact with TRP 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P ILE* 4.3 14.1 - - + -
102P GLY* 4.3 20.0 - - - -
103P LEU* 4.6 9.2 - - + -
108P TYR* 3.2 47.1 - + + +
110P TYR 3.0 10.4 + - - +
111P LYS* 3.2 9.6 - - - +
113P THR* 1.3 77.8 - - - +
115P ASN* 1.3 68.3 + - - +
117P GLY* 3.0 16.3 + - - -
118P VAL* 3.0 21.5 + - + +
302P LEU* 2.7 52.3 + - + -
303P PHE* 5.0 0.2 - - - -
305P ILE* 4.4 9.6 - - + -
306P PRO* 3.6 20.1 - - + +
502P HEM 3.6 45.0 - - + +
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Residues in contact with ASN 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P LYS* 2.8 38.4 + - - +
112P GLU* 4.1 7.0 - - - +
114P TRP* 1.3 75.7 - - - +
116P THR* 1.3 68.7 + - + +
117P GLY 3.0 1.6 - - - -
118P VAL* 3.0 14.1 + - - +
119P ILE* 3.0 17.3 + - + +
303P PHE* 3.2 38.7 - - + +
306P PRO* 5.3 1.8 - - - +
307P PHE* 6.4 0.4 - - - -
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Residues in contact with THR 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P GLU 3.0 16.6 + - - +
113P THR* 2.9 10.2 + - - -
115P ASN* 1.3 74.5 - - + +
117P GLY* 1.3 57.5 + - - +
119P ILE* 2.9 16.7 + - + +
120P LEU* 2.8 28.7 + - - +
193P ILE* 4.4 10.2 - - + +
196P ILE* 4.0 13.5 - - + -
197P HIS* 2.7 40.6 + - - -
200P PHE* 3.8 27.4 - - + -
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Residues in contact with GLY 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P THR 3.0 2.0 + - - -
114P TRP 3.0 10.3 + - - -
116P THR* 1.3 83.9 + - - +
118P VAL* 1.3 60.6 + - - +
120P LEU* 3.1 4.6 + - - +
121P LEU 3.1 10.6 + - - -
197P HIS* 3.5 13.5 - - - -
502P HEM 2.8 42.2 - - - +
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Residues in contact with VAL 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P TRP* 3.0 28.6 + - - +
115P ASN* 3.0 1.5 + - - -
117P GLY* 1.3 74.9 - - - +
119P ILE* 1.3 58.5 + - - +
121P LEU* 3.2 7.6 + - + +
122P LEU* 3.0 36.1 + - + +
299P VAL* 4.7 5.8 - - + +
302P LEU* 4.2 26.0 - - + -
303P PHE* 3.4 51.1 - - + -
502P HEM 3.7 15.5 - - + -
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Residues in contact with ILE 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P ASN* 3.0 14.7 + - + +
116P THR* 2.9 16.0 + - + +
118P VAL* 1.3 74.5 - - - +
120P LEU* 1.3 65.1 + - - +
122P LEU* 3.3 10.0 + - + +
123P THR* 2.9 32.5 + - - +
193P ILE* 3.5 33.2 - - + -
303P PHE* 4.5 13.5 - - + -
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Residues in contact with LEU 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P ILE* 4.9 1.1 - - - -
116P THR 2.8 13.4 + - - +
117P GLY 3.1 8.3 + - - +
119P ILE* 1.3 76.9 - - - +
121P LEU* 1.3 55.9 + - - +
123P THR* 3.3 3.3 + - - -
124P LEU* 2.9 31.7 + - - +
190P ILE* 3.6 43.0 - - + +
193P ILE* 3.7 20.0 - - + -
194P THR* 3.7 11.9 - - - +
197P HIS* 3.9 34.5 - - + +
502P HEM 3.8 38.8 - - + +
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Residues in contact with LEU 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P PHE* 4.7 7.9 - - + -
95P ILE* 3.7 34.3 - - + -
96P PHE* 4.9 6.5 - - + -
99P ILE* 3.9 15.7 - - + -
117P GLY 3.1 11.0 + - - +
118P VAL* 3.2 9.8 + - + +
120P LEU* 1.3 75.3 - - - +
122P LEU* 1.3 66.7 + - - +
124P LEU* 3.2 2.2 + - + +
125P MET* 2.9 47.0 + - + +
299P VAL* 4.0 14.4 - - + -
302P LEU* 3.8 28.5 - - + -
502P HEM 4.0 9.6 - - + +
3007P PEE 5.1 6.7 - - + -
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Residues in contact with LEU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P VAL* 3.0 28.0 + - + +
119P ILE* 3.3 9.6 + - + +
121P LEU* 1.3 75.9 - - - +
123P THR* 1.3 63.0 + - - +
125P MET* 3.2 14.0 + - - +
126P ALA* 3.1 22.0 + - - +
299P VAL* 3.5 34.1 - - + -
300P LEU* 4.2 22.2 - - + -
303P PHE* 4.8 7.6 - - + -
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Residues in contact with THR 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P ILE* 2.9 27.5 + - - +
120P LEU* 3.7 5.2 - - - -
122P LEU* 1.3 75.3 - - - +
124P LEU* 1.3 52.4 + - - +
126P ALA* 3.2 7.5 + - - +
127P THR* 2.8 39.5 + - - +
186P LEU* 4.0 24.9 - - + +
189P ALA* 4.6 5.4 - - + -
190P ILE* 3.2 31.9 - - + +
193P ILE* 4.3 6.7 - - - +
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Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P PHE* 3.4 41.7 - - + -
92P PHE* 3.7 29.8 - - + -
95P ILE* 3.7 23.3 - - + -
120P LEU 2.9 17.4 + - - +
121P LEU* 3.5 4.9 - - - +
123P THR* 1.3 73.4 - - - +
125P MET* 1.3 66.3 + - - +
127P THR* 3.2 1.3 + - - -
128P ALA* 3.0 20.6 + - - +
190P ILE* 3.8 12.7 - - + +
501P HEM 3.8 35.2 - - + -
502P HEM 6.0 1.6 - - + -
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Residues in contact with MET 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92P PHE* 4.1 19.3 - - + -
121P LEU* 2.9 42.1 + - + +
122P LEU* 3.5 18.8 - - + +
124P LEU* 1.3 74.3 - - - +
126P ALA* 1.3 58.9 + - - +
128P ALA* 3.1 4.3 + - - +
129P PHE* 2.9 29.8 + - - +
274P TYR 5.5 0.2 - - - +
275P PHE* 3.8 16.1 - - + -
277P PHE* 5.1 9.6 - - + -
278P ALA* 5.3 0.2 - - + -
295P LEU* 6.3 0.4 - - + -
299P VAL* 4.2 26.0 - - + -
3001P JZZ 3.4 41.5 - - + -
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Residues in contact with ALA 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P LEU 3.1 9.7 + - - +
123P THR* 3.5 10.3 - - - +
125P MET* 1.3 77.4 - - - +
127P THR* 1.3 64.5 + - - +
129P PHE* 3.2 7.2 + - - +
130P VAL* 3.1 30.3 + - + +
186P LEU* 4.2 15.7 - - + -
3001P JZZ 6.2 0.4 - - - -
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Residues in contact with THR 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P THR 2.8 23.8 + - - -
124P LEU* 3.2 12.1 + - - -
126P ALA* 1.3 72.9 - - - +
128P ALA* 1.3 57.3 + - - +
130P VAL* 3.0 15.4 - - - +
131P GLY 3.0 2.3 + - - -
183P HIS* 2.8 31.5 + - - +
186P LEU* 3.1 22.8 - - - +
187P PRO* 3.8 15.7 - - + -
190P ILE* 3.5 9.5 - - - +
501P HEM 3.5 40.8 - - + -
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Residues in contact with ALA 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ALA* 5.5 0.4 - - + -
92P PHE* 3.9 24.5 - - + -
124P LEU 3.0 12.4 + - - +
125P MET 3.7 6.3 - - - +
127P THR* 1.3 73.4 - - - +
129P PHE* 1.3 68.5 + - - +
131P GLY 3.1 0.2 + - - -
132P TYR* 2.9 26.9 + - - +
274P TYR* 4.1 19.3 - - + +
275P PHE* 4.6 1.1 - - + -
501P HEM 3.6 23.6 - - + +
3001P JZZ 4.3 2.0 - - - -
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Residues in contact with PHE 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P MET 2.9 16.1 + - - +
126P ALA* 3.5 8.7 - - - +
128P ALA* 1.3 80.1 - - - +
130P VAL* 1.3 70.5 + - + +
133P VAL* 3.5 5.7 + - - +
144P ALA* 4.0 13.2 - - - -
147P ILE* 3.7 41.7 - - + -
148P THR* 4.4 11.4 - - + -
179P PHE* 4.4 17.5 - + - -
275P PHE* 4.3 4.4 - + + -
3001P JZZ 3.0 89.0 - + + +
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Residues in contact with VAL 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ALA* 3.1 14.8 + - + +
127P THR* 3.0 23.6 - - - +
129P PHE* 1.3 82.0 - - + +
131P GLY* 1.3 67.5 + - - +
133P VAL* 3.2 12.6 + - - +
134P LEU* 3.6 14.6 + - - +
179P PHE* 4.0 41.1 - - + +
182P LEU* 4.4 15.9 - - + -
183P HIS* 3.4 30.5 - - + +
186P LEU* 4.9 3.6 - - + -
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Residues in contact with GLY 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P THR 3.0 5.1 + - - -
128P ALA 3.1 1.8 + - - -
130P VAL* 1.3 84.1 - - - +
132P TYR* 1.3 62.3 + - - +
134P LEU* 3.1 22.5 + - - +
135P PRO* 3.6 0.3 - - - +
183P HIS* 3.1 36.8 - - - -
501P HEM 3.4 18.7 - - - +
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Residues in contact with TYR 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P ALA 2.9 12.2 + - - +
129P PHE 3.7 0.4 - - - +
131P GLY* 1.3 76.3 - - - +
133P VAL* 1.3 61.3 + - - +
135P PRO* 3.0 14.7 - - - +
139P MET* 3.6 28.9 - - - +
140P SER* 3.1 14.4 + - - -
253P ASP* 4.5 6.2 + - - +
256P ASN* 3.5 27.7 + - - +
272P GLU* 3.4 29.5 + - + -
274P TYR* 5.5 0.2 - - - -
501P HEM 3.7 33.6 - - + +
3001P JZZ 3.1 75.4 - + - +
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Residues in contact with VAL 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P PHE* 3.5 8.0 + - + +
130P VAL 3.2 7.7 + - - +
131P GLY 3.2 1.2 - - - -
132P TYR* 1.3 78.3 - - - +
134P LEU* 1.3 63.2 + - - +
136P TRP* 2.9 47.1 + - + -
140P SER* 3.5 12.7 - - - +
144P ALA* 3.7 20.6 - - + -
171P VAL* 5.3 0.9 - - + -
175P THR* 6.3 0.7 - - + -
176P LEU* 4.5 7.4 - - + -
179P PHE* 3.9 26.9 - - + -
3001P JZZ 3.2 25.8 - - - -
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Residues in contact with LEU 134 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P TYR* 2.6 43.1 + - + +
63P ALA* 3.5 6.2 - - - +
130P VAL 3.6 8.7 - - - +
131P GLY* 3.1 14.4 + - - +
133P VAL* 1.3 77.1 - - - +
135P PRO* 1.3 63.3 - - + +
136P TRP* 3.0 2.1 + - - +
176P LEU* 4.0 11.2 - - + +
179P PHE* 4.4 2.0 - - + -
180P PHE* 3.7 46.4 - - + +
183P HIS* 3.6 33.4 - - + -
501P HEM 3.6 22.9 - - + -
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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