Contacts of the helix formed by residues 109 - 133 (chain P) in PDB entry 1PP9
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 PHE 109 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P SER 3.0 10.5 + - - +
107P TYR 2.9 2.5 - - - -
108P THR* 1.3 78.1 + - - +
110P LEU* 1.3 58.2 + - - +
111P GLU* 3.5 5.4 - - - -
112P THR* 3.4 17.3 + - - +
113P TRP* 2.9 28.2 + - - +
200P LEU* 3.9 15.5 - - + -
203P THR* 3.3 33.4 - - + +
204P GLY 3.4 26.5 - - - -
205P SER 4.3 1.8 - - - -
206P ASN* 3.8 16.6 - - + -
313P ARG* 3.3 37.9 - - - -
502P HEM 3.9 15.3 - - + -
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P TYR 3.5 10.8 - - - +
108P THR* 2.9 17.9 + - - +
109P PHE* 1.3 70.1 - - - +
111P GLU* 1.3 69.8 + - - +
113P TRP* 3.8 0.8 - - - +
114P ASN* 2.9 46.1 + - - +
305P PRO* 3.4 36.1 - - + -
306P LEU* 6.3 2.5 - - + -
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Residues in contact with GLU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P PHE* 4.3 2.8 - - - -
110P LEU* 1.3 85.1 + - + +
112P THR* 1.3 66.8 + - - +
114P ASN* 3.9 2.9 - - - +
115P ILE* 3.0 33.3 + - + +
199P PHE* 3.5 41.1 - - + -
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Residues in contact with THR 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P PHE* 3.4 20.0 + - - +
111P GLU* 1.3 79.2 + - - +
113P TRP* 1.3 64.6 + - - +
115P ILE* 3.4 1.9 + - - +
116P GLY 3.0 17.0 + - - -
196P HIS* 3.1 45.6 + - + +
199P PHE* 3.5 10.2 + - - +
200P LEU* 3.2 34.6 + - + -
502P HEM 3.7 24.7 - - + -
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Residues in contact with TRP 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P VAL* 4.3 9.0 - - + -
101P GLY* 4.1 21.1 - - - -
102P LEU* 3.6 35.9 - - + -
107P TYR* 3.2 36.3 - - + +
109P PHE 2.9 18.8 + - - +
110P LEU 3.8 2.7 - - - +
112P THR* 1.3 77.1 - - - +
114P ASN* 1.3 73.3 + - - +
116P GLY* 2.9 18.0 + - - -
117P VAL* 3.0 15.0 + - + +
301P LEU* 2.7 40.7 + - + -
304P ILE* 4.5 2.0 - - + -
305P PRO* 4.0 18.4 - - + +
502P HEM 3.8 51.5 - - + +
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Residues in contact with ASN 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P LEU* 2.9 36.9 + - - +
111P GLU* 4.2 4.4 - - - +
113P TRP* 1.3 87.2 - - - +
115P ILE* 1.3 62.5 + - + +
117P VAL* 3.2 16.2 + - - +
118P ILE* 3.2 20.6 + - + +
302P ALA* 4.0 24.9 + - - +
305P PRO* 5.5 0.7 - - - +
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Residues in contact with ILE 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P GLU* 3.0 20.8 + - + +
112P THR 3.6 3.8 - - - +
114P ASN* 1.3 76.8 - - + +
116P GLY* 1.3 58.7 + - - +
118P ILE* 3.1 15.3 + - + +
119P LEU* 2.8 26.6 + - + +
192P ILE* 3.7 34.8 - - + +
195P VAL* 3.6 21.1 - - + +
196P HIS* 3.8 17.0 - - + +
199P PHE* 3.3 36.3 - - + -
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Residues in contact with GLY 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P THR 3.0 11.1 + - - -
113P TRP 2.9 9.6 + - - -
115P ILE* 1.3 78.4 - - - +
117P VAL* 1.3 56.9 + - - +
119P LEU* 3.1 4.5 + - - +
120P LEU 2.9 24.8 + - - -
196P HIS* 3.9 4.0 - - - -
502P HEM 3.0 42.6 - - - +
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Residues in contact with VAL 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P TRP* 3.0 23.1 + - + +
114P ASN* 3.2 12.5 + - - +
116P GLY* 1.3 75.7 - - - +
118P ILE* 1.3 64.7 + - + +
120P LEU* 3.3 6.3 + - - +
121P LEU* 3.2 34.9 + - + +
298P ILE* 4.6 17.0 - - + +
299P LEU* 4.8 9.6 - - + -
301P LEU* 4.0 20.4 - - + -
302P ALA* 4.3 15.7 - - + +
502P HEM 3.8 16.2 - - + -
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Residues in contact with ILE 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P ASN* 3.2 15.7 + - + +
115P ILE* 3.1 17.9 + - + +
117P VAL* 1.3 77.0 - - + +
119P LEU* 1.3 62.6 + - - +
121P LEU* 3.3 11.8 + - + +
122P THR* 2.8 38.9 + - - +
192P ILE* 4.4 21.5 - - + -
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Residues in contact with LEU 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P ILE* 2.8 19.0 + - + +
116P GLY* 3.1 8.9 + - - +
118P ILE* 1.3 77.8 - - - +
120P LEU* 1.3 60.6 + - - +
122P THR* 3.3 4.3 + - - -
123P VAL* 2.9 30.7 + - - +
189P ILE* 3.7 35.9 - - + +
192P ILE* 3.5 24.9 - - + -
193P ALA* 3.9 5.4 - - - +
196P HIS* 3.8 37.5 - - + +
502P HEM 4.0 33.7 - - + -
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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
----------------------------------------------------------
91P PHE* 5.0 0.4 - - + -
94P LEU* 4.0 29.2 - - + -
95P TYR* 4.4 14.1 - - + -
98P VAL* 4.7 10.3 - - + -
116P GLY 2.9 6.4 + - - +
117P VAL* 3.6 8.7 - - - +
118P ILE 3.3 0.2 - - - -
119P LEU* 1.3 75.5 - - - +
121P LEU* 1.3 57.9 + - - +
123P VAL* 3.4 3.9 + - - +
124P MET* 3.0 57.9 + - + +
298P ILE* 4.2 13.7 - - + -
301P LEU* 3.7 31.0 - - + -
502P HEM 3.7 17.1 - - + +
3007P PEE 5.0 9.4 - - + -
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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
----------------------------------------------------------
117P VAL* 3.2 21.3 + - + +
118P ILE* 3.7 10.8 - - + +
120P LEU* 1.3 75.7 - - - +
122P THR* 1.3 61.8 + - - +
124P MET* 3.4 5.1 + - - -
125P ALA* 3.0 25.1 + - - +
298P ILE* 3.6 32.8 - - + -
299P LEU* 4.1 25.1 - - + -
3001P SMA 3.5 32.8 - - - +
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Residues in contact with THR 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P ILE* 2.8 28.0 + - - +
119P LEU* 3.3 5.8 + - - -
121P LEU* 1.3 73.0 - - - +
123P VAL* 1.3 60.5 + - - +
125P ALA* 3.3 5.5 + - - +
126P THR* 2.8 33.5 + - - -
185P LEU* 3.5 28.5 - - + -
188P ILE* 5.3 0.2 - - + -
189P ILE* 3.2 29.2 - - + -
192P ILE* 4.6 10.9 - - + +
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Residues in contact with VAL 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P PHE* 4.0 37.7 - - + -
91P PHE* 3.9 13.9 - - + -
94P LEU* 3.7 24.7 - - + -
119P LEU 2.9 21.5 + - - +
120P LEU 3.9 3.6 - - - +
122P THR* 1.3 73.0 - - - +
124P MET* 1.3 61.5 + - - +
126P THR* 3.6 1.5 - - - -
127P ALA* 2.9 28.6 + - - +
189P ILE* 3.8 20.6 - - + -
501P HEM 4.6 7.4 - - + -
502P HEM 4.2 12.1 - - + -
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Residues in contact with MET 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P PHE* 3.9 21.5 - - + -
95P TYR* 3.8 22.7 - - + +
120P LEU* 3.0 43.3 + - + +
121P LEU* 3.6 8.7 - - - +
122P THR 3.3 0.2 - - - -
123P VAL* 1.3 77.4 - - - +
125P ALA* 1.3 63.5 + - - +
127P ALA 3.9 0.2 - - - -
128P PHE* 3.0 23.7 + - - +
274P PHE* 3.7 17.6 - - + -
276P PHE* 4.6 6.5 - - + -
298P ILE* 3.7 33.2 - - + -
3001P SMA 3.9 37.0 - - + +
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Residues in contact with ALA 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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121P LEU 3.0 17.1 + - - +
122P THR* 3.7 6.5 - - - +
124P MET* 1.3 75.6 - - - +
126P THR* 1.3 61.8 + - - +
128P PHE* 3.3 6.9 + - - +
129P MET* 3.1 32.1 + - - +
185P LEU* 4.5 11.7 - - + -
3001P SMA 3.8 33.1 + - + +
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Residues in contact with THR 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P THR 2.8 23.1 + - - -
123P VAL* 3.6 8.1 - - - -
124P MET 3.2 0.2 - - - -
125P ALA* 1.3 75.7 - - - +
127P ALA* 1.3 61.3 + - - +
129P MET* 3.3 5.1 + - - -
130P GLY 3.1 6.2 + - - -
182P HIS* 2.9 44.9 + - + +
185P LEU* 3.0 28.6 - - + +
186P PRO* 3.9 13.5 - - + -
189P ILE* 3.4 6.8 - - - +
501P HEM 3.8 26.9 - - + -
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Residues in contact with ALA 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P ALA* 5.3 0.4 - - + -
91P PHE* 3.7 26.9 - - + -
123P VAL 2.9 20.3 + - - +
124P MET 3.9 3.4 - - - +
126P THR* 1.3 71.4 - - - +
128P PHE* 1.3 64.8 + - - +
130P GLY 3.3 0.3 + - - -
131P TYR* 3.1 23.7 + - - +
271P GLU* 5.3 0.9 - - - -
273P TYR* 4.2 15.3 + - + +
274P PHE* 4.8 0.9 - - + -
501P HEM 3.7 28.4 - - + +
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Residues in contact with PHE 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P MET 3.0 14.3 + - - +
125P ALA 3.4 6.7 - - - +
126P THR 3.2 0.2 - - - -
127P ALA* 1.3 78.9 - - - +
129P MET* 1.3 74.9 + - + +
131P TYR* 3.1 15.0 + + + +
132P VAL* 3.4 13.3 + - + +
142P GLY* 3.4 28.0 - - - -
143P ALA* 3.8 9.4 - - - -
146P ILE* 3.4 40.2 - - + -
147P THR* 4.2 5.8 - - - -
178P PHE* 3.7 26.2 - + - -
271P GLU* 4.7 5.2 - - - -
274P PHE* 4.5 10.7 - - + -
3001P SMA 3.8 44.9 - - + -
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Residues in contact with MET 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P ALA* 3.1 19.8 + - - +
126P THR* 3.8 4.3 - - - +
128P PHE* 1.3 90.0 - - + +
130P GLY* 1.3 62.9 + - - +
132P VAL* 3.2 14.3 + - - +
133P LEU* 3.4 16.4 - - - +
178P PHE* 3.4 34.1 - - + +
181P PHE* 2.9 53.4 - - + -
182P HIS* 4.1 15.5 - - + +
185P LEU* 4.7 10.8 - - - -
3001P SMA 3.7 20.9 - - + -
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Residues in contact with GLY 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P THR 3.1 11.1 + - - -
127P ALA 3.3 1.7 + - - -
128P PHE 3.2 0.2 - - - -
129P MET* 1.3 76.0 - - - +
131P TYR* 1.3 63.3 - - - +
133P LEU* 3.1 21.7 + - - +
134P PRO* 3.4 5.4 - - - +
182P HIS* 3.3 30.2 + - - -
501P HEM 3.4 21.5 - - - +
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Residues in contact with TYR 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P ALA 3.1 11.7 + - - +
128P PHE* 3.1 11.9 + + + +
130P GLY* 1.3 76.3 - - - +
132P VAL* 1.3 53.4 + - + +
134P PRO* 3.2 7.8 - - - +
138P MET* 3.6 42.5 - - + +
139P SER* 2.6 28.4 + - - -
142P GLY* 6.0 2.0 - - - -
252P ASP* 3.6 23.3 + - - +
255P ASN* 3.8 19.2 - - + +
269P LYS 6.1 0.4 - - - -
270P PRO 6.1 0.2 - - - -
271P GLU* 3.4 38.2 - - + +
273P TYR* 5.6 0.2 - - - +
501P HEM 3.7 22.7 - - + -
3001P SMA 4.9 3.6 - - - -
3009P GOL 3.6 35.4 + - - -
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Residues in contact with VAL 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P PHE* 3.6 35.0 - - + +
129P MET 3.2 8.0 + - - +
130P GLY 3.1 0.8 - - - -
131P TYR* 1.3 78.2 - - + +
133P LEU* 1.3 65.9 + - - +
134P PRO 3.4 0.2 - - - -
135P TRP* 3.0 42.1 + - + -
139P SER* 3.2 28.0 - - - +
142P GLY* 4.9 0.7 - - - -
143P ALA* 3.8 11.7 - - + +
174P THR* 5.7 0.9 - - + -
175P LEU* 4.3 7.6 - - + -
178P PHE* 4.0 22.4 - - + -
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Residues in contact with LEU 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P TYR* 2.7 40.5 + - + +
62P ALA* 3.7 6.6 - - - +
129P MET 3.4 14.4 - - - +
130P GLY 3.1 9.5 + - - +
132P VAL* 1.3 76.2 - - - +
134P PRO* 1.3 62.9 - - + +
135P TRP 3.0 1.3 + - - -
175P LEU* 3.8 14.1 - - + +
178P PHE* 4.0 4.7 - - + -
179P PHE* 3.7 43.3 - - + +
182P HIS* 3.7 33.4 - - + -
501P HEM 3.7 25.8 - - + -
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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