Contacts of the helix formed by residues 97 - 123 (chain D) in PDB entry 5XVO
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 THR 97 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA 3.9 9.4 - - - +
96D TRP* 1.3 72.5 - - - +
98D GLU* 1.3 64.1 + - - +
99D GLU* 3.8 4.0 + - - +
100D ARG* 3.1 26.0 + - - +
101D LYS* 3.1 23.1 + - - +
278D GLN* 3.9 24.7 + - - +
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TRP 3.9 1.0 + - - -
97D THR* 1.3 72.6 - - - +
99D GLU* 1.3 64.2 + - + +
101D LYS* 3.6 17.5 + - - +
102D GLY 3.1 16.8 + - - -
142D PHE* 3.6 26.6 - - + -
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D THR* 3.2 3.9 + - - +
98D GLU* 1.3 81.1 - - + +
100D ARG* 1.3 57.9 + - - +
102D GLY* 3.1 4.4 + - - -
103D GLN* 2.9 42.9 + - - +
141D LEU* 4.5 21.9 - - + +
142D PHE* 5.6 0.4 - - - -
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TRP* 6.0 0.4 - - + -
97D THR* 3.1 23.1 + - - +
99D GLU* 1.3 75.6 - - - +
101D LYS* 1.3 58.4 + - - +
103D GLN* 2.9 27.9 + - - +
104D VAL* 2.9 37.8 + - - +
275D VAL* 2.8 38.0 + - - +
276D LEU* 3.9 19.5 - - + +
278D GLN* 3.0 42.3 - - + +
280D GLU 4.0 8.7 + - - -
281D GLU* 3.5 23.1 + - - -
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Residues in contact with LYS 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TRP* 4.0 39.6 + - + +
97D THR 3.1 14.9 + - - +
98D GLU* 3.8 28.7 - - - +
100D ARG* 1.3 76.3 - - - +
102D GLY* 1.3 53.1 + - - +
104D VAL* 3.9 0.5 - - - +
105D TRP* 2.7 37.8 + - - +
142D PHE* 3.9 2.9 - - + -
201D GLY 4.7 7.1 + - - +
202D LEU* 4.0 38.5 + - + +
276D LEU* 4.0 16.4 - - + -
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLU 3.1 7.7 + - - -
99D GLU* 3.1 7.8 + - - -
101D LYS* 1.3 72.9 - - - +
103D GLN* 1.3 63.1 + - - +
106D THR* 2.6 33.0 + - - -
141D LEU* 3.8 9.9 - - - -
142D PHE* 3.2 33.6 - - - -
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Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLU* 2.9 31.2 + - + +
100D ARG* 2.9 39.2 + - - +
102D GLY* 1.3 74.4 - - - +
104D VAL* 1.3 59.1 + - + +
106D THR* 3.8 2.1 - - - -
107D ALA* 2.9 31.6 + - - +
141D LEU* 3.9 17.6 - - + +
283D VAL* 5.5 0.9 - - - -
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ARG* 2.9 26.2 + - - +
101D LYS 3.9 2.0 - - - +
103D GLN* 1.3 75.5 - - + +
105D TRP* 1.3 65.2 + - - +
107D ALA* 3.3 2.1 + - - +
108D ILE* 3.0 42.3 + - + +
202D LEU* 3.8 12.8 - - + -
272D VAL* 4.0 17.3 - - + -
275D VAL* 3.7 30.5 - - + -
276D LEU* 3.9 17.9 - - + -
283D VAL* 3.9 15.0 - - + -
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Residues in contact with TRP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LYS 2.7 23.0 + - - +
102D GLY 4.0 1.6 - - - +
104D VAL* 1.3 72.7 - - - +
106D THR* 1.3 74.0 + - + +
108D ILE* 3.2 9.3 + - + +
109D ILE* 2.9 59.4 + - + +
142D PHE* 3.6 35.9 - + + -
143D ASP* 3.7 20.6 - - + -
148D GLU* 4.0 12.8 - - - -
202D LEU* 4.0 22.2 - - + +
203D LYS* 3.6 37.5 - - + +
216D ASP* 3.5 39.6 + - + +
219D GLU* 5.9 1.0 - - - +
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Residues in contact with THR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLY 2.6 22.1 + - - -
103D GLN* 3.9 2.2 - - - -
105D TRP* 1.3 85.0 - - + +
107D ALA* 1.3 66.7 + - - +
109D ILE* 3.4 2.3 + - - +
110D ALA* 3.0 23.6 + - - +
139D LEU* 3.8 29.6 - - + +
140D ARG* 3.9 16.6 - - - +
141D LEU* 3.6 7.3 - - + -
142D PHE 3.1 22.5 + - - +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLN 2.9 18.9 + - - +
104D VAL 3.4 5.8 - - - +
106D THR* 1.3 74.7 - - - +
108D ILE* 1.3 62.8 + - - +
110D ALA* 3.3 9.3 - - - +
111D GLN* 3.2 27.6 + - - +
283D VAL* 4.2 25.6 - - + -
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D VAL* 3.0 34.0 + - + +
105D TRP* 3.4 12.1 - - + +
107D ALA* 1.3 74.4 - - - +
109D ILE* 1.3 67.0 + - + +
111D GLN* 3.0 22.0 + - - +
112D LYS* 3.1 9.2 + - - +
202D LEU* 5.0 2.9 - - + -
216D ASP* 3.5 22.2 - - + +
217D LEU* 4.1 26.2 - - + -
219D GLU* 4.1 5.2 - - + -
220D PRO* 3.7 23.3 - - + +
268D TYR* 3.9 14.8 - - - +
272D VAL* 4.3 8.3 - - + -
283D VAL* 4.3 11.2 - - + -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 2.9 52.2 + - + +
106D THR* 3.9 2.9 - - - +
108D ILE* 1.3 77.3 - - + +
110D ALA* 1.3 63.8 + - - +
112D LYS* 3.0 9.7 + - + +
113D ILE* 2.9 39.6 + - + +
139D LEU* 4.2 13.5 - - + -
148D GLU* 3.2 47.8 - - + +
219D GLU* 3.7 24.5 - - + +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D THR* 3.0 15.1 + - + +
107D ALA* 3.3 14.4 - - - +
109D ILE* 1.3 77.0 - - - +
111D GLN* 1.3 57.5 + - + +
113D ILE* 3.2 3.4 + - - +
114D THR* 2.8 32.7 + - - +
136D ARG* 3.7 24.5 - - + +
139D LEU* 4.1 15.9 - - + -
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Residues in contact with GLN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ALA* 3.4 15.3 + - - +
108D ILE* 3.0 9.9 + - - +
110D ALA* 1.3 76.8 - - + +
112D LYS* 1.3 61.3 + - - +
114D THR* 2.5 23.5 + - - +
115D ASN* 3.0 18.3 + - - -
220D PRO* 4.0 9.7 - - + +
268D TYR* 3.3 17.9 + - - -
283D VAL* 4.1 14.5 + - - +
284D PRO 2.8 23.2 + - - +
285D GLU* 3.5 23.0 - - + +
286D PHE 3.1 28.1 + - - +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ILE 3.1 6.1 + - - +
109D ILE* 3.0 16.9 + - + +
111D GLN* 1.3 77.1 - - - +
113D ILE* 1.3 52.6 + - + +
115D ASN* 3.0 5.6 + - - +
116D GLN* 2.8 66.1 + - + +
148D GLU* 3.0 29.1 + - + +
152D ALA* 5.2 6.8 - - - +
219D GLU* 2.8 54.8 + - + +
220D PRO* 3.8 10.2 - - - +
222D ARG* 3.9 21.0 - - - +
223D PRO* 4.3 3.9 - - + +
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 2.9 32.9 + - + +
110D ALA 3.7 6.3 - - - +
112D LYS* 1.3 79.1 - - + +
114D THR* 1.3 56.7 + - - +
116D GLN* 3.1 18.1 + - - +
117D SER* 2.9 27.5 + - - -
132D LEU* 3.6 36.1 - - + +
133D LEU* 4.9 0.4 - - - +
135D MET 5.2 0.2 - - - -
136D ARG* 4.0 17.0 - - + +
139D LEU* 4.3 16.4 - - + -
147D ARG* 4.6 3.4 - - + +
148D GLU* 4.1 21.3 - - - +
151D ALA* 4.3 15.9 - - + -
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Residues in contact with THR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA 2.8 11.6 + - - +
111D GLN* 2.5 32.0 + - - +
113D ILE* 1.3 71.3 - - - +
115D ASN* 1.3 61.6 + - - +
117D SER* 3.1 8.3 + - - -
118D LEU* 2.8 36.8 + - - +
133D LEU* 4.6 8.6 - - + +
136D ARG* 3.1 45.8 - - - +
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Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLN 3.0 20.2 + - - +
112D LYS 3.5 3.6 - - - +
114D THR* 1.3 77.1 + - - +
116D GLN* 1.3 64.6 + - - +
118D LEU* 3.9 7.9 - - - +
119D HIS* 3.0 20.1 + - - +
220D PRO* 3.0 23.4 + - - +
223D PRO* 3.7 17.6 - - + +
286D PHE* 3.0 25.7 + - - +
287D GLY* 3.2 20.6 - - - -
288D ILE* 3.3 30.4 + - + +
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LYS* 2.8 48.2 + - + +
113D ILE* 3.4 25.7 - - - +
115D ASN* 1.3 72.2 - - - +
117D SER* 1.3 63.3 + - - +
119D HIS* 3.3 1.8 + - - -
120D LEU* 3.0 18.0 + - - +
132D LEU* 3.7 6.1 - - + -
148D GLU 4.8 1.2 - - - +
151D ALA* 4.3 12.1 - - - +
152D ALA* 4.1 15.0 + - - +
155D TYR* 3.2 63.7 - - + -
156D PHE* 4.4 4.8 - - - -
222D ARG* 6.3 0.6 - - - +
223D PRO* 4.3 9.0 - - + -
226D ASP* 4.9 2.0 + - - -
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ILE 2.9 10.7 + - - -
114D THR 3.1 8.5 + - - -
116D GLN* 1.3 76.6 - - - +
118D LEU* 1.3 56.5 + - - +
120D LEU* 2.8 7.1 + - - +
121D ALA* 2.8 27.1 + - - +
129D ALA* 2.7 35.8 + - - +
132D LEU* 3.8 14.1 - - - +
133D LEU* 3.2 26.5 - - - +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D THR* 2.8 23.3 + - - +
115D ASN* 3.8 25.4 - - - +
117D SER* 1.3 73.0 + - - +
119D HIS* 1.3 57.4 + - - +
121D ALA* 3.4 10.8 + - + +
122D GLN* 2.9 28.5 + - - +
133D LEU* 6.5 0.2 - - + -
287D GLY* 5.1 2.5 - - - -
288D ILE* 4.1 27.6 - - + +
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Residues in contact with HIS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ASN 3.0 18.1 + - - +
116D GLN 3.5 4.9 - - - +
118D LEU* 1.3 73.6 - - - +
120D LEU* 1.3 64.6 + - - +
122D GLN* 3.2 20.0 - - - +
123D ARG* 3.2 42.6 + - - +
155D TYR* 2.8 28.6 + - - +
159D LEU* 3.7 21.0 - - + +
223D PRO* 4.7 2.0 + - + -
226D ASP* 3.8 7.2 - - - +
227D GLN* 3.5 39.8 - - + -
230D TYR* 4.3 4.7 - - + +
288D ILE* 3.9 12.5 - - + +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLN 3.0 11.7 + - - +
117D SER 2.8 7.8 + - - +
119D HIS* 1.3 73.0 - - - +
121D ALA* 1.3 63.6 + - - +
123D ARG* 2.9 15.4 + - - +
125D TYR* 3.1 27.1 + - + +
128D LYS* 4.1 17.3 - - + +
129D ALA* 4.1 9.2 - - + +
132D LEU* 3.7 38.8 - - + -
154D SER 5.7 0.2 - - - -
155D TYR* 3.8 17.0 - - + +
158D THR* 3.8 30.3 - - + +
159D LEU* 3.8 26.5 - - + -
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D SER 2.8 15.0 + - - +
118D LEU* 3.4 17.5 - - + +
120D LEU* 1.3 71.1 - - - +
122D GLN* 1.3 58.4 + - - +
124D ASP* 2.8 26.7 + - - +
125D TYR 4.5 6.1 - - - +
126D GLY* 4.7 5.5 + - - +
129D ALA* 3.9 15.5 - - + +
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU 2.9 15.3 + - - +
119D HIS* 3.2 15.2 - - - +
121D ALA* 1.3 75.4 - - - +
123D ARG* 1.3 93.6 + - - +
124D ASP* 3.5 7.8 + - - +
227D GLN* 3.0 29.1 + - - +
231D GLU* 4.5 2.3 - - - +
288D ILE* 5.1 6.1 + - - +
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D HIS* 3.2 34.9 + - - +
120D LEU 2.9 7.9 + - - +
122D GLN* 1.3 100.8 + - - +
124D ASP* 1.3 70.4 + - - +
125D TYR* 3.3 30.0 - - + -
159D LEU* 4.2 12.1 - - + -
227D GLN* 3.5 11.7 + - - +
230D TYR* 3.2 36.1 - - + +
231D GLU* 3.1 41.0 + - - +
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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