Contacts of the helix formed by residues 109 - 141 (chain D) in PDB entry 5X11
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 109 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C PHE* 4.1 0.9 - - - -
108D LEU* 1.3 74.8 - - - +
110D ARG* 1.3 58.5 + - - +
111D GLN* 3.3 9.6 + - - +
112D GLU* 2.8 44.3 + - - +
113D ALA* 2.9 27.5 + - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C SER* 6.2 0.4 - - - -
147C PHE* 3.6 45.4 - - + +
148C SER* 3.7 21.2 + - - -
109D SER* 1.3 72.4 - - - +
111D GLN* 1.3 56.9 + - - +
113D ALA* 3.5 2.3 + - - +
114D SER* 3.0 26.5 + - - -
178D MET 4.8 2.6 + - - -
179D ILE* 2.6 44.7 + - + +
180D ASP* 4.1 15.5 + - - +
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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
----------------------------------------------------------
109D SER* 3.1 8.3 + - - +
110D ARG* 1.3 76.7 - - - +
112D GLU* 1.3 66.2 + - + +
114D SER* 3.1 15.0 + - - -
115D ASP* 3.0 26.7 + - + +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C HIS* 3.2 33.8 + - - -
85C ILE* 4.3 15.2 - - + +
107D SER 4.6 0.2 - - - +
108D LEU* 3.7 19.8 - - + +
109D SER* 2.8 40.2 + - - +
111D GLN* 1.3 77.3 - - + +
113D ALA* 1.3 57.0 + - - +
115D ASP* 3.4 7.5 + - - +
116D LEU* 3.1 27.2 + - - +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C PHE* 3.9 16.2 - - + -
105D ILE* 3.7 28.7 - - + -
108D LEU* 4.3 12.7 - - + +
109D SER 2.9 16.6 + - - +
110D ARG 3.9 2.7 - - - +
112D GLU* 1.3 73.8 - - - +
114D SER* 1.3 64.9 + - - +
115D ASP 3.4 0.2 - - - -
116D LEU* 3.9 3.4 - - - -
117D PHE* 3.1 30.6 + - + +
176D LEU* 4.7 0.5 - - - +
179D ILE* 5.5 5.8 - - + +
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Residues in contact with SER 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG 3.0 14.1 + - - -
111D GLN* 3.1 23.2 + - - -
113D ALA* 1.3 77.4 - - - +
115D ASP* 1.3 52.9 + - - +
117D PHE 3.5 0.3 + - - -
118D THR* 2.8 45.8 + - - -
176D LEU* 3.9 7.6 - - - +
179D ILE* 5.4 2.7 - - - +
180D ASP* 3.2 32.4 + - - -
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Residues in contact with ASP 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 3.9 11.9 + - + +
111D GLN* 3.0 19.0 + - + +
112D GLU* 3.8 7.0 - - - +
114D SER* 1.3 77.9 - - - +
116D LEU* 1.3 56.9 + - - +
118D THR* 4.2 5.5 - - - +
119D ASP* 3.1 27.2 + - - +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU 3.4 27.6 - - - +
85C ILE* 4.9 4.3 - - - -
86C ARG 4.5 7.2 - - - +
87C HIS* 4.8 11.2 - - + -
98D PHE* 3.8 26.2 - - + -
101D LYS* 4.2 30.1 - - + +
105D ILE* 5.9 0.2 - - + -
108D LEU* 4.2 17.5 - - + -
112D GLU 3.1 16.6 + - - +
113D ALA* 4.1 4.7 - - - +
114D SER 3.3 0.4 - - - -
115D ASP* 1.3 76.1 - - - +
117D PHE* 1.3 73.6 + - + +
119D ASP* 3.5 5.9 + - - +
120D GLN* 3.2 23.6 + - - +
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 4.2 7.6 - - + -
98D PHE* 3.9 25.8 - + - -
102D ALA* 4.1 20.6 - - + -
105D ILE* 3.7 22.7 - - + -
113D ALA* 3.1 23.2 + - + +
116D LEU* 1.3 88.3 - - + +
118D THR* 1.3 60.3 + - - +
120D GLN* 3.8 5.1 - - - +
121D LEU* 3.0 29.5 + - - +
171D TRP* 4.0 11.2 - + - -
172D LEU* 3.6 22.5 - - + +
175D ILE* 3.5 37.7 - - + -
176D LEU* 3.5 24.9 - - + +
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Residues in contact with THR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D SER* 2.8 29.3 + - - -
115D ASP* 4.2 4.9 - - - -
117D PHE* 1.3 75.4 - - - +
119D ASP* 1.3 58.8 + - - +
121D LEU* 3.4 6.5 + - + +
122D LEU* 2.9 35.4 + - + +
176D LEU* 3.4 22.1 - - + +
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Residues in contact with ASP 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 3.2 49.7 + - + +
88C GLN 4.8 1.2 + - - +
115D ASP 3.1 20.9 + - - +
116D LEU* 3.8 5.6 - - - +
117D PHE 3.4 0.2 - - - -
118D THR* 1.3 77.7 - - - +
120D GLN* 1.3 62.2 + - - +
122D LEU* 3.5 8.1 + - - +
123D LYS* 3.0 56.6 + - - +
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Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLN 4.8 8.9 + - - -
90C ILE* 3.5 15.0 - - - +
98D PHE* 3.3 50.0 - - + +
116D LEU* 3.2 16.5 + - - +
117D PHE 3.8 4.3 - - - +
118D THR 3.3 0.2 - - - -
119D ASP* 1.3 81.7 + - - +
121D LEU* 1.3 60.6 + - - +
123D LYS* 3.4 4.9 + - - +
124D ARG* 2.9 66.2 + - - +
168D TYR* 4.2 1.1 + - + -
172D LEU* 3.7 19.1 - - + -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PHE 3.0 17.9 + - - +
118D THR* 3.7 5.6 - - + +
120D GLN* 1.3 73.7 - - - +
122D LEU* 1.3 60.0 + - - +
124D ARG* 3.4 1.0 + - - +
125D LYS* 2.9 67.1 + - - +
169D VAL* 3.5 34.8 - - + +
172D LEU* 3.8 15.4 - - + +
173D GLU* 3.9 20.6 - - + +
176D LEU* 4.0 28.0 - - + -
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D THR* 2.9 23.4 + - + +
119D ASP* 3.5 11.4 - - - +
121D LEU* 1.3 77.2 - - - +
123D LYS* 1.3 66.4 + - + +
125D LYS* 3.5 9.7 + - + +
126D ALA* 3.2 21.5 + - + +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 4.2 13.7 - - - -
88C GLN 4.5 17.0 - - - +
89C PRO* 4.9 8.1 - - + -
90C ILE* 3.6 27.5 - - + +
119D ASP* 3.0 49.6 + - - +
120D GLN* 3.8 6.7 - - - +
122D LEU* 1.3 84.8 - - + +
124D ARG* 1.3 56.2 + - - +
126D ALA* 3.2 9.7 + - - +
127D LYS 3.0 21.1 + - - -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ILE* 3.8 26.6 - - + +
91C PRO* 4.8 8.5 + - - +
94C VAL* 6.1 4.8 - - - +
96D ASP* 4.7 7.3 + - - -
98D PHE* 5.6 0.4 - - - +
120D GLN* 2.9 43.7 + - - +
121D LEU 4.2 1.1 - - - +
123D LYS* 1.3 72.2 - - - +
125D LYS* 1.3 61.4 + - - +
126D ALA 3.2 0.2 - - - -
127D LYS* 3.6 12.2 - - - +
128D LEU* 2.9 30.5 + - - +
164D ARG* 6.3 0.6 - - - +
165D GLU* 2.8 47.1 + - - +
168D TYR* 3.4 56.7 + - - -
169D VAL* 3.7 16.3 - - + +
172D LEU* 4.1 6.1 - - + -
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 2.9 48.4 + - + +
122D LEU* 3.7 8.7 - - + +
124D ARG* 1.3 75.2 - - - +
126D ALA* 1.3 58.0 - - - +
128D LEU* 3.5 7.3 + - + +
129D SER* 2.9 30.8 + - - -
169D VAL* 3.8 20.1 - - + +
173D GLU* 4.5 13.9 + - - -
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 3.2 13.1 + - + +
123D LYS* 3.2 12.9 + - - +
124D ARG 3.2 0.4 - - - -
125D LYS* 1.3 75.9 - - - +
127D LYS* 1.3 64.2 + - - +
129D SER* 3.6 6.6 + - - -
130D ASP* 3.2 22.0 + - - +
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ILE* 3.7 22.2 - - + -
91C PRO 3.4 16.5 + - - -
92C GLU* 3.3 28.9 + - - +
94C VAL* 5.2 4.0 - - - +
32D GLN* 3.6 23.5 + - - +
123D LYS 3.0 13.8 + - - +
124D ARG* 3.6 12.2 - - - +
125D LYS 3.3 0.2 - - - -
126D ALA* 1.3 73.4 - - - +
128D LEU* 1.3 65.5 + - - +
130D ASP* 3.1 9.9 + - + +
131D LEU* 3.0 28.5 + - + +
164D ARG* 4.7 5.1 - - - +
165D GLU* 3.4 29.9 + - + +
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ARG 2.9 21.2 + - - +
125D LYS* 3.7 7.2 - - + +
127D LYS* 1.3 71.4 - - - +
129D SER* 1.3 58.3 + - - +
131D LEU* 3.3 4.3 + - - +
132D GLN* 2.8 30.3 + - + +
162D LEU* 3.2 37.5 - - + +
165D GLU* 3.8 13.4 - - + +
166D LYS* 3.7 42.6 - - + +
169D VAL* 4.2 19.7 - - + -
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Residues in contact with SER 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LYS 2.9 19.1 + - - -
126D ALA* 3.8 7.9 - - - -
127D LYS 3.2 0.2 - - - -
128D LEU* 1.3 76.7 - - - +
130D ASP* 1.3 57.1 + - - +
132D GLN* 3.3 8.8 + - - +
133D GLY* 3.0 23.9 + - - -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA 3.2 10.3 + - - +
127D LYS* 3.1 12.2 + - + +
129D SER* 1.3 77.5 + - - +
131D LEU* 1.3 61.4 + - + +
133D GLY* 3.3 4.0 + - - -
134D SER* 3.2 23.1 + - - -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 4.1 28.0 - - + +
127D LYS* 3.0 27.1 + - + +
128D LEU* 3.6 6.7 - - - +
130D ASP* 1.3 72.7 - - + +
132D GLN* 1.3 64.6 + - - +
133D GLY 3.0 1.8 - - - -
134D SER* 3.0 8.7 + - - +
135D TYR* 3.0 23.6 + - - +
158D LEU* 4.1 20.9 - - + +
161D ALA* 3.5 43.5 - - + +
162D LEU* 3.7 15.4 - - + +
165D GLU* 4.2 15.5 - - + +
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Residues in contact with GLN 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 2.8 24.3 + - + +
129D SER* 3.3 10.3 + - - +
131D LEU* 1.3 71.7 - - - +
133D GLY* 1.3 59.8 - - - +
135D TYR* 3.6 28.2 + - - +
136D GLU* 3.2 52.2 + - - +
162D LEU* 3.8 23.2 - - + +
166D LYS* 4.1 14.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D SER 3.0 12.6 + - - -
130D ASP* 3.3 5.6 + - - -
131D LEU 3.0 0.8 - - - -
132D GLN* 1.3 76.5 - - - +
134D SER* 1.3 61.5 + - - +
136D GLU* 3.4 6.4 + - - +
137D LYS* 3.2 22.9 + - - +
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Residues in contact with SER 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP 3.2 13.8 + - - -
131D LEU* 3.0 10.7 + - - +
133D GLY* 1.3 73.5 - - - +
135D TYR* 1.3 60.7 + - - +
137D LYS* 3.4 7.2 + - - +
138D LEU* 3.0 29.3 + - - +
158D LEU* 3.9 24.2 - - - +
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Residues in contact with TYR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D LEU 3.0 16.0 + - - +
132D GLN* 3.8 25.6 - - - +
133D GLY 3.3 0.2 - - - -
134D SER* 1.3 78.2 - - - +
136D GLU* 1.3 61.7 + - + +
138D LEU* 3.7 4.0 + - + +
139D MET* 3.1 58.2 + - + +
155D TYR* 3.9 30.7 + + - -
158D LEU* 4.4 19.5 - - + +
159D THR* 4.1 14.9 - - + +
162D LEU* 4.0 22.9 - - + -
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D GLN* 3.2 47.1 + - - +
133D GLY* 3.4 5.7 + - - +
134D SER 3.2 0.2 - - - -
135D TYR* 1.3 80.4 - - + +
137D LYS* 1.3 65.0 + - - +
138D LEU 3.3 0.2 - - - -
139D MET* 3.4 6.1 + - + +
140D ALA* 3.1 24.6 + - - +
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D GLY 3.2 17.0 + - - +
134D SER* 3.4 7.4 + - - +
136D GLU* 1.3 79.0 - - - +
138D LEU* 1.3 58.3 + - - +
140D ALA* 3.8 6.8 + - - +
141D SER* 3.8 15.8 + - - -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER 3.0 17.4 + - - +
135D TYR* 3.9 6.1 - - + +
137D LYS* 1.3 77.4 - - - +
139D MET* 1.3 69.9 + - - +
141D SER* 3.4 21.7 + - - +
145D MET* 4.7 6.1 - - + +
151D ASP* 4.1 30.1 - - + +
154D HIS* 4.2 19.7 - - + +
155D TYR* 3.9 42.2 - - + +
158D LEU* 4.0 20.0 - - + -
----------------------------------------------------------
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Residues in contact with MET 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D TYR* 3.1 51.3 + - + +
136D GLU* 3.4 7.3 + - - +
138D LEU* 1.3 86.0 - - - +
140D ALA* 1.3 65.9 + - - +
141D SER 3.3 5.5 + - - -
144D PRO* 5.1 11.5 - - + +
145D MET* 4.0 25.8 - - + +
155D TYR* 3.7 31.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLU 3.1 17.0 + - - +
137D LYS* 4.0 8.3 - - - +
138D LEU 3.4 0.2 - - - -
139D MET* 1.3 75.0 - - - +
141D SER* 1.3 60.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LYS 3.8 9.0 + - - -
138D LEU* 3.4 22.2 + - - +
139D MET 3.2 9.1 - - - -
140D ALA* 1.3 82.6 - - - +
144D PRO* 5.9 7.8 - - - +
151D ASP* 4.7 11.5 - - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il