Contacts of the helix formed by residues 109 - 141 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.8 1.8 - - - -
108B LEU* 1.3 74.3 - - - +
110B ARG* 1.3 67.5 + - - +
111B GLN* 3.9 7.5 + - - +
112B GLU* 3.0 37.3 + - - +
113B ALA* 3.0 20.6 + - - +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.5 35.2 - - + -
109B SER* 1.3 70.8 - - - +
111B GLN* 1.3 56.3 + - - +
113B ALA 3.6 0.2 + - - -
114B SER* 3.0 31.1 + - - -
179B ILE* 3.6 17.1 - - - +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 3.1 8.8 + - - +
110B ARG* 1.3 79.7 - - - +
112B GLU* 1.3 57.7 - - + +
114B SER* 3.4 12.2 + - - -
115B ASP* 3.0 30.4 + - + +
180B ASP* 5.4 1.2 + - - -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A HIS* 3.4 28.0 + - - -
85A ILE* 4.3 14.2 - - + +
107B SER 4.3 1.6 - - - +
108B LEU* 3.6 23.1 - - + +
109B SER* 3.0 38.1 + - - +
111B GLN* 1.3 80.4 - - + +
113B ALA* 1.3 57.6 + - - +
115B ASP* 3.5 6.5 + - - +
116B LEU* 2.9 29.0 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 4.0 11.9 - - + -
105B ILE* 4.0 31.2 - - + -
108B LEU* 4.1 15.0 - - + +
109B SER 3.0 14.9 + - - +
110B ARG 3.9 3.1 - - - +
112B GLU* 1.3 74.7 - - - +
114B SER* 1.3 59.2 + - - +
116B LEU* 3.6 2.0 - - - +
117B PHE* 2.8 38.3 + - + +
179B ILE* 4.0 6.7 - - + -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG 3.0 19.8 + - - -
111B GLN* 3.6 15.2 + - - -
113B ALA* 1.3 74.5 - - - +
115B ASP* 1.3 52.3 + - - +
117B PHE 3.7 0.2 - - - -
118B THR* 2.6 46.1 + - - -
176B LEU* 3.8 5.8 - - - +
179B ILE* 3.7 14.1 - - - +
180B ASP* 2.7 35.1 + - - -
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.1 10.3 + - + +
111B GLN* 3.0 20.8 + - + +
112B GLU* 3.6 7.0 - - - +
114B SER* 1.3 76.0 - - - +
116B LEU* 1.3 61.3 + - - +
118B THR* 3.9 5.7 - - - -
119B ASP* 3.2 24.6 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.6 25.6 - - - +
85A ILE* 5.0 3.8 - - - +
86A ARG 4.1 15.0 - - - +
87A HIS* 4.2 16.1 + - + -
98B PHE* 4.0 24.2 - - + -
101B LYS* 4.1 24.0 - - + +
108B LEU* 4.2 17.3 - - + -
112B GLU 2.9 19.6 + - - +
113B ALA* 3.3 5.6 + - - +
115B ASP* 1.3 77.6 - - - +
117B PHE* 1.3 72.9 + - + +
119B ASP* 3.3 5.6 + - - +
120B GLN* 3.2 21.5 + - - +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.1 17.5 - - + -
98B PHE* 3.7 23.6 - + - -
102B ALA* 4.3 11.4 - - + -
105B ILE* 3.8 19.7 - - + -
108B LEU* 6.0 0.7 - - + -
113B ALA* 2.8 29.9 + - + +
116B LEU* 1.3 81.2 - - + +
118B THR* 1.3 65.6 + - - +
120B GLN* 3.3 7.3 + - - +
121B LEU* 3.1 22.9 + - - +
171B TRP* 3.9 18.2 - + - -
172B LEU* 3.6 22.9 - - + +
175B ILE* 3.6 29.6 - - + -
176B LEU* 3.9 20.3 - - + +
179B ILE* 3.7 9.4 - - + -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 2.6 36.8 + - - -
115B ASP* 3.9 6.2 - - - -
117B PHE* 1.3 71.0 - - - +
119B ASP* 1.3 64.2 + - - +
121B LEU* 3.1 17.4 + - + +
122B LEU* 3.1 27.9 + - + +
176B LEU* 3.7 22.5 - - + +
180B ASP* 4.9 0.2 + - - -
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 3.4 42.3 + - + +
88A GLN 5.0 0.3 - - - +
115B ASP 3.2 12.2 + - - +
116B LEU* 3.3 10.1 + - - +
118B THR* 1.3 78.9 - - - +
120B GLN* 1.3 68.2 + - - +
122B LEU* 3.4 10.7 + - - +
123B LYS* 3.1 57.6 + - - +
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN 4.7 8.1 + - - -
90A ILE* 3.4 17.2 - - - +
98B PHE* 3.7 47.3 - - + +
116B LEU* 3.2 12.3 + - - +
117B PHE 3.5 8.7 - - - +
118B THR 3.2 0.2 - - - -
119B ASP* 1.3 83.9 + - - +
121B LEU* 1.3 52.7 + - - +
123B LYS* 3.3 6.0 + - - +
124B ARG* 2.8 69.9 + - + +
168B TYR* 4.4 1.0 + - + -
172B LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE 3.1 10.2 + - - +
118B THR* 3.4 12.8 - - + +
120B GLN* 1.3 80.4 - - - +
122B LEU* 1.3 55.1 + - + +
124B ARG* 3.1 1.6 + - - +
125B LYS* 2.8 50.2 + - + +
169B VAL* 3.8 36.8 - - + +
172B LEU* 3.9 17.0 - - + +
173B GLU* 3.7 36.1 - - + +
176B LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.1 24.3 + - + +
119B ASP* 3.8 11.2 - - - +
121B LEU* 1.3 81.9 - - + +
123B LYS* 1.3 62.0 + - + +
125B LYS* 3.7 11.3 + - + +
126B ALA* 3.2 22.3 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.6 7.3 - - - +
88A GLN 3.9 22.0 - - - +
89A PRO* 4.8 3.8 - - + -
90A ILE* 4.2 32.1 - - + +
119B ASP* 3.1 43.4 + - - +
120B GLN* 3.6 9.4 - - - +
121B LEU 3.2 0.4 - - - -
122B LEU* 1.3 76.1 - - + +
124B ARG* 1.3 60.5 + - - +
126B ALA* 3.0 9.0 + - - +
127B LYS* 2.9 29.3 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.9 26.4 - - + +
91A PRO* 4.7 12.9 + - - +
94A VAL* 5.9 5.3 - - - +
96B ASP* 4.4 7.7 + - - -
98B PHE* 5.3 0.8 - - - +
120B GLN* 2.8 49.0 + - + +
121B LEU* 3.7 6.1 - - - +
123B LYS* 1.3 72.4 - - - +
125B LYS* 1.3 57.5 + - - +
127B LYS* 3.6 4.3 + - - +
128B LEU* 3.0 25.8 + - - +
164B ARG* 6.0 0.4 - - - +
165B GLU* 2.7 54.3 + - - +
168B TYR* 3.6 42.2 + - - -
169B VAL* 3.9 18.5 - - + +
172B LEU* 3.9 15.0 - - + -
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 2.8 37.7 + - + +
122B LEU* 4.0 12.8 - - + +
124B ARG* 1.3 73.9 - - - +
126B ALA* 1.3 60.5 + - - +
128B LEU* 3.2 14.7 + - + +
129B SER* 2.9 31.6 + - - -
169B VAL* 4.0 22.7 - - + -
173B GLU* 4.5 11.8 + - - +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU 3.2 14.7 + - - +
123B LYS* 3.0 11.8 + - - +
125B LYS* 1.3 77.6 - - - +
127B LYS* 1.3 60.3 + - - +
129B SER* 3.3 9.1 + - - -
130B ASP* 3.2 20.1 + - - +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.7 21.3 - - + +
91A PRO 3.7 13.3 + - - -
92A GLU* 3.6 19.6 + - - +
32B GLN* 3.2 35.2 + - - +
123B LYS 2.9 15.2 + - - +
124B ARG* 3.7 5.9 - - - +
126B ALA* 1.3 74.0 - - - +
128B LEU* 1.3 60.0 + - - +
130B ASP* 3.3 8.0 + - + +
131B LEU* 3.0 34.4 + - + +
164B ARG* 4.6 4.4 - - - +
165B GLU* 3.4 36.7 + - + +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG 3.0 17.7 + - - +
125B LYS* 3.2 15.5 + - + +
127B LYS* 1.3 74.2 - - - +
129B SER* 1.3 59.4 + - - +
131B LEU* 3.3 4.8 + - + -
132B GLN* 2.8 45.0 + - - +
162B LEU* 3.8 34.3 - - + +
165B GLU* 4.3 9.2 - - + -
166B LYS* 3.8 26.5 - - + +
169B VAL* 4.1 26.5 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS 2.9 13.9 + - - -
126B ALA* 3.4 12.7 - - - -
127B LYS 3.3 0.2 - - - -
128B LEU* 1.3 75.0 - - - +
130B ASP* 1.3 63.0 + - - +
132B GLN* 3.1 8.0 + - - +
133B GLY* 2.9 22.3 + - - -
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 3.2 10.1 + - - +
127B LYS* 3.3 10.5 + - + +
129B SER* 1.3 78.5 - - - +
131B LEU* 1.3 58.6 + - + +
133B GLY* 3.4 1.8 + - - -
134B SER* 3.1 31.7 + - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 4.4 15.5 - - + +
127B LYS* 3.0 29.8 + - + +
128B LEU* 3.7 5.2 - - - +
130B ASP* 1.3 75.4 - - + +
132B GLN* 1.3 63.7 + - - +
134B SER* 3.3 8.5 + - - +
135B TYR* 3.1 22.5 + - - +
158B LEU* 3.7 19.6 - - + +
161B ALA* 3.4 45.1 - - + +
162B LEU* 4.0 14.0 - - + +
165B GLU* 3.7 22.0 - - + -
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Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 2.8 35.2 + - - +
129B SER* 3.6 6.9 + - - +
131B LEU* 1.3 72.0 - - - +
133B GLY* 1.3 63.2 + - - +
135B TYR* 3.3 8.4 + - + +
136B GLU* 3.3 34.8 + - + +
162B LEU* 3.8 23.1 - - + +
166B LYS* 3.8 28.5 - - - +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER 2.9 13.0 + - - -
130B ASP* 3.8 3.4 - - - -
132B GLN* 1.3 77.7 - - - +
134B SER* 1.3 61.2 + - - +
136B GLU* 3.3 13.7 + - - +
137B LYS* 3.1 21.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP 3.1 15.7 + - - -
131B LEU* 3.6 13.3 - - - +
132B GLN 3.3 0.2 - - - -
133B GLY* 1.3 71.6 - - - +
135B TYR* 1.3 66.3 + - - +
137B LYS* 3.2 9.5 + - - +
138B LEU* 3.0 23.4 + - - +
158B LEU* 3.9 17.0 - - - +
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU 3.1 12.5 + - - +
132B GLN* 3.3 13.0 - - + +
133B GLY 3.3 0.2 - - - -
134B SER* 1.3 76.1 - - - +
136B GLU* 1.3 65.2 + - + +
138B LEU* 3.0 6.3 + - + +
139B MET* 2.9 66.0 + - + +
155B TYR* 3.8 20.4 + + - -
158B LEU* 3.9 19.7 - - + +
159B THR* 3.7 27.3 - - + +
162B LEU* 3.8 23.3 - - + -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 3.7 24.6 - - + +
133B GLY* 3.3 11.2 + - - +
134B SER 3.3 0.2 - - - -
135B TYR* 1.3 87.3 - - + +
137B LYS* 1.3 61.6 + - - +
139B MET* 3.1 17.4 + - - +
140B ALA* 3.3 15.2 + - - +
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 3.1 14.0 + - - +
134B SER* 3.2 12.3 + - - +
136B GLU* 1.3 76.4 - - - +
138B LEU* 1.3 59.4 + - - +
140B ALA* 4.7 3.5 - - - +
141B SER* 3.7 17.7 + - - -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER 3.0 12.8 + - - +
135B TYR* 3.0 9.4 + - + +
137B LYS* 1.3 76.8 - - - +
139B MET* 1.3 72.2 + - - +
141B SER* 3.3 22.4 + - - -
145B MET* 5.1 13.0 - - + +
151B ASP* 5.2 8.4 - - + +
154B HIS* 4.5 32.5 - - + +
155B TYR* 5.2 6.5 - - + +
158B LEU* 4.2 11.9 - - + -
----------------------------------------------------------
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 2.9 61.9 + - + +
136B GLU* 3.1 7.9 + - - +
138B LEU* 1.3 81.1 - - - +
140B ALA* 1.3 63.6 + - - +
141B SER 3.4 3.8 + - - -
145B MET* 4.2 24.2 - - + -
155B TYR* 3.4 27.4 - - + +
----------------------------------------------------------
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU 3.3 11.9 + - - +
137B LYS* 4.7 4.3 - - - +
139B MET* 1.3 78.6 - - - +
141B SER* 1.3 60.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS 3.7 13.7 + - - -
138B LEU* 3.3 20.6 + - - -
139B MET 3.2 3.7 - - - -
140B ALA* 1.3 83.9 - - - +
151B ASP* 4.9 13.3 - - - +
----------------------------------------------------------
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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