Contacts of the helix formed by residues 113 - 140 (chain B) in PDB entry 4IVR
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 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.7 1.3 - - - -
112B ILE* 1.3 79.5 - - - +
114B ALA* 1.3 56.9 - - - +
115B GLY* 3.4 4.4 + - - -
116B ASP* 3.0 35.9 + - - +
117B ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.6 19.4 - - + +
113B SER* 1.3 73.9 - - - +
115B GLY* 1.3 56.8 + - - +
117B ALA* 3.4 3.4 + - - +
118B ALA* 3.0 29.8 + - - +
180B GLY 4.2 16.9 - - - +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 3.1 6.7 + - - -
114B ALA* 1.3 75.3 - - - +
116B ASP* 1.3 65.7 + - - +
118B ALA* 3.3 15.0 + - - +
119B VAL* 3.4 19.7 + - - +
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.3 16.0 - - + +
113B SER* 3.0 30.1 + - - +
115B GLY* 1.3 76.5 - - - +
117B ALA* 1.3 62.7 + - - +
119B VAL* 3.1 24.6 - - - +
120B VAL* 3.5 11.4 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 4.0 11.1 - - + +
107B LEU* 4.0 26.2 - - + -
112B ILE* 4.0 19.2 - - + +
113B SER 2.9 16.6 + - - +
114B ALA 3.6 5.6 - - - +
115B GLY 3.2 0.2 - - - -
116B ASP* 1.3 76.2 - - - +
118B ALA* 1.3 53.1 + - - +
120B VAL* 3.3 3.5 + - - +
121B MET* 2.8 37.8 + - - +
181B SER* 3.9 11.0 - - - -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA 3.0 16.9 + - - +
115B GLY* 3.3 8.0 + - - +
117B ALA* 1.3 77.2 - - - +
119B VAL* 1.3 55.4 + - + +
121B MET* 3.7 0.7 - - - +
122B THR* 2.7 39.3 + - - +
181B SER 3.2 17.0 + - - +
182B MET* 3.8 7.3 - - - +
183B THR* 4.2 26.0 - - + +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 5.8 4.9 - - - +
119A VAL* 4.3 16.2 - - + +
120A VAL* 4.8 17.3 - - + +
123A SER* 2.8 37.2 + - - +
115B GLY 3.4 10.7 + - - +
116B ASP* 3.1 20.2 - - - +
118B ALA* 1.3 74.5 - - + +
120B VAL* 1.3 75.2 + - + +
123B SER* 3.0 19.2 + - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 4.3 22.2 - - + -
99B ASN* 3.7 23.5 + - - +
100B ILE* 5.8 0.2 - - - -
103B THR* 3.4 33.2 - - + +
112B ILE* 6.0 2.0 - - + -
116B ASP 3.5 12.8 - - - +
117B ALA 3.3 7.1 + - - +
119B VAL* 1.3 78.8 - - + +
121B MET* 1.3 60.6 + - - +
123B SER* 3.3 5.4 + - - -
124B ALA* 2.9 28.8 + - + +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.1 48.9 - - + +
103B THR* 4.3 6.1 - - + -
104B GLN* 3.9 13.7 - - + +
117B ALA 2.8 13.8 + - - +
118B ALA 3.7 0.2 - - - +
120B VAL* 1.3 79.3 - - - +
122B THR* 1.3 61.9 + - - +
124B ALA* 4.1 1.9 - - - +
125B GLN* 3.1 34.6 + - - +
176B ARG* 3.6 39.7 - - - +
181B SER* 3.2 39.3 - - - +
182B MET* 3.3 10.8 - - + -
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR 5.2 0.2 - - - +
123A SER* 3.2 34.0 + - - +
126A ILE* 4.7 10.1 - - + -
118B ALA* 2.7 23.2 + - - +
120B VAL 3.3 0.2 - - - -
121B MET* 1.3 80.0 - - - +
123B SER* 1.3 62.0 + - - +
125B GLN* 3.4 0.6 + - - -
126B ILE* 3.3 21.4 + - + +
182B MET* 3.2 20.7 - - - +
186B ALA* 3.9 15.1 - - + +
190B PHE* 3.6 25.7 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 2.7 49.2 + - - -
122A THR* 3.3 24.0 - - - +
123A SER 3.7 1.6 + - - -
119B VAL 3.0 13.9 + - - -
120B VAL 3.7 2.9 - - - -
122B THR* 1.3 78.2 - - - +
124B ALA* 1.3 62.1 + - - +
126B ILE* 3.4 17.9 + - - +
127B THR* 3.5 9.2 + - - -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 3.5 9.8 - - + +
99B ASN* 3.8 23.3 - - - +
100B ILE* 3.8 23.8 - - + -
120B VAL* 2.9 18.7 + - + +
121B MET* 4.2 2.5 - - - +
122B THR 3.3 0.2 - - - -
123B SER* 1.3 76.7 - - - +
125B GLN* 1.3 58.1 + - - +
127B THR* 3.1 10.5 + - - -
128B MET* 3.0 27.8 + - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 4.3 14.1 - - + +
121B MET* 3.1 23.7 + - - +
122B THR 4.0 3.4 - - - +
123B SER 3.3 0.2 - - - -
124B ALA* 1.3 75.1 - - - +
126B ILE* 1.3 65.1 + - - +
128B MET* 3.3 4.2 + - - +
129B GLY* 3.1 19.1 + - - -
168B ALA* 4.5 3.8 - - - +
172B TYR* 3.4 10.7 + - - +
173B PRO* 3.3 28.8 - - - +
176B ARG* 3.8 19.3 - - - +
182B MET* 3.6 19.2 - - - +
190B PHE* 4.1 15.7 - - + -
401B N50 3.2 37.5 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 4.6 11.2 - - + -
126A ILE* 4.2 23.1 - - + -
186A ALA* 5.0 6.3 - - + +
189A ALA* 3.6 26.8 - - + +
190A PHE* 4.4 14.8 - - + -
193A LEU* 4.5 16.2 - - + -
122B THR* 3.3 16.7 + - + +
123B SER* 3.4 9.9 - - - +
125B GLN* 1.3 75.7 - - - +
127B THR* 1.3 65.4 + - - +
129B GLY* 3.0 11.7 + - - -
130B MET* 3.1 13.9 + - - +
169B LEU* 5.5 3.8 - - + -
190B PHE* 3.7 28.7 - - + -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA* 5.8 3.8 - - - +
189A ALA* 5.6 0.9 - - - -
87B TYR* 3.5 39.4 - - + +
88B TRP* 4.1 1.3 - - - -
92B GLY* 4.2 7.3 + - - -
93B ALA* 4.2 20.4 - - + +
96B THR* 3.6 25.8 - - + +
123B SER 3.5 9.4 + - - -
124B ALA* 3.1 13.3 + - - -
126B ILE* 1.3 81.2 - - - +
128B MET* 1.3 63.3 + - - +
129B GLY 3.3 0.7 + - - -
130B MET* 3.6 6.3 + - - -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP* 2.9 65.5 + - + +
96B THR* 3.5 25.1 - - + -
97B ILE* 3.5 26.0 - - + -
100B ILE* 3.9 16.2 - - + -
124B ALA 3.0 19.2 + - - +
125B GLN* 3.6 8.7 - - - +
126B ILE 3.2 0.4 - - - -
127B THR* 1.3 76.3 - - - +
129B GLY* 1.3 59.6 + - - +
130B MET 3.8 0.3 + - - -
131B PRO* 3.8 3.3 - - - +
132B TYR* 4.0 6.4 - - - -
168B ALA* 4.5 1.1 - - - -
401B N50 3.7 42.0 - - + +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLN 3.1 8.2 + - - -
126B ILE* 3.0 6.8 + - - -
128B MET* 1.3 77.8 - - - +
130B MET* 1.3 65.1 - - - +
131B PRO* 3.4 1.1 - - - -
132B TYR* 3.0 10.1 + - - +
133B ALA* 3.0 23.7 + - - +
168B ALA* 3.5 24.9 - - - -
169B LEU* 6.2 2.2 - - - -
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Residues in contact with MET 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.5 14.1 - - + -
189A ALA* 3.6 29.8 - - + +
192A ALA* 5.1 0.4 - - + -
307A VAL* 3.6 23.8 - - + +
308A PHE* 3.7 25.4 - - + -
311A ALA* 4.5 2.7 - - + -
87B TYR* 3.3 33.9 - - + +
126B ILE 3.1 13.0 + - - +
127B THR* 3.8 6.5 - - - +
128B MET 3.5 0.2 - - - -
129B GLY* 1.3 75.3 - - - +
131B PRO* 1.3 70.6 - - + +
133B ALA* 3.2 6.4 + - - +
134B VAL* 2.9 44.3 + - + +
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Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 4.5 0.4 - - + -
84B PRO* 3.9 33.9 - - + -
87B TYR* 3.7 28.7 - - + -
88B TRP* 4.5 0.9 - - - +
127B THR 3.9 6.3 - - - +
128B MET 3.8 9.9 - - - +
129B GLY 3.5 4.7 - - - -
130B MET* 1.3 96.6 - - + +
132B TYR* 1.3 60.4 + - - +
134B VAL* 3.1 10.9 - - + +
135B THR* 2.9 31.4 + - - -
368B PHE* 4.0 13.9 - - + -
372B MET* 4.2 5.2 - - - -
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO 5.6 0.7 - - - -
83B GLU* 5.2 0.7 - - - +
84B PRO* 3.9 19.1 - - + +
88B TRP* 3.1 29.0 - + - -
128B MET 4.0 14.1 - - - -
129B GLY* 3.0 7.2 + - - +
131B PRO* 1.3 78.6 - - + +
133B ALA* 1.3 62.3 + - - +
135B THR* 3.5 5.9 + - - -
136B ASP* 3.1 23.4 + - - +
162B ASP* 3.4 20.0 + - - -
163B ARG* 3.3 33.9 - - + +
164B HIS 4.3 10.5 - - - -
165B PRO* 3.8 25.0 - - + +
167B ALA* 5.1 0.4 - - + -
168B ALA* 4.0 18.8 - - + -
368B PHE* 5.5 4.5 - + - -
401B N50 3.9 22.0 - - + -
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 4.3 11.7 - - + +
193A LEU* 3.7 34.3 - - + -
129B GLY 3.0 13.0 + - - +
130B MET* 3.7 9.0 - - - +
132B TYR* 1.3 74.9 - - - +
134B VAL* 1.3 64.8 + - - +
136B ASP* 3.4 6.3 + - - +
137B ALA* 3.1 22.7 + - - +
165B PRO* 4.9 5.6 - - + +
169B LEU* 5.3 5.2 - - + -
195B PRO* 5.4 5.2 - - + +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 3.4 25.4 - - + -
307A VAL* 3.8 20.9 - - + +
310A TRP* 4.6 16.8 - - + -
311A ALA* 4.3 10.5 - - + +
314A VAL* 4.6 1.5 - - - +
130B MET* 2.9 44.7 + - + +
131B PRO* 3.1 22.0 - - + +
133B ALA* 1.3 71.8 - - - +
135B THR* 1.3 69.7 + - - +
137B ALA* 3.2 5.7 + - - +
138B VAL* 3.1 29.3 + - - +
368B PHE* 5.5 0.7 - - + -
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 5.2 1.9 - - - -
81B VAL* 5.0 7.2 - - + -
131B PRO 2.9 19.9 + - - -
132B TYR* 3.6 6.7 - - - +
133B ALA 3.2 0.2 - - - -
134B VAL* 1.3 79.2 - - - +
136B ASP* 1.3 67.2 - - - +
138B VAL* 3.4 10.0 - - - +
139B LEU* 3.1 25.9 + - + +
161B PHE* 4.0 29.6 - - + -
364B LEU* 4.6 16.0 - - + +
368B PHE* 3.4 23.4 - - - -
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 5.8 0.9 + - - -
53B TYR* 4.6 12.2 + - + +
132B TYR 3.1 13.6 + - - +
133B ALA 3.8 4.0 - - - +
134B VAL 3.4 0.2 - - - -
135B THR* 1.3 81.5 - - - +
137B ALA* 1.3 61.0 + - - +
139B LEU* 3.8 4.3 - - - +
140B ALA* 3.1 31.9 + - - +
164B HIS* 5.2 5.5 + - - -
165B PRO* 4.1 18.2 - - + +
195B PRO* 3.2 33.1 - - + +
196B PRO* 4.9 5.6 - - - +
198B LEU* 4.7 12.4 - - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 4.3 11.9 - - - +
314A VAL* 3.7 27.6 - - + -
318A ARG* 4.4 17.1 + - - +
133B ALA 3.1 16.6 + - - +
134B VAL* 3.6 5.2 - - - +
135B THR 3.1 1.0 - - - -
136B ASP* 1.3 83.1 - - - +
138B VAL* 1.3 59.4 + - - +
140B ALA* 3.8 5.1 + - - +
141B PRO* 3.6 15.4 - - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 3.8 41.1 - - + +
313A ASP* 4.7 8.1 - - + +
314A VAL* 4.1 6.3 - - + -
134B VAL 3.1 13.1 + - - +
135B THR* 3.4 19.1 - - - +
137B ALA* 1.3 75.5 - - - +
139B LEU* 1.3 62.4 + - + +
140B ALA 3.5 0.2 - - - -
141B PRO* 3.7 6.9 - - - +
142B HIS* 3.5 18.9 + - - -
364B LEU* 3.8 31.4 - - + -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 4.8 5.2 - - - +
53B TYR* 6.0 0.7 - - - +
135B THR* 3.1 22.1 + - + +
136B ASP* 3.3 6.3 + - - +
137B ALA 3.3 0.4 - - - -
138B VAL* 1.3 80.2 - - + +
140B ALA* 1.3 66.7 + - - +
141B PRO 3.4 0.4 - - - -
142B HIS* 3.0 18.7 + - + +
143B ILE* 3.5 25.3 - - + +
159B LEU* 4.7 19.5 - - + -
161B PHE* 5.2 5.2 - - + -
198B LEU* 6.1 0.4 - - + -
361B ILE* 4.9 15.3 - - + -
364B LEU* 6.2 3.4 - - + -
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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
----------------------------------------------------------
318A ARG* 6.4 0.2 - - - +
136B ASP* 3.1 19.0 + - - +
137B ALA* 4.0 5.8 - - - +
139B LEU* 1.3 77.5 - - - +
141B PRO* 1.3 63.1 - - + +
143B ILE* 3.0 27.0 + - - +
198B LEU* 3.6 32.9 - - + +
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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