Contacts of the helix formed by residues 154 - 179 (chain A) in PDB entry 2VT4
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 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.4 15.8 - - - +
150A GLN 5.7 1.1 - - - +
151A SER 5.0 4.9 - - - +
152A LEU 3.4 11.7 + - - +
153A MET* 1.3 79.9 - - - +
155A ARG* 1.3 60.1 + - - +
156A ALA* 3.7 7.8 + - - +
157A ARG* 3.2 31.8 + - - +
158A ALA* 3.0 21.7 + - - +
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Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 4.5 29.6 - - - +
74A THR 6.2 0.6 - - - -
75A LEU* 4.0 8.7 - - + +
78A LEU* 4.0 36.0 - - + +
154A THR* 1.3 72.0 - - - +
156A ALA* 1.3 66.6 + - - +
157A ARG 3.1 0.2 - - - -
158A ALA* 3.4 1.7 + - - +
159A LYS* 3.0 64.9 + - - +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 3.4 7.2 + - - +
155A ARG* 1.3 78.4 - - - +
157A ARG* 1.3 63.1 + - - +
159A LYS* 3.5 10.6 + - - +
160A VAL* 3.2 25.4 + - - +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER 4.3 3.8 + - - -
152A LEU* 2.7 57.9 + - - +
153A MET* 4.7 7.0 - - - +
154A THR* 3.2 26.6 + - - +
155A ARG 3.1 0.4 - - - -
156A ALA* 1.3 78.9 - - - +
158A ALA* 1.3 65.4 + - - +
160A VAL* 3.0 12.9 + - + +
161A ILE* 2.9 28.9 + - + +
205B ARG* 5.0 11.8 - - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.2 9.4 - - + +
78A LEU* 4.1 18.6 - - + -
79A PHE* 4.0 22.3 - - + -
153A MET* 4.5 3.1 - - - -
154A THR 3.0 17.2 + - - +
155A ARG 3.8 4.5 - - - +
157A ARG* 1.3 76.4 - - - +
159A LYS* 1.3 57.4 + - - +
161A ILE* 3.1 16.1 + - - +
162A ILE* 2.8 32.9 + - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.5 16.6 - - + -
155A ARG* 3.0 56.7 + - - +
156A ALA* 3.7 11.7 - - - +
158A ALA* 1.3 73.2 - - - +
160A VAL* 1.3 65.9 + - + +
162A ILE* 3.2 14.6 + - + +
163A CYS* 3.0 33.1 + - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA 3.2 12.2 + - - +
157A ARG* 3.0 15.1 + - + +
159A LYS* 1.3 77.1 - - - +
161A ILE* 1.3 61.2 + - + +
163A CYS* 3.2 6.8 + - - +
164A THR* 2.9 31.9 + - - +
206B ALA* 4.0 27.4 - - + +
402B SOG 4.7 22.0 - - - +
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 4.6 7.0 - - + -
134A VAL* 4.0 34.8 - - + -
153A MET* 4.0 27.4 - - + -
157A ARG* 2.9 23.8 + - + +
158A ALA* 3.1 15.0 + - - +
160A VAL* 1.3 78.3 - - + +
162A ILE* 1.3 61.5 + - - +
164A THR* 3.5 8.3 + - - -
165A VAL* 3.1 24.0 + - + +
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.6 37.7 - - + +
79A PHE* 4.0 17.3 - - + -
82A SER* 3.6 28.5 - - - +
131A THR* 6.2 0.2 - - + -
158A ALA 2.8 19.7 + - - +
159A LYS* 3.5 19.5 - - + +
161A ILE* 1.3 72.6 - - - +
163A CYS* 1.3 65.1 + - - +
165A VAL* 3.2 7.8 + - - +
166A TRP* 3.0 40.3 + - + +
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Residues in contact with CYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 3.0 23.5 + - - +
160A VAL* 3.7 5.2 - - - +
162A ILE* 1.3 81.4 - - - +
164A THR* 1.3 57.6 + - - +
166A TRP* 3.7 7.4 - - - +
167A ALA* 2.7 36.1 + - - +
402B SOG 3.7 39.7 + - - +
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 2.9 18.4 + - - +
161A ILE* 3.7 9.1 - - - -
163A CYS* 1.3 75.7 - - - +
165A VAL* 1.3 58.2 + - + +
167A ALA* 3.4 5.7 - - - +
168A ILE* 2.9 40.6 + - + +
206B ALA* 3.3 27.8 - - + +
210B ALA* 3.8 29.2 - - + -
402B SOG 4.0 18.5 - - + -
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 5.7 0.2 - - - +
127A ALA* 4.2 5.8 - - + +
130A GLU* 3.4 31.3 - - + +
131A THR* 3.8 22.0 - - - +
134A VAL* 3.8 28.0 - - + -
161A ILE* 3.1 18.3 + - + +
162A ILE* 3.3 12.1 - - - +
164A THR* 1.3 78.0 - - + +
166A TRP* 1.3 62.3 + - + +
168A ILE* 4.7 4.9 - - + -
169A SER* 2.8 34.4 + - - +
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Residues in contact with TRP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 3.0 31.9 + - - +
85A CYS* 4.5 8.5 - - + -
86A ALA* 3.8 35.9 - - + -
89A VAL* 5.4 6.1 - - + -
123A LEU* 3.9 36.9 - - + +
124A CYS* 5.1 6.1 - - - -
127A ALA* 4.0 27.5 - - + +
131A THR* 5.0 1.4 + - - -
162A ILE* 3.0 37.6 + - + +
163A CYS* 3.2 7.4 + - - +
165A VAL* 1.3 76.5 - - + +
167A ALA* 1.3 60.6 + - - +
169A SER* 3.2 5.1 + - - -
170A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS 2.7 21.3 + - - +
164A THR* 3.4 8.1 - - - +
166A TRP* 1.3 70.2 - - - +
168A ILE* 1.3 66.4 + - - +
169A SER 3.1 0.3 + - - -
170A ALA* 3.2 7.5 + - - +
171A LEU* 3.0 22.5 + - - +
181B TRP* 3.9 25.4 - - + -
402B SOG 4.3 16.6 - - + +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.8 20.6 - - - +
164A THR* 2.9 31.5 + - + +
165A VAL* 3.8 7.9 - - + +
167A ALA* 1.3 71.7 - - - +
169A SER* 1.3 61.9 + - - +
171A LEU* 3.2 14.3 - - + +
172A VAL* 3.2 32.0 + - + +
406A D10 5.7 3.6 - - + -
181B TRP* 5.2 0.9 - - - -
210B ALA* 3.8 20.9 - - + -
214B ILE* 3.6 33.7 - - + -
402B SOG 4.2 18.8 - - + -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.7 13.5 - - - -
126A THR* 3.7 18.4 - - - +
127A ALA* 3.4 25.9 + - - -
130A GLU* 3.3 11.6 + - - -
165A VAL 2.8 22.1 + - - -
166A TRP* 3.4 8.3 - - - -
167A ALA 3.0 0.2 - - - -
168A ILE* 1.3 79.9 - - - +
170A ALA* 1.3 55.5 + - - +
172A VAL* 3.4 2.8 + - - +
173A SER* 2.6 34.1 + - - -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.5 6.8 - - + +
166A TRP 2.9 18.3 + - - +
167A ALA* 3.2 4.9 + - - +
169A SER* 1.3 68.3 - - - +
171A LEU* 1.3 63.2 + - - +
173A SER* 3.5 7.2 - - - -
174A PHE* 2.8 60.0 + - + +
175A LEU* 3.4 3.1 + - - +
181B TRP* 5.8 2.2 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 3.0 11.9 + - - +
168A ILE* 3.2 17.5 - - + +
170A ALA* 1.3 78.7 - - - +
172A VAL* 1.3 64.0 + - + +
175A LEU* 3.2 50.1 - - + +
176A PRO* 3.3 6.6 - - - +
171B LEU* 3.6 36.4 - - + +
172B VAL* 4.4 11.2 - - + -
175B LEU* 4.8 5.2 - - + -
176B PRO* 3.9 19.5 - - + -
179B MET* 4.9 2.0 - - - -
181B TRP* 4.4 20.7 - - + -
214B ILE* 6.5 0.4 - - + -
402B SOG 4.6 10.5 - - + -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.9 1.7 - - - +
126A THR* 3.9 15.0 - - + -
130A GLU* 4.9 2.2 - - - +
168A ILE* 3.2 25.7 + - + +
169A SER 3.7 9.0 - - - +
171A LEU* 1.3 84.0 - - + +
173A SER* 1.3 58.9 + - - +
176A PRO* 3.9 12.7 - - - +
207A TYR* 5.4 2.9 + - - -
211A SER* 5.4 4.7 - - - -
214A ILE* 3.9 25.3 - - + +
215A SER* 3.9 23.9 + - - +
402A SOG 4.8 6.9 - - + +
406A D10 6.4 2.2 - - + -
171B LEU* 4.2 16.4 - - + -
172B VAL* 5.1 9.0 - - + -
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 4.6 4.1 + - - -
122A VAL* 3.5 32.6 - - - +
123A LEU* 3.5 30.0 - - - +
126A THR* 4.6 1.8 - - - -
169A SER 2.6 21.7 + - - -
171A LEU 3.3 0.6 - - - -
172A VAL* 1.3 83.8 - - - +
174A PHE* 1.3 75.3 + - - +
175A LEU 3.5 0.6 + - - -
176A PRO* 4.0 3.8 - - - +
177A ILE* 3.4 21.8 - - - +
207A TYR* 5.3 1.7 + - - -
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 5.0 2.0 - - + -
119A SER* 3.5 44.5 + - - -
120A LEU* 3.9 15.0 - - + -
123A LEU* 3.6 27.1 - - + -
170A ALA* 2.8 43.1 + - + +
173A SER* 1.3 77.8 + - - +
175A LEU* 1.3 60.1 + - + +
177A ILE* 3.1 7.4 + - - +
178A MET* 2.9 41.3 + - - +
403A SOG 4.1 26.2 - - + +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA 3.4 3.6 + - - +
171A LEU* 3.2 47.8 - - + +
174A PHE* 1.3 79.7 - - + +
176A PRO* 1.3 63.6 - - + +
178A MET* 3.3 26.2 + - + +
179A MET* 3.1 37.5 + - + +
171B LEU* 4.2 7.6 - - + -
175B LEU* 4.1 15.7 - - + -
179B MET* 4.1 25.1 - - + -
181B TRP* 5.5 0.9 - - + -
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Residues in contact with PRO 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU 3.3 13.7 - - - +
172A VAL 3.9 17.9 - - - +
173A SER 4.0 2.9 - - - +
174A PHE 3.8 1.1 - - - -
175A LEU* 1.3 91.2 - - + +
177A ILE* 1.3 58.9 + - - +
179A MET* 4.7 0.4 - - + -
180A HIS 3.1 2.4 + - - -
181A TRP* 2.8 59.8 + - + +
182A TRP* 3.8 3.1 - - - -
207A TYR* 4.1 18.8 - - + -
402A SOG 4.7 6.5 - - + -
171B LEU* 3.9 25.8 - - + -
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 4.0 8.9 - - + +
118A THR* 3.8 30.5 - - + -
119A SER* 3.6 23.6 - - - +
122A VAL* 5.2 3.1 - - + -
173A SER 3.4 16.8 - - - +
174A PHE 3.1 8.8 + - - +
176A PRO* 1.3 78.3 - - + +
178A MET* 1.3 62.5 + - - +
180A HIS* 3.1 11.1 + - - -
182A TRP* 3.7 25.3 + - + +
201A PHE* 4.0 17.5 - - + -
207A TYR* 4.6 10.1 - - - +
403A SOG 3.8 27.2 - - + +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 2.9 31.8 + - - +
175A LEU* 3.5 33.0 - - + +
177A ILE* 1.3 76.6 - - - +
179A MET* 1.3 59.3 + - + +
180A HIS* 3.2 14.1 + - - -
403A SOG 2.9 82.1 + - + +
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Residues in contact with MET 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.1 27.7 + - + +
176A PRO* 5.3 0.2 - - - -
178A MET* 1.3 76.3 - - + +
180A HIS* 1.3 74.8 + - - +
181A TRP* 3.1 55.3 + - + +
402A SOG 4.2 1.9 + - - -
171B LEU* 5.9 0.4 - - - -
175B LEU* 4.5 25.1 - - + -
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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