Contacts of the helix formed by residues 135 - 159 (chain A) in PDB entry 1VGO
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 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ALA* 3.9 13.4 - - + +
133A SER 3.6 0.2 - - - -
134A LYS* 1.3 87.6 + - - +
136A PRO* 1.3 74.6 - - + +
137A LEU* 3.1 27.6 - - + +
138A ALA* 3.1 11.6 + - + +
139A ARG* 2.8 33.6 + - - +
302A BNG 4.2 4.7 - - - +
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Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 6.0 2.7 - - + -
76A ALA* 5.2 7.9 - - + +
77A SER* 6.0 2.2 - - - +
134A LYS 4.5 2.7 - - - +
135A THR* 1.3 86.9 - - + +
137A LEU* 1.3 54.5 + - - +
139A ARG* 4.3 8.7 - - + -
140A TYR* 2.9 66.1 + - + +
302A BNG 3.5 24.2 - - - +
304A BNG 5.1 4.3 - - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.1 15.1 - - + +
136A PRO* 1.3 78.4 - - - +
138A ALA* 1.3 57.0 + - - +
140A TYR 4.1 0.2 - - - -
141A THR* 2.6 41.8 + - - +
302A BNG 3.8 51.4 + - + +
303A BNG 4.5 5.4 - - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 3.7 19.1 - - - +
134A LYS 4.8 1.1 - - - +
135A THR* 3.1 19.6 + - - +
137A LEU* 1.3 78.9 - - - +
139A ARG* 1.3 63.0 + - - +
141A THR* 3.5 4.4 + - - -
142A TRP* 2.9 36.7 + - + +
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Residues in contact with ARG 139 (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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73A VAL* 5.0 0.6 - - - +
75A LEU* 3.9 24.8 - - - +
81A LEU* 4.2 11.0 - - - +
83A ILE* 5.4 0.8 - - - +
130A GLY* 3.3 19.5 + - - +
131A ALA* 3.1 25.5 + - - +
133A SER* 3.0 32.5 + - - +
135A THR 2.8 29.8 + - - +
136A PRO* 3.9 7.9 - - - +
138A ALA* 1.3 74.9 - - - +
140A TYR* 1.3 69.0 + - + +
142A TRP* 4.0 2.3 - - - +
143A TRP* 3.0 27.6 + - - +
194A TRP* 4.0 13.2 - - + -
199A GLU* 3.2 53.1 + - - +
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 2.9 36.5 + - + +
139A ARG* 1.3 85.4 + - + +
141A THR* 1.3 59.1 + - - +
143A TRP* 3.8 7.2 - - - +
144A LEU* 3.1 27.9 + - - +
194A TRP* 4.7 2.7 - + - -
195A ILE* 4.1 11.9 - - + -
199A GLU 3.9 18.9 + - - -
200A GLY* 3.3 19.4 + - - -
302A BNG 3.7 33.4 - - + +
304A BNG 2.9 75.7 + - + +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 2.6 30.5 + - - +
138A ALA* 3.7 7.4 - - - -
139A ARG 3.2 0.2 - - - -
140A TYR* 1.3 77.0 - - - +
142A TRP* 1.3 71.9 + - + +
144A LEU* 3.4 5.2 + - - +
145A PHE* 3.0 29.5 + - + +
302A BNG 3.9 26.9 - - + +
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Residues in contact with TRP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 3.4 50.8 - - + +
129A ILE* 3.8 18.7 - - + +
130A GLY* 3.6 13.9 - - - -
133A SER* 3.7 17.4 + - - -
138A ALA* 2.9 29.2 + - - +
141A THR* 1.3 82.2 - - + +
143A TRP* 1.3 61.6 + - - +
145A PHE* 3.2 15.2 + + + +
146A SER* 2.8 32.8 + - - -
301A BNG 3.7 41.3 - - + +
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Residues in contact with TRP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 5.6 1.8 - - - -
130A GLY* 5.0 0.8 - - - -
139A ARG 3.0 18.6 + - - +
140A TYR* 3.8 6.1 - - - +
142A TRP* 1.3 77.6 - - - +
144A LEU* 1.3 81.5 + - + +
146A SER* 3.3 6.1 + - - -
147A THR* 2.6 55.2 + - + -
191A PRO* 3.1 30.6 + - + -
194A TRP* 3.2 36.3 - + + -
195A ILE* 3.8 28.1 - - + +
260A RET 3.3 26.4 - - + +
304A BNG 3.8 34.3 - - + -
305A BNG 4.0 33.4 - - + -
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Residues in contact with LEU 144 (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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140A TYR 3.1 17.1 + - - +
141A THR* 3.6 4.7 - - - +
142A TRP 3.2 0.2 - - - -
143A TRP* 1.3 90.5 - - + +
145A PHE* 1.3 59.5 + - - +
147A THR* 3.3 5.8 + - + -
148A ILE* 3.0 44.7 + - + +
302A BNG 3.7 33.4 - - + -
303A BNG 3.7 32.8 - - + -
304A BNG 3.9 14.1 - - + -
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.9 18.6 - - + -
126A THR* 4.3 18.4 - - + -
141A THR* 3.0 19.9 + - + +
142A TRP* 3.7 18.8 - + + +
144A LEU* 1.3 76.9 - - - +
146A SER* 1.3 59.2 + - - +
148A ILE* 3.1 21.4 + - + +
149A ALA* 3.1 25.3 + - + +
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Residues in contact with SER 146 (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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123A MET* 2.7 28.3 + - - +
126A THR* 3.3 20.8 + - - -
127A GLY* 3.9 8.3 + - - -
142A TRP 2.8 17.1 + - - -
143A TRP 3.6 4.5 - - - -
145A PHE* 1.3 74.2 - - - +
147A THR* 1.3 60.8 - - - +
149A ALA* 3.3 7.8 + - - +
150A PHE 3.1 20.4 + - - -
260A RET 3.1 25.1 - - - +
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Residues in contact with THR 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 2.6 44.6 + - + -
144A LEU* 3.6 12.3 - - + -
145A PHE 3.2 0.2 - - - -
146A SER* 1.3 75.0 - - - +
148A ILE* 1.3 65.1 + - + +
150A PHE* 3.1 4.1 + - + +
151A LEU* 3.1 25.5 + - + +
191A PRO* 4.0 6.9 - - + +
260A RET 3.6 16.2 - - + +
305A BNG 3.8 37.5 - - + -
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Residues in contact with ILE 148 (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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144A LEU* 3.0 40.3 + - + +
145A PHE* 3.1 22.6 + - + +
147A THR* 1.3 75.4 - - + +
149A ALA* 1.3 65.3 + - - +
151A LEU* 3.1 17.6 + - + +
152A PHE* 3.0 47.6 + - + -
303A BNG 3.8 31.9 - - + -
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Residues in contact with ALA 149 (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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119A VAL* 3.5 20.2 - - + +
122A LEU* 4.9 10.3 - - + -
123A MET* 3.8 23.3 - - + +
126A THR* 5.5 0.4 - - - +
145A PHE* 3.1 13.4 + - + +
146A SER* 3.5 10.1 - - - +
147A THR 3.2 0.2 - - - -
148A ILE* 1.3 79.1 - - - +
150A PHE* 1.3 60.2 + - - +
152A PHE* 3.0 13.8 + - - +
153A VAL* 3.0 21.6 + - - +
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Residues in contact with PHE 150 (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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123A MET* 3.7 29.1 - - - -
146A SER 3.1 9.8 + - - +
147A THR 3.2 9.2 - - - +
149A ALA* 1.3 77.4 - - - +
151A LEU* 1.3 62.6 + - + +
153A VAL* 3.2 6.3 + - + +
154A LEU* 2.9 56.2 + - + +
183A VAL 4.7 0.2 - - - -
187A TRP* 3.4 31.4 - + + -
188A THR* 3.5 42.8 - - - -
191A PRO* 4.6 6.5 - - + -
260A RET 3.9 13.7 - - + -
305A BNG 3.7 26.7 - - + -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.1 12.8 + - + +
148A ILE* 3.3 20.2 - - + +
150A PHE* 1.3 91.6 - - + +
152A PHE* 1.3 58.5 + - + +
154A LEU* 3.4 11.3 + - + +
155A TYR* 2.8 29.3 + - - +
305A BNG 3.7 30.1 - - + -
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Residues in contact with PHE 152 (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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119A VAL* 3.7 25.8 - - + -
148A ILE* 3.0 44.7 + - + -
149A ALA* 3.0 13.3 + - - +
151A LEU* 1.3 77.2 - - + +
153A VAL* 1.3 65.5 + - - +
155A TYR* 3.3 7.3 + - - +
156A TYR* 3.0 38.7 + + + -
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.3 18.6 - - + -
116A LEU* 4.2 26.2 - - + -
119A VAL* 4.2 7.0 - - + -
120A ASP* 4.1 31.6 - - + +
123A MET* 4.9 3.6 - - - -
149A ALA 3.0 16.5 + - - +
150A PHE* 3.2 14.3 + - + +
152A PHE* 1.3 76.0 - - - +
154A LEU* 1.3 64.4 + - + +
156A TYR* 3.1 14.3 + - - +
157A LEU* 3.2 23.5 + - + +
187A TRP* 4.4 14.6 - - + -
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Residues in contact with LEU 154 (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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150A PHE* 2.9 50.6 + - + +
151A LEU* 3.5 17.5 - - + +
153A VAL* 1.3 78.8 - - + +
155A TYR* 1.3 61.0 + - - +
157A LEU* 3.3 10.7 + - + +
158A LEU* 3.1 62.7 + - + +
180A THR* 5.9 1.3 - - + +
183A VAL* 4.6 10.5 - - + -
184A ALA* 4.4 28.5 - - + -
188A THR* 5.0 1.1 - - - +
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Residues in contact with TYR 155 (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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151A LEU 2.8 18.0 + - - +
152A PHE* 3.5 8.7 - - - +
153A VAL 3.2 0.2 - - - -
154A LEU* 1.3 76.7 - - - +
156A TYR* 1.3 73.6 + + - +
158A LEU* 3.5 4.2 + - - -
159A THR* 2.6 65.2 + - + +
160A SER* 5.6 1.6 - - - -
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Residues in contact with TYR 156 (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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112A THR* 3.7 33.0 - - + -
115A THR* 3.1 35.4 + - + +
116A LEU* 4.2 30.3 - - + -
119A VAL* 6.0 4.5 - - + -
152A PHE* 3.0 29.2 + + + +
153A VAL 3.1 8.0 + - - +
155A TYR* 1.3 91.3 - + - +
157A LEU* 1.3 59.5 + - + +
159A THR* 4.0 3.4 - - - -
160A SER* 3.2 17.9 + - - +
161A LEU* 3.0 29.6 + - + +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.8 4.0 - - + -
102A LEU* 4.1 27.6 - - + -
116A LEU* 4.4 17.0 - - + -
153A VAL* 3.2 26.9 + - + +
154A LEU* 3.5 14.6 - - + +
155A TYR 3.3 0.2 - - - -
156A TYR* 1.3 81.5 - - + +
158A LEU* 1.3 58.0 + - + +
161A LEU* 4.1 20.4 - - + -
162A ARG* 3.0 30.0 + - - +
176A PHE* 3.9 7.6 - - + -
180A THR* 4.0 23.9 - - + +
183A VAL* 4.0 26.9 - - + -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.1 43.2 + - + +
155A TYR* 4.2 3.8 - - - +
157A LEU* 1.3 78.1 - - - +
159A THR* 1.3 64.7 + - + +
162A ARG* 3.1 34.3 + - + -
180A THR* 4.1 20.9 - - + -
184A ALA* 5.9 3.8 - - + -
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 2.6 59.8 + - + +
156A TYR* 3.8 0.5 + - - -
157A LEU 3.2 1.0 - - - -
158A LEU* 1.3 86.2 - - + +
160A SER* 1.3 66.7 + - - +
161A LEU 3.6 0.2 - - - -
162A ARG* 3.4 7.9 + - - +
163A SER* 2.7 39.0 + - - -
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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) + - + + + + + -
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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