Contacts of the helix formed by residues 135 - 159 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.6 14.6 - - + -
134B LYS* 1.3 85.9 - - + +
136B PRO* 1.3 67.2 - - + +
137B LEU* 3.1 8.4 - - - +
138B ALA* 3.0 39.1 + - - +
139B ARG* 3.1 15.6 + - - +
312B BNG 4.8 0.2 - - - -
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Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 5.4 2.5 - - + -
135B THR* 1.3 86.5 - - + +
137B LEU* 1.3 60.4 + - + +
139B ARG* 3.6 21.5 - - + +
140B TYR* 3.4 6.4 + - - +
312B BNG 3.2 80.4 - - + +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR* 3.0 7.9 + - - +
136B PRO* 1.3 79.4 - - + +
138B ALA* 1.3 64.5 + - - +
140B TYR* 3.5 10.6 + - + +
141B THR* 3.1 29.3 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B SER* 3.7 20.2 - - - +
134B LYS 5.3 0.2 - - - +
135B THR* 3.0 22.5 + - - +
137B LEU* 1.3 78.0 - - - +
139B ARG* 1.3 65.0 + - - +
141B THR* 3.1 7.3 + - - -
142B TRP* 3.1 34.3 + - + +
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.0 25.2 - - - +
130B GLY* 3.2 28.0 - - - +
133B SER* 2.9 21.2 + - - +
134B LYS 2.7 27.2 + - - -
135B THR 3.1 8.1 + - - +
136B PRO* 3.6 26.7 - - - +
137B LEU 3.4 0.2 - - - -
138B ALA* 1.3 78.0 - - - +
140B TYR* 1.3 56.0 + - - +
142B TRP* 4.1 0.7 - - - +
143B TRP* 3.0 27.3 + - - +
194B TRP* 3.7 12.5 - - + -
198B THR 5.4 0.4 + - - -
199B GLU* 3.1 46.5 + - - -
200B GLY* 4.9 3.6 + - - -
312B BNG 3.3 41.9 + - + +
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Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO 3.4 14.6 + - - +
137B LEU* 3.9 10.5 - - + +
138B ALA 3.1 0.8 - - - -
139B ARG* 1.3 77.3 - - - +
141B THR* 1.3 64.5 + - - +
143B TRP* 3.5 28.8 - + - +
144B LEU* 2.7 60.9 + - + +
195B ILE* 4.8 3.1 - - + -
312B BNG 3.4 28.4 - - + +
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Residues in contact with THR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.1 17.1 + - - +
138B ALA* 3.1 11.0 + - - -
140B TYR* 1.3 86.6 - - - +
142B TRP* 1.3 68.3 + - + +
144B LEU* 3.3 5.9 + - - +
145B PHE* 2.9 37.5 + - + +
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Residues in contact with TRP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 3.8 37.4 - - + +
127B GLY* 5.6 0.9 - - - -
129B ILE* 3.4 37.4 - - + +
130B GLY* 3.4 24.2 - - - +
133B SER* 3.5 20.9 + - - -
138B ALA* 3.1 26.3 + - + +
139B ARG 4.3 0.4 - - - +
141B THR* 1.3 88.2 - - + +
143B TRP* 1.3 58.2 + - - +
145B PHE* 3.5 22.3 + + + +
146B SER* 3.0 29.1 + - - -
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 6.0 1.1 - - - -
139B ARG 3.0 22.5 + - - +
140B TYR* 3.5 34.5 - + - +
142B TRP* 1.3 75.6 - - - +
144B LEU* 1.3 81.6 + - + +
146B SER* 3.3 5.8 + - - -
147B THR* 2.7 63.0 + - + -
191B PRO* 3.1 34.5 + - + +
192B ILE* 5.3 1.6 - - + -
194B TRP* 3.4 32.5 - + + -
195B ILE* 3.8 27.2 - - + +
261B RET 3.4 19.3 - - + -
312B BNG 5.0 0.2 - - + -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 2.7 51.8 + - + +
141B THR* 3.7 5.2 - - - +
143B TRP* 1.3 85.0 - - + +
145B PHE* 1.3 66.0 + - + +
147B THR* 4.4 4.7 - - + +
148B ILE* 2.9 66.4 + - + +
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Residues in contact with PHE 145 (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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122B LEU* 4.4 11.9 - - + +
126B THR* 3.7 25.8 - - + -
141B THR* 2.9 24.6 + - + +
142B TRP* 3.5 25.8 - + + +
144B LEU* 1.3 80.0 - - + +
146B SER* 1.3 59.8 + - - +
148B ILE* 3.6 10.9 + - + +
149B ALA* 3.4 19.2 + - - +
310B BNG 4.0 24.4 - - + +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 2.8 23.4 + - - +
126B THR* 3.1 19.7 + - - -
127B GLY* 4.0 6.3 + - - -
142B TRP 3.0 15.6 + - - -
143B TRP* 3.6 1.1 - - - -
144B LEU 3.1 0.2 - - - -
145B PHE* 1.3 73.8 - - - +
147B THR* 1.3 65.3 + - - +
148B ILE 3.1 1.6 - - - -
149B ALA* 3.3 6.8 + - - +
150B PHE* 3.0 22.0 + - - +
261B RET 3.1 29.8 - - - +
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 2.7 63.6 + - + -
144B LEU* 3.3 9.2 + - + -
146B SER* 1.3 72.7 - - - +
148B ILE* 1.3 57.7 + - - +
150B PHE* 3.5 4.2 + - + +
151B LEU* 2.9 53.4 + - + +
191B PRO* 4.0 6.3 - - + +
261B RET 3.7 17.9 - - + +
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Residues in contact with ILE 148 (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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144B LEU* 2.9 59.3 + - + +
145B PHE* 3.7 10.8 - - + +
146B SER 3.1 0.2 - - - -
147B THR* 1.3 75.5 - - - +
149B ALA* 1.3 67.3 + - - +
151B LEU* 2.9 25.2 + - + +
152B PHE* 2.9 34.7 + - + -
310B BNG 4.0 15.5 - - + -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.1 41.8 - - + +
122B LEU* 4.0 16.6 - - + -
123B MET* 3.9 8.7 - - + -
145B PHE 3.4 9.8 + - - +
146B SER 3.3 8.5 + - - +
148B ILE* 1.3 78.9 - - - +
150B PHE* 1.3 57.3 + - - +
152B PHE* 3.0 3.5 + - - -
153B VAL* 2.9 26.1 + - - +
310B BNG 4.1 8.5 - - + +
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Residues in contact with PHE 150 (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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123B MET* 3.4 32.9 - - - -
146B SER 3.0 10.9 + - - +
147B THR* 3.5 8.1 - - + +
149B ALA* 1.3 77.4 - - - +
151B LEU* 1.3 70.4 + - + +
153B VAL* 3.1 8.7 + - + +
154B LEU* 2.9 65.2 + - + +
184B ALA 4.7 0.4 - - - -
187B TRP* 3.6 49.8 - + + -
188B THR* 3.8 21.5 - - + -
191B PRO* 4.9 6.3 - - + -
261B RET 3.8 19.5 - - + -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B THR* 2.9 44.2 + - + +
148B ILE* 2.9 19.6 + - + +
150B PHE* 1.3 88.7 - - + +
152B PHE* 1.3 57.5 + - + +
154B LEU* 3.4 11.8 + - + +
155B TYR* 2.8 28.5 + - - +
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Residues in contact with PHE 152 (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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119B VAL* 3.7 11.4 - - + -
148B ILE* 2.9 41.7 + - + -
149B ALA 3.2 9.0 - - - +
151B LEU* 1.3 76.6 - - + +
153B VAL* 1.3 65.6 + - - +
155B TYR* 3.1 18.5 + + + +
156B TYR* 3.0 57.5 + + + -
310B BNG 4.2 33.2 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.3 11.7 - - + -
116B LEU* 4.2 18.2 - - + +
119B VAL* 4.1 4.0 - - + -
120B ASP* 4.1 36.3 - - + +
123B MET* 4.8 3.1 - - - -
149B ALA 2.9 18.9 + - - +
150B PHE* 3.2 15.5 - - + +
152B PHE* 1.3 79.8 - - - +
154B LEU* 1.3 68.5 + - + +
156B TYR* 3.3 8.3 + - - +
157B LEU* 3.1 35.8 + - + +
187B TRP* 4.5 12.6 - - + -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 2.9 57.6 + - + +
151B LEU* 3.6 16.2 - - + +
152B PHE 3.3 0.2 - - - -
153B VAL* 1.3 78.4 - - + +
155B TYR* 1.3 56.7 + - - +
157B LEU* 3.3 17.6 + - + +
158B LEU* 2.8 51.4 + - + +
183B VAL* 4.7 4.9 - - + -
184B ALA* 4.4 23.1 - - + +
188B THR* 4.4 7.4 - - - +
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Residues in contact with TYR 155 (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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151B LEU 2.8 15.0 + - - +
152B PHE* 3.3 23.6 - + + +
153B VAL 3.1 0.2 - - - -
154B LEU* 1.3 74.6 - - - +
156B TYR* 1.3 90.0 + + - +
158B LEU* 3.2 3.7 + - - -
159B THR* 2.7 64.6 + - + +
160B SER* 5.6 0.7 - - - -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 5.1 7.9 - - - +
115B THR* 3.7 21.1 - - + -
116B LEU* 4.5 25.6 - - + -
119B VAL* 4.0 16.2 - - + -
152B PHE* 3.0 46.5 + + + -
153B VAL* 4.0 7.0 - - - +
155B TYR* 1.3 95.8 - + - +
157B LEU* 1.3 58.4 + - - +
159B THR* 3.8 4.5 - - - -
160B SER* 3.3 16.4 + - - +
161B LEU* 3.0 35.3 + - + +
310B BNG 3.2 42.3 + - - +
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Residues in contact with LEU 157 (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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99B LEU* 4.3 5.8 - - + -
102B LEU* 3.9 35.4 - - + -
116B LEU* 4.2 18.8 - - + -
153B VAL* 3.1 27.1 + - + +
154B LEU* 3.4 16.6 - - + +
155B TYR 3.1 0.4 - - - -
156B TYR* 1.3 79.5 - - - +
158B LEU* 1.3 59.9 + - + +
161B LEU* 3.6 22.3 - - + +
162B ARG* 3.2 26.7 + - - +
176B PHE* 3.7 7.0 - - + -
180B THR* 4.3 18.2 - - + +
183B VAL* 4.1 22.7 - - + -
184B ALA 6.0 0.2 - - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 2.8 41.6 + - + +
155B TYR* 4.1 3.4 - - - +
157B LEU* 1.3 74.5 - - + +
159B THR* 1.3 63.2 + - + +
162B ARG* 3.8 32.6 + - - +
180B THR* 3.9 25.4 - - + +
181B ALA* 6.4 0.2 - - - -
184B ALA* 5.5 9.4 - - + -
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR* 2.7 55.9 + - + +
156B TYR* 3.8 1.0 - - - -
157B LEU 3.4 0.2 - - - -
158B LEU* 1.3 84.6 - - + +
160B SER* 1.3 69.2 + - - +
161B LEU 3.6 0.2 - - - -
162B ARG* 3.5 1.1 + - - +
163B SER* 2.8 38.6 + - - -
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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