Contacts of the helix formed by residues 182 - 196 (chain B) in PDB entry 2VUX
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B PHE* 1.3 66.5 + - - +
184B GLY* 3.5 9.2 + - - -
185B GLU* 2.7 56.6 + - - +
186B ARG* 2.9 36.8 + - - +
244B ASN 5.5 1.8 + - - -
246B PRO* 4.2 9.1 - - + +
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Residues in contact with PHE 183 (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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34B LEU* 4.7 10.5 - - + -
35B LEU* 3.9 39.3 - - + -
111B PHE* 3.4 34.3 - + - -
114B GLU* 4.2 17.9 - - + -
115B VAL* 3.7 26.9 - - + -
124B TYR* 5.5 2.7 - - - -
182B THR* 1.3 73.1 - - - +
184B GLY* 1.3 56.6 + - - +
186B ARG* 3.0 23.3 + - + +
187B VAL* 2.9 47.6 + - + +
238B MET* 5.4 5.8 - - + -
242B LEU* 3.7 24.2 - - + -
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Residues in contact with GLY 184 (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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182B THR* 2.9 6.7 + - - -
183B PHE* 1.3 75.9 - - - +
185B GLU* 1.3 63.4 + - - +
187B VAL* 3.3 4.5 + - - +
188B VAL* 3.2 27.7 + - - +
239B PHE* 4.2 1.2 - - - -
242B LEU* 3.4 31.1 - - - +
244B ASN 5.3 2.1 + - - -
246B PRO* 4.1 13.9 - - - -
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Residues in contact with GLU 185 (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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182B THR* 2.7 52.2 + - - +
184B GLY* 1.3 69.9 - - - -
186B ARG* 1.3 61.0 + - - +
188B VAL* 3.1 7.5 + - - +
189B ALA* 2.9 29.9 + - - +
246B PRO* 4.0 19.5 - - + +
250B ARG* 3.0 42.9 + - + +
254B ILE* 4.9 16.1 - - + +
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Residues in contact with ARG 186 (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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107B LEU* 5.0 8.4 - - + +
110B ARG* 3.4 33.5 - - - +
111B PHE* 3.4 19.1 - - + -
114B GLU* 5.4 2.8 + - - -
182B THR* 2.9 33.9 + - - +
183B PHE* 3.0 35.0 + - - +
185B GLU* 1.3 81.3 - - - +
187B VAL* 1.3 56.5 + - - +
189B ALA* 3.8 8.1 - - + +
190B PHE* 2.9 30.7 + - - +
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Residues in contact with VAL 187 (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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111B PHE* 4.1 5.4 - - + -
124B TYR* 5.7 1.3 - - - +
183B PHE* 2.9 47.2 + - + +
184B GLY* 3.5 12.1 - - - +
185B GLU 3.2 0.4 - - - -
186B ARG* 1.3 75.7 - - - +
188B VAL* 1.3 52.4 + - - +
190B PHE* 3.2 11.3 + - + +
191B ALA* 2.6 34.4 + - + +
235B ALA* 3.3 33.9 - - + +
238B MET* 4.2 11.7 - - + -
239B PHE* 4.5 10.3 - - + +
242B LEU* 4.5 5.4 - - + -
297B LEU* 6.0 0.9 - - + -
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Residues in contact with VAL 188 (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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184B GLY 3.2 12.8 + - - +
185B GLU* 3.1 9.7 + - - +
187B VAL* 1.3 73.6 - - - +
189B ALA* 1.3 55.8 + - - +
191B ALA* 3.1 7.9 + - - +
192B ALA* 2.6 34.7 + - - +
239B PHE* 3.8 25.6 - - + -
246B PRO* 5.3 1.6 - - + -
251B VAL* 4.2 23.1 - - + -
254B ILE* 4.0 17.3 - - + -
255B ILE* 3.6 25.9 - - + +
297B LEU* 4.2 16.4 - - + -
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Residues in contact with ALA 189 (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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107B LEU* 5.6 2.2 - - + -
171B TRP* 3.3 27.6 - - + -
185B GLU 2.9 14.6 + - - +
186B ARG* 3.9 9.0 - - + +
188B VAL* 1.3 76.6 - - - +
190B PHE* 1.3 56.2 + - - +
192B ALA* 3.4 0.2 - - - +
193B VAL* 3.1 33.2 + - - +
254B ILE* 3.7 20.1 - - + +
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Residues in contact with PHE 190 (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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107B LEU* 4.1 17.4 - - + +
108B VAL* 4.0 16.2 - - + -
111B PHE* 3.4 26.9 - + + -
124B TYR* 4.0 22.2 - + - -
127B GLN* 3.3 28.7 - - - -
186B ARG 2.9 20.4 + - - +
187B VAL* 3.2 7.2 - - + +
189B ALA* 1.3 73.4 - - - +
191B ALA* 1.3 63.6 + - - +
193B VAL* 3.0 19.9 + - + +
194B GLU* 3.0 40.2 + - + +
231B HIS 4.6 5.2 - - - -
234B PHE* 5.3 0.4 - + - -
235B ALA* 3.8 31.9 - - + -
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Residues in contact with ALA 191 (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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187B VAL 2.6 16.7 + - - +
188B VAL* 3.4 11.7 - - - +
190B PHE* 1.3 72.9 - - - +
192B ALA* 1.3 51.6 + - - +
194B GLU* 3.3 8.7 + - - +
195B GLY* 2.8 34.0 + - - -
232B CYS* 4.2 10.0 - - - +
235B ALA* 3.8 20.9 - - + -
236B CYS* 5.2 0.2 - - - -
293B LEU* 4.2 25.2 - - + +
297B LEU* 5.1 7.2 - - + -
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Residues in contact with ALA 192 (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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171B TRP* 3.9 19.5 - - + -
188B VAL 2.6 19.1 + - - +
189B ALA* 3.4 9.9 - - - +
190B PHE 3.2 0.2 - - - -
191B ALA* 1.3 74.3 - - - +
193B VAL* 1.3 56.6 - - - +
196B VAL* 2.7 28.1 + - + +
197B PHE* 3.1 11.2 + - - -
254B ILE* 4.6 1.3 - - + -
255B ILE* 4.2 15.9 - - + -
258B ALA* 4.3 10.8 - - + -
293B LEU* 4.2 10.3 - - - +
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Residues in contact with VAL 193 (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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104B ASN* 5.8 11.2 - - + +
107B LEU* 5.5 7.2 - - + -
171B TRP* 3.9 19.3 - - + -
189B ALA 3.1 18.1 + - - +
190B PHE* 3.0 12.8 + - + +
192B ALA* 1.3 72.5 - - - +
194B GLU* 1.3 69.2 + - + +
197B PHE* 3.2 38.2 - - + +
198B PHE* 4.8 10.7 - - + +
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Residues in contact with GLU 194 (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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127B GLN* 3.2 12.0 + - - -
131B GLU* 4.2 1.0 - - - +
190B PHE* 3.0 45.0 + - + +
191B ALA* 3.6 5.4 - - - +
193B VAL* 1.3 83.2 - - - +
195B GLY* 1.3 59.5 + - - +
197B PHE 3.9 5.9 - - - +
202B PHE* 4.5 8.8 - - - -
228B GLU* 3.0 29.4 - - - +
231B HIS* 4.1 8.5 - - + +
232B CYS* 3.7 29.6 - - + +
1315B FE 2.6 25.4 - - - -
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Residues in contact with GLY 195 (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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191B ALA 2.8 19.1 + - - -
194B GLU* 1.3 75.5 - - - +
196B VAL* 1.3 59.4 + - - +
197B PHE 4.2 0.2 - - - -
199B SER* 3.2 14.2 - - - -
232B CYS* 4.3 14.4 - - - -
289B VAL* 3.2 26.1 - - - +
293B LEU* 5.0 4.9 - - - -
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Residues in contact with VAL 196 (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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192B ALA* 2.7 19.4 + - - +
195B GLY* 1.3 71.5 - - - -
197B PHE* 1.3 62.5 + - - +
198B PHE 3.5 0.3 + - - -
199B SER* 2.5 23.5 + - - -
255B ILE* 4.3 11.4 - - + -
258B ALA* 3.5 41.7 - - + +
259B VAL* 3.6 12.6 - - + +
262B GLU* 3.5 13.9 - - + +
286B ILE* 4.5 5.1 - - + +
289B VAL* 4.7 1.8 - - + -
290B ALA* 4.0 34.3 - - + +
293B LEU* 4.6 9.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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