Contacts of the helix formed by residues 186 - 202 (chain A) in PDB entry 2VWK
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 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TRP* 3.5 12.1 - - + +
184A VAL* 3.5 5.4 - - - +
185A SER* 1.3 85.4 - - - +
187A GLU* 1.3 61.1 + - - +
188A LYS* 3.8 11.8 + - - +
189A GLU* 3.3 25.8 + - - +
190A MET* 3.0 26.7 + - - +
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Residues in contact with GLU 187 (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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156A PRO* 3.4 8.5 - - - +
157A ILE* 2.9 39.6 + - - +
173A TRP* 3.6 29.9 - - + +
186A THR* 1.3 72.9 - - - +
188A LYS* 1.3 59.1 + - - +
190A MET* 3.1 7.4 + - + +
191A ILE* 2.9 39.9 + - + +
222A ARG* 2.9 44.1 + - - +
226A LEU* 3.5 15.9 - - + +
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A THR* 3.3 10.6 - - - +
187A GLU* 1.3 78.9 - - - +
189A GLU* 1.3 59.3 + - + +
191A ILE* 3.4 4.7 + - - +
192A LYS* 3.0 50.1 + - + +
226A LEU* 2.6 52.7 + - + +
227A GLY* 3.3 18.5 + - - -
228A VAL* 3.8 13.6 - - + +
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Residues in contact with GLU 189 (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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184A VAL* 4.0 14.9 - - + +
185A SER* 4.4 12.3 - - - +
186A THR* 3.3 26.3 + - - +
187A GLU 3.3 0.2 - - - -
188A LYS* 1.3 78.9 - - + +
190A MET* 1.3 60.1 + - - +
192A LYS* 3.3 36.4 + - - +
193A ARG* 2.9 29.8 + - - +
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Residues in contact with MET 190 (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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157A ILE* 3.2 42.4 - - + +
158A LEU 3.5 25.4 - - - +
159A MET 3.8 1.3 - - - -
160A ILE* 3.9 19.3 - - + -
171A ILE* 3.5 35.2 - - + +
172A THR* 3.9 3.1 - - - -
173A TRP* 4.1 4.0 - - + -
184A VAL* 3.6 14.5 - - + +
186A THR 3.0 14.6 + - - +
187A GLU* 3.2 23.3 - - + +
189A GLU* 1.3 74.0 - - - +
191A ILE* 1.3 66.4 + - + +
193A ARG* 3.2 4.7 + - - +
194A PHE* 3.0 22.0 + - - +
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Residues in contact with ILE 191 (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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157A ILE* 5.0 3.6 - - + -
160A ILE* 3.9 19.1 - - + -
187A GLU* 2.9 45.9 + - + +
188A LYS* 3.8 4.5 - - - +
190A MET* 1.3 74.7 - - + +
192A LYS* 1.3 64.9 + - - +
194A PHE* 3.0 6.5 + - - +
195A LEU* 3.0 23.1 + - + +
219A LEU* 4.5 9.6 - - + -
222A ARG* 4.6 12.8 - - + -
223A SER* 3.9 22.0 - - - +
226A LEU* 3.9 16.2 - - + -
228A VAL* 4.3 15.9 - - + -
230A PHE* 4.4 17.9 - - + -
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Residues in contact with LYS 192 (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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188A LYS* 3.0 39.6 + - + +
189A GLU* 3.3 35.6 + - - +
191A ILE* 1.3 75.2 - - - +
193A ARG* 1.3 58.0 + - - +
195A LEU* 3.4 13.0 + - + +
196A LYS* 3.0 27.0 + - - +
228A VAL* 3.7 21.8 - - + -
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Residues in contact with ARG 193 (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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162A TYR* 5.0 2.6 + - - -
171A ILE* 4.1 25.1 - - + -
182A ASP* 4.4 27.8 + - + +
184A VAL* 4.6 11.7 - - + -
189A GLU 2.9 19.4 + - - +
190A MET* 3.2 6.3 + - - +
192A LYS* 1.3 72.3 - - - +
194A PHE* 1.3 59.4 + - - +
196A LYS* 3.2 22.1 + - - +
197A VAL* 3.0 58.4 + - + +
200A GLU* 6.0 0.2 + - - -
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Residues in contact with PHE 194 (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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138A LEU* 5.4 1.8 - - + -
140A PHE* 3.5 56.5 - + + -
160A ILE* 3.5 30.7 - - + -
162A TYR* 4.5 15.0 - + + -
171A ILE* 3.7 18.3 - - + +
190A MET 3.0 12.8 + - - +
191A ILE* 3.3 8.3 - - + +
193A ARG* 1.3 77.0 - - - +
195A LEU* 1.3 72.0 + - + +
197A VAL* 3.3 3.6 + - + +
198A VAL* 3.1 53.8 + - + +
206A LEU* 5.5 0.2 - - + -
219A LEU* 4.7 11.7 - - + -
230A PHE* 5.1 0.2 - + - -
232A LEU* 4.5 18.4 - - + -
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Residues in contact with LEU 195 (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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191A ILE* 3.0 19.0 + - + +
192A LYS* 3.7 9.2 - - + +
193A ARG 3.3 0.4 - - - -
194A PHE* 1.3 81.4 - - + +
196A LYS* 1.3 57.0 + - - +
198A VAL* 4.0 0.9 - - - +
199A LYS* 3.1 32.1 + - - +
228A VAL* 4.2 18.8 - - + -
229A LYS 3.5 24.7 - - - +
230A PHE* 3.6 37.2 - - + -
231A ILE* 4.1 12.6 - - + +
232A LEU* 3.8 27.1 - - + +
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Residues in contact with LYS 196 (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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192A LYS 3.0 13.8 + - - +
193A ARG* 3.5 30.5 - - - +
194A PHE 3.2 0.2 - - - -
195A LEU* 1.3 78.4 - - - +
197A VAL* 1.3 59.2 + - + +
199A LYS* 3.8 5.3 + - - +
200A GLU* 3.2 29.6 + - + +
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Residues in contact with VAL 197 (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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138A LEU* 5.8 0.9 - - + -
162A TYR* 3.6 39.9 - - + +
171A ILE* 4.8 0.9 - - + -
193A ARG* 3.0 50.8 + - + +
194A PHE* 3.8 7.2 - - + +
196A LYS* 1.3 75.9 - - + +
198A VAL* 1.3 65.5 + - + +
200A GLU* 3.5 12.9 - - - +
201A LYS* 3.1 43.9 + - + +
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Residues in contact with VAL 198 (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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138A LEU* 4.1 17.9 - - + -
194A PHE* 3.1 51.4 + - + +
195A LEU 4.0 0.9 - - - +
197A VAL* 1.3 76.9 - - + +
199A LYS* 1.3 64.7 - - - +
200A GLU 3.0 0.3 + - - -
201A LYS 3.2 1.7 + - - -
202A ASP* 2.9 21.8 + - - -
203A PRO* 3.3 24.0 - - + +
206A LEU* 4.5 9.4 - - + -
232A LEU* 3.8 24.5 - - + +
255A ARG* 4.4 14.8 + - - +
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Residues in contact with LYS 199 (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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195A LEU 3.1 17.4 + - - +
196A LYS* 4.2 5.8 - - - +
197A VAL 3.4 0.2 - - - -
198A VAL* 1.3 78.9 - - - +
200A GLU* 1.3 59.1 + - - +
202A ASP* 4.0 15.1 + - - +
231A ILE* 5.8 11.9 - - + +
232A LEU* 5.7 0.2 - - - +
255A ARG* 4.3 14.8 + - - +
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Residues in contact with GLU 200 (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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193A ARG* 6.0 0.2 + - - -
196A LYS* 3.2 21.0 + - + +
197A VAL* 3.5 16.2 - - - +
198A VAL 3.0 0.8 - - - -
199A LYS* 1.3 78.4 - - - +
201A LYS* 1.3 75.5 + - - +
202A ASP* 3.2 3.7 - - - +
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Residues in contact with LYS 201 (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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136A LYS* 5.0 7.8 - - - +
138A LEU* 4.4 13.9 - - + -
162A TYR* 3.9 16.9 - - - -
164A ASP* 2.7 43.1 + - - +
166A GLU* 4.6 12.1 - - - +
197A VAL* 3.1 40.7 + - + +
198A VAL* 3.9 2.7 - - - +
200A GLU* 1.3 85.7 - - - +
202A ASP* 1.3 68.6 + - - +
203A PRO* 3.5 9.6 - - + +
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Residues in contact with ASP 202 (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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26A PHE* 5.5 3.1 - - - +
136A LYS* 4.4 7.1 - - - +
198A VAL 2.9 10.9 + - - -
199A LYS 4.2 11.3 - - - +
200A GLU 3.2 3.9 - - - +
201A LYS* 1.3 80.6 - - - +
203A PRO* 1.3 68.0 - - - +
204A ASP* 3.6 1.9 + - - +
234A ARG* 3.5 28.2 + - - +
255A ARG* 2.8 27.7 + - - +
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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