Contacts of the helix formed by residues 202 - 217 (chain W) in PDB entry 1MVW
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 202 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2859 CYS 3.6 2.7 - - - +
2879 ILE* 0.6 286.4 - - + +
2909 ARG* 2.2 60.8 - - - +
201W VAL* 1.3 73.3 - - - +
203W THR* 1.3 52.5 + - - -
205W GLU* 2.9 17.3 + - - +
206W ARG* 3.1 11.5 + - - +
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Residues in contact with THR 203 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2869 ASP* 2.3 34.1 - - - +
2879 ILE* 1.4 35.8 - - - +
2889 ASP* 1.3 77.3 + - + +
62W ARG* 3.7 26.2 + - + +
202W THR 1.3 66.3 - - - -
204W ALA* 1.3 50.9 + - - -
205W GLU 3.2 0.4 - - - -
206W ARG* 3.7 11.6 - - - +
207W GLU* 3.3 27.0 + - - +
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Residues in contact with ALA 204 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2879 ILE* 2.8 33.1 - - + +
2889 ASP* 2.7 20.0 + - - +
2919 LYS* 5.6 4.0 - - + -
203W THR* 1.3 74.0 - - - +
205W GLU* 1.3 62.9 + - - +
207W GLU* 4.6 2.9 - - - -
208W ILE* 3.6 11.4 - - - +
243W PRO* 3.5 32.1 - - + +
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Residues in contact with GLU 205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2879 ILE* 3.0 28.4 - - + +
2909 ARG* 5.3 2.9 + - - -
199W SER 4.3 3.9 - - - +
200W PHE* 3.4 34.8 - - + -
201W VAL* 3.5 17.1 - - + +
202W THR* 2.9 15.4 + - - +
204W ALA* 1.3 85.2 - - - +
206W ARG* 1.3 67.8 + - - +
208W ILE* 3.1 21.4 - - - +
209W VAL 3.7 2.9 + - - -
242W LEU* 3.7 23.2 - - - +
243W PRO* 4.4 5.4 - - - +
244W ASP* 5.1 3.1 - - - +
246W GLN* 5.6 1.4 - - - +
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Residues in contact with ARG 206 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62W ARG* 4.4 12.9 - - - +
183W ARG* 6.1 2.8 - - - +
186W THR* 4.6 11.6 - - - +
187W ASP* 3.4 32.8 + - - -
190W MET* 3.7 27.2 - - + +
200W PHE* 4.2 4.2 - - + +
201W VAL 5.9 0.4 - - - +
202W THR 3.1 8.4 + - - +
203W THR* 3.5 15.0 + - - +
205W GLU* 1.3 77.1 - - - +
207W GLU* 1.3 67.6 + - - +
209W VAL* 3.0 30.0 + - - +
210W ARG* 5.1 0.2 - - - +
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Residues in contact with GLU 207 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2889 ASP* 4.1 11.0 - - - +
59W GLN* 3.8 12.5 - - - +
62W ARG* 2.9 38.1 + - - +
203W THR 3.3 13.0 + - - +
204W ALA* 5.1 2.0 - - - -
206W ARG* 1.3 82.9 - - - +
208W ILE* 1.3 58.1 + - - +
210W ARG* 3.1 39.8 + - - +
211W ASP* 3.8 2.1 + - - +
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Residues in contact with ILE 208 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200W PHE* 5.4 2.9 - - + -
204W ALA 3.6 15.0 + - - +
205W GLU* 3.1 19.7 - - - +
207W GLU* 1.3 75.5 - - - +
209W VAL* 1.4 57.4 + - - +
210W ARG 3.1 2.2 - - - -
211W ASP* 3.0 11.1 + - + +
212W ILE* 2.9 32.4 + - + +
240W TYR* 3.2 40.8 - - + +
242W LEU* 4.4 14.1 - - + -
243W PRO* 3.9 29.2 - - + -
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Residues in contact with VAL 209 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186W THR* 3.6 22.2 - - + +
189W LEU* 3.5 22.1 - - + +
190W MET* 3.2 48.0 - - + +
193W LEU* 4.1 13.2 - - + -
200W PHE* 5.1 5.4 - - + -
205W GLU 3.7 2.9 + - - +
206W ARG* 3.0 24.8 + - - +
208W ILE* 1.4 77.7 - - - +
210W ARG* 1.3 59.7 + - + +
212W ILE* 3.2 12.2 + - - +
213W LYS* 2.9 24.6 + - - +
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Residues in contact with ARG 210 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16W LEU* 6.1 3.0 - - - +
186W THR* 3.7 31.4 - - + +
206W ARG* 6.2 0.2 - - - +
207W GLU* 3.1 23.5 + - - +
209W VAL* 1.3 83.5 - - + +
211W ASP* 1.3 61.7 + - - +
213W LYS* 3.4 13.1 - - - +
214W GLU* 2.8 69.4 + - - +
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Residues in contact with ASP 211 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207W GLU 3.8 1.7 + - - +
208W ILE* 3.0 18.7 + - + +
210W ARG* 1.3 82.3 + - - +
212W ILE* 1.3 60.1 + - - +
214W GLU* 4.0 13.1 - - - +
215W LYS* 2.7 62.9 + - - +
240W TYR* 2.9 20.6 + - - +
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Residues in contact with ILE 212 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189W LEU* 3.7 17.5 - - + -
193W LEU* 4.2 23.1 - - + -
200W PHE* 5.1 8.5 - - + -
208W ILE* 2.9 20.5 + - + +
209W VAL* 3.2 12.3 + - - +
211W ASP* 1.3 73.8 - - - +
213W LYS* 1.4 62.3 + - - +
215W LYS 3.2 1.0 + - - -
216W LEU* 2.9 42.1 + - + +
217W CYS* 3.7 2.4 + - - -
240W TYR* 3.9 39.3 - - + -
242W LEU* 5.2 1.3 - - + -
248W ILE* 4.3 15.3 - - + -
250W ILE* 4.5 15.9 - - + -
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Residues in contact with LYS 213 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157W ASP* 5.8 0.4 + - - -
182W GLY* 2.8 25.6 + - - +
185W LEU 4.1 2.9 - - - -
186W THR* 2.7 40.6 + - - +
189W LEU* 3.6 17.5 - - + -
209W VAL 2.9 9.3 + - - +
210W ARG* 3.4 20.6 - - - +
212W ILE* 1.4 73.2 - - - +
214W GLU* 1.3 77.0 + - - +
217W CYS* 3.0 31.7 + - - +
257W CYS* 4.2 13.5 - - - -
303W THR* 5.1 1.2 + - - -
306W TYR* 3.7 32.3 + - + +
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Residues in contact with GLU 214 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210W ARG* 2.8 57.8 + - - +
211W ASP* 4.2 11.1 - - - +
213W LYS* 1.3 92.9 + - - +
215W LYS* 1.3 65.1 + - + +
217W CYS 4.3 5.7 + - - +
306W TYR* 5.6 4.3 - - - -
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Residues in contact with LYS 215 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211W ASP* 2.7 53.3 + - - +
212W ILE 4.1 0.4 - - - +
214W GLU* 1.3 78.5 - - + +
216W LEU* 1.3 73.5 + - + +
217W CYS 4.9 0.7 - - - +
218W TYR* 4.8 6.9 - - - -
240W TYR* 4.1 14.9 + - + -
254W ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212W ILE* 2.9 26.6 + - + +
215W LYS* 1.3 86.0 - - + +
217W CYS* 1.3 61.9 + - - +
218W TYR* 3.3 5.0 - - - -
238W LYS* 3.8 46.4 - - + +
239W SER 5.8 0.7 - - - +
240W TYR* 3.9 31.6 - - + +
250W ILE* 4.6 12.1 - - + -
254W ARG* 2.9 43.5 + - + +
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Residues in contact with CYS 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189W LEU* 4.6 7.4 - - - -
212W ILE* 3.7 2.7 + - - -
213W LYS* 3.0 36.4 + - - +
214W GLU 4.6 4.3 - - - +
215W LYS 3.8 0.7 - - - +
216W LEU* 1.3 73.0 - - - +
218W TYR* 1.3 73.8 + - - +
250W ILE* 6.2 0.2 - - - -
253W GLU 4.7 0.4 - - - -
254W ARG* 2.9 27.1 - - - +
257W CYS* 4.2 19.3 - - - -
258W PRO* 4.1 2.7 - - + -
306W TYR* 4.0 21.9 - - + -
307W PRO* 3.4 17.7 - - - +
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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