Contacts of the helix formed by residues 202 - 217 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285X CYS 2.7 6.5 - - - +
286X ASP* 0.7 164.5 + - + +
287X ILE* 0.9 103.9 + - - +
288X ASP 2.7 6.6 + - - -
201Z VAL* 1.3 34.3 - - + +
203Z THR* 1.3 55.5 + - - +
205Z GLU 2.9 12.1 + - - -
206Z ARG* 3.1 9.1 + - - +
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Residues in contact with THR 203 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286X ASP* 2.9 9.1 + - + +
270Y GLU* 5.0 21.8 + - + +
62Z ARG* 3.7 30.3 + - + +
202Z THR* 1.3 73.4 - - - +
204Z ALA* 1.3 62.4 + - + +
206Z ARG* 3.7 11.7 - - - +
207Z GLU* 3.3 28.1 + - - +
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Residues in contact with ALA 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166X TYR* 5.9 2.2 - - + +
286X ASP* 2.8 17.4 + - - +
288X ASP* 1.0 101.1 + - + +
289X ILE* 4.1 7.2 - - + -
203Z THR* 1.3 76.5 - - + +
205Z GLU* 1.3 18.2 - - - +
207Z GLU* 4.6 5.1 - - - +
208Z ILE* 3.6 9.3 - - - +
243Z PRO* 3.5 13.6 - - + +
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Residues in contact with GLU 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287X ILE* 1.3 87.2 - - + +
288X ASP* 0.4 106.3 + - - +
200Z PHE* 3.4 28.0 - - + -
202Z THR* 2.9 4.6 + - - +
204Z ALA* 1.3 40.9 - - - +
206Z ARG* 1.3 68.0 + - - +
207Z GLU 3.4 0.2 - - - -
208Z ILE* 3.1 18.5 - - - +
209Z VAL 3.7 2.8 + - - -
242Z LEU* 3.7 9.5 - - + +
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Residues in contact with ARG 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z ARG* 4.4 13.9 - - - +
183Z ARG* 6.1 2.6 - - - +
186Z THR* 4.6 10.8 - - - +
187Z ASP* 3.4 31.8 + - - -
190Z MET* 3.7 26.7 - - + +
200Z PHE* 4.2 4.1 - - + +
201Z VAL 5.9 0.4 - - - +
202Z THR 3.1 7.9 + - - +
203Z THR* 3.7 15.7 - - - +
205Z GLU* 1.3 75.8 - - - +
207Z GLU* 1.3 67.7 + - - +
209Z VAL* 3.0 29.9 + - - +
210Z ARG* 5.1 0.9 - - - +
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Residues in contact with GLU 207 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z GLN* 3.8 13.0 - - - +
62Z ARG* 2.9 39.2 + - - +
203Z THR 3.3 14.3 + - - +
204Z ALA* 5.1 4.3 - - - -
205Z GLU 3.4 0.4 - - - -
206Z ARG* 1.3 83.5 - - - +
208Z ILE* 1.3 57.6 + - - +
210Z ARG* 3.1 39.3 + - - +
211Z ASP* 3.8 2.1 + - - +
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Residues in contact with ILE 208 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288X ASP* 3.2 15.9 - - - +
200Z PHE* 5.4 3.1 - - + -
204Z ALA 4.0 3.6 - - - +
205Z GLU* 3.1 17.9 - - - +
207Z GLU* 1.3 75.7 - - + +
209Z VAL* 1.4 57.5 + - - +
210Z ARG 3.1 2.2 - - - -
211Z ASP* 3.0 11.1 + - + +
212Z ILE* 2.9 32.3 + - + +
240Z TYR* 3.2 41.5 - - + +
242Z LEU* 4.4 10.8 - - + -
243Z PRO* 3.9 28.9 - - + -
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Residues in contact with VAL 209 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Z THR* 3.6 22.9 - - + +
189Z LEU* 3.5 22.2 - - + +
190Z MET* 3.2 47.8 - - + +
193Z LEU* 4.1 13.2 - - + -
200Z PHE* 5.1 5.6 - - + -
205Z GLU 4.5 2.7 - - - +
206Z ARG* 3.0 24.6 + - - +
208Z ILE* 1.4 78.4 - - - +
210Z ARG* 1.3 58.7 + - - +
212Z ILE* 3.2 12.1 + - - +
213Z LYS* 2.9 24.4 + - - +
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Residues in contact with ARG 210 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z LEU* 6.1 2.8 - - - +
186Z THR* 3.7 31.2 - - + +
206Z ARG* 5.1 0.9 - - - +
207Z GLU* 3.1 25.2 + - - +
209Z VAL* 1.3 82.4 - - + +
211Z ASP* 1.3 61.8 + - - +
213Z LYS* 3.4 13.5 - - - +
214Z GLU* 2.8 67.4 + - - +
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Residues in contact with ASP 211 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Z GLU 3.8 1.3 + - - +
208Z ILE* 3.0 20.3 + - + +
210Z ARG* 1.3 82.6 + - - +
212Z ILE* 1.3 60.8 + - - +
214Z GLU* 4.0 13.4 - - - +
215Z LYS* 2.7 63.3 + - - +
240Z TYR* 2.9 22.3 + - - +
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Residues in contact with ILE 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Z LEU* 3.7 17.0 - - + -
193Z LEU* 4.2 24.0 - - + -
200Z PHE* 5.1 7.9 - - + -
208Z ILE* 2.9 19.6 + - + +
209Z VAL* 3.2 12.5 + - - +
211Z ASP* 1.3 75.1 - - - +
213Z LYS* 1.4 60.2 + - - +
215Z LYS 3.2 1.0 + - - -
216Z LEU* 2.9 42.5 + - + +
217Z CYS* 3.7 2.1 + - - -
240Z TYR* 3.9 40.2 - - + -
242Z LEU* 5.2 1.6 - - + -
248Z ILE* 4.3 15.5 - - + -
250Z ILE* 4.5 15.5 - - + -
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Residues in contact with LYS 213 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Z ASP* 5.8 0.6 + - - -
182Z GLY* 2.8 24.8 + - - +
185Z LEU 4.1 3.4 - - - -
186Z THR* 2.7 41.3 + - - +
189Z LEU* 3.5 18.1 - - + +
209Z VAL 2.9 8.5 + - - +
210Z ARG* 3.4 20.4 - - - +
212Z ILE* 1.4 73.4 - - - +
214Z GLU* 1.3 77.0 + - - +
217Z CYS* 3.0 31.0 + - - +
257Z CYS* 4.2 13.0 - - - -
303Z THR* 5.1 1.4 + - - -
306Z TYR* 3.7 32.6 - - + +
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Residues in contact with GLU 214 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Z ARG* 2.8 56.0 + - - +
211Z ASP* 4.2 10.7 - - - +
212Z ILE 3.3 0.2 - - - -
213Z LYS* 1.3 95.1 + - - +
215Z LYS* 1.3 64.1 + - + +
217Z CYS 4.3 6.1 + - - +
306Z TYR* 5.6 4.0 - - - -
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Residues in contact with LYS 215 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211Z ASP* 2.7 53.0 + - - +
212Z ILE* 4.1 1.1 - - - +
214Z GLU* 1.3 78.6 - - + +
216Z LEU* 1.3 73.0 + - + +
217Z CYS 4.9 0.6 - - - +
218Z TYR* 4.8 7.1 - - - -
240Z TYR* 4.1 15.4 + - + -
254Z ARG* 5.4 0.3 + - - -
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Residues in contact with LEU 216 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Z ILE* 2.9 25.3 + - + +
215Z LYS* 1.3 85.8 - - + +
217Z CYS* 1.3 62.5 + - - +
218Z TYR* 3.3 6.0 - - - -
238Z LYS* 3.8 46.2 - - + +
239Z SER 5.8 0.9 - - - +
240Z TYR* 3.9 32.5 - - + +
250Z ILE* 4.6 11.9 - - + -
254Z ARG* 2.9 43.0 + - + +
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Residues in contact with CYS 217 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Z LEU* 4.6 7.6 - - - -
212Z ILE* 3.7 2.9 + - - -
213Z LYS* 3.0 36.1 + - - +
214Z GLU 4.6 4.5 - - - +
215Z LYS 3.8 0.7 - - - +
216Z LEU* 1.3 72.8 - - - +
218Z TYR* 1.3 73.7 + - - +
250Z ILE* 6.2 0.7 - - - -
253Z GLU 4.7 0.2 - - - -
254Z ARG* 2.9 26.7 - - - +
257Z CYS* 4.2 19.5 - - - -
258Z PRO* 4.1 3.4 - - + -
306Z TYR* 4.0 21.5 - - + -
307Z 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