Contacts of the helix formed by residues 202 - 217 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285W CYS 2.5 13.9 - - - +
286W ASP* 1.8 36.1 - - - +
287W ILE* 0.7 431.8 - - + +
290W ARG* 3.0 9.6 - - - +
201Y VAL* 1.3 56.2 - - + +
203Y THR* 1.3 50.6 + - - +
205Y GLU* 2.9 14.0 + - - +
206Y ARG* 3.1 11.5 + - - +
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Residues in contact with THR 203 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286W ASP* 2.1 50.5 + - - +
287W ILE* 2.2 1.4 - - - +
288W ASP* 1.0 46.5 - - + +
62Y ARG* 3.7 30.3 + - + +
202Y THR* 1.3 67.2 - - - +
204Y ALA* 1.3 23.5 + - - -
206Y ARG* 3.7 11.7 - - - +
207Y GLU* 3.3 27.2 + - - +
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Residues in contact with ALA 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288W ASP* 0.5 296.1 + - + +
291W LYS* 5.4 0.2 - - - -
203Y THR* 1.3 35.5 - - - +
205Y GLU* 1.3 61.4 + - - +
207Y GLU 4.6 0.9 - - - -
208Y ILE* 3.6 11.3 - - - +
243Y PRO* 3.5 23.8 - - + +
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Residues in contact with GLU 205 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W ILE* 1.5 129.4 - - + +
290W ARG* 4.7 4.0 + - - -
199Y SER 4.3 4.1 - - - +
200Y PHE* 3.4 33.2 - - + -
201Y VAL* 3.5 10.7 - - + +
202Y THR 2.9 4.3 + - - +
204Y ALA* 1.3 82.7 - - - +
206Y ARG* 1.3 67.8 + - - +
208Y ILE* 3.1 22.0 - - - +
209Y VAL* 3.7 2.8 + - - +
242Y LEU* 3.7 23.4 - - + +
243Y PRO* 4.4 4.5 - - - +
244Y ASP* 5.1 3.2 - - - +
246Y GLN* 5.6 1.4 - - - +
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Residues in contact with ARG 206 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Y ARG* 4.4 13.8 - - - +
183Y ARG* 6.1 3.0 - - - +
186Y THR* 4.6 12.1 - - - +
187Y ASP* 3.4 31.0 + - - -
190Y MET* 3.7 27.4 - - + +
200Y PHE* 4.2 3.6 - - + +
201Y VAL 5.9 0.4 - - - +
202Y THR 3.1 8.6 + - - +
203Y THR* 3.7 15.3 - - - +
205Y GLU* 1.3 76.9 - - - +
207Y GLU* 1.3 66.9 + - - +
209Y VAL* 3.0 29.9 + - - +
210Y ARG* 5.1 0.6 - - - +
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Residues in contact with GLU 207 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288W ASP* 4.6 6.5 - - - +
59Y GLN* 3.8 12.8 - - - +
62Y ARG* 2.9 38.7 + - - +
203Y THR 3.3 14.1 + - - +
205Y GLU 3.4 0.2 - - - -
206Y ARG* 1.3 83.5 - - - +
208Y ILE* 1.3 56.8 + - - +
210Y ARG* 3.1 39.2 + - - +
211Y ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Y PHE* 5.4 3.4 - - + -
204Y ALA 3.6 14.5 + - - +
205Y GLU* 3.1 20.8 - - - +
207Y GLU* 1.3 75.8 - - + +
209Y VAL* 1.4 58.4 + - - +
210Y ARG 3.1 2.0 - - - -
211Y ASP* 3.0 11.1 + - + +
212Y ILE* 2.9 32.8 + - + +
240Y TYR* 3.2 41.1 - - + +
242Y LEU* 4.4 13.7 - - + -
243Y PRO* 3.9 29.2 - - + -
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Residues in contact with VAL 209 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Y THR* 3.6 22.4 - - + +
189Y LEU* 3.5 22.1 - - + +
190Y MET* 3.2 48.5 - - + +
193Y LEU* 4.1 13.0 - - + -
200Y PHE* 5.1 5.8 - - + -
205Y GLU 3.7 3.1 + - - +
206Y ARG* 3.0 24.8 + - - +
208Y ILE* 1.4 78.2 - - - +
210Y ARG* 1.3 59.0 + - - +
212Y ILE* 3.2 12.0 + - - +
213Y LYS* 2.9 24.6 + - - +
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Residues in contact with ARG 210 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Y LEU* 6.1 2.8 - - - +
186Y THR* 3.7 31.0 - - + +
206Y ARG* 5.1 0.7 - - - +
207Y GLU* 3.1 24.2 + - - +
208Y ILE 3.1 0.2 - - - -
209Y VAL* 1.3 82.0 - - + +
211Y ASP* 1.3 61.4 + - - +
213Y LYS* 3.4 13.7 - - - +
214Y GLU* 2.8 69.0 + - - +
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Residues in contact with ASP 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Y GLU 3.8 1.3 + - - +
208Y ILE* 3.0 19.8 + - + +
210Y ARG* 1.3 82.9 + - - +
212Y ILE* 1.3 60.3 + - - +
214Y GLU* 4.0 13.1 - - - +
215Y LYS* 2.7 63.3 + - - +
240Y TYR* 2.9 22.4 + - - +
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Residues in contact with ILE 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Y LEU* 3.7 17.0 - - + -
193Y LEU* 4.2 24.5 - - + -
200Y PHE* 5.1 7.9 - - + -
208Y ILE* 2.9 19.4 + - + +
209Y VAL* 3.2 13.0 + - - +
211Y ASP* 1.3 75.1 - - - +
213Y LYS* 1.4 60.1 + - - +
215Y LYS 3.2 1.2 + - - -
216Y LEU* 2.9 42.8 + - + +
217Y CYS* 3.7 2.4 + - - -
240Y TYR* 3.9 40.2 - - + -
242Y LEU* 5.2 1.8 - - + -
248Y ILE* 4.3 15.5 - - + -
250Y ILE* 4.5 15.5 - - + -
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Residues in contact with LYS 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Y ASP* 5.8 0.4 + - - -
182Y GLY* 2.8 25.0 + - - +
185Y LEU 4.1 3.4 - - - -
186Y THR* 2.7 41.3 + - - +
189Y LEU* 3.5 17.7 - - + +
209Y VAL 2.9 9.3 + - - +
210Y ARG* 3.4 20.4 - - - +
212Y ILE* 1.4 73.4 - - - +
214Y GLU* 1.3 76.0 + - - +
217Y CYS* 3.0 30.8 + - - +
257Y CYS* 4.2 13.0 - - - -
303Y THR* 5.1 1.4 + - - -
306Y TYR* 3.7 31.9 - - + +
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Residues in contact with GLU 214 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y ARG* 2.8 55.7 + - - +
211Y ASP* 4.2 10.1 - - - +
212Y ILE 3.3 0.4 - - - -
213Y LYS* 1.3 95.3 + - - +
215Y LYS* 1.3 64.4 + - + +
217Y CYS 4.3 5.5 + - - +
306Y TYR* 5.6 4.0 - - - -
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Residues in contact with LYS 215 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211Y ASP* 2.7 53.0 + - - +
212Y ILE* 4.1 1.3 - - - +
214Y GLU* 1.3 78.4 - - + +
216Y LEU* 1.3 73.1 + - + +
217Y CYS 4.9 0.9 - - - +
218Y TYR* 4.8 6.6 - - - -
240Y TYR* 4.1 14.7 + - + -
254Y ARG* 5.4 0.3 + - - -
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Residues in contact with LEU 216 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Y ILE* 2.9 25.9 + - + +
215Y LYS* 1.3 86.0 - - + +
217Y CYS* 1.3 62.7 + - - +
218Y TYR* 3.3 5.1 - - - -
238Y LYS* 3.8 46.2 - - + +
239Y SER 5.8 1.1 - - - +
240Y TYR* 3.9 32.5 - - + +
250Y ILE* 4.6 11.7 - - + -
254Y ARG* 2.9 43.6 + - + +
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Residues in contact with CYS 217 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Y LEU* 4.6 7.6 - - - -
212Y ILE* 3.7 2.4 + - - -
213Y LYS* 3.0 36.1 + - - +
214Y GLU 4.6 4.3 - - - +
215Y LYS 3.8 1.1 - - - +
216Y LEU* 1.3 73.3 - - - +
218Y TYR* 1.3 73.9 + - - +
250Y ILE* 6.2 0.4 - - - -
253Y GLU 4.7 0.2 - - - -
254Y ARG* 2.9 26.7 - - - +
257Y CYS* 4.2 19.5 - - - -
258Y PRO* 4.1 3.4 - - + -
306Y TYR* 4.0 21.7 - - + -
307Y 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