Contacts of the helix formed by residues 181 - 195 (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 ALA 181 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Y SER* 4.5 1.3 - - - +
156Y GLY 3.3 15.0 - - - +
157Y ASP 3.4 17.9 - - - +
158Y GLY 3.7 14.1 + - - -
159Y VAL 3.8 9.6 - - - +
160Y THR* 4.3 2.7 - - - +
180Y LEU* 1.3 77.5 - - - +
182Y GLY* 1.3 61.1 + - - +
183Y ARG 3.2 2.5 + - - -
184Y ASP* 3.2 11.2 + - - +
185Y LEU* 3.0 33.6 + - - +
303Y THR* 4.2 6.7 - - - -
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Residues in contact with GLY 182 (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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156Y GLY 3.0 11.0 + - - -
157Y ASP* 4.4 4.7 - - - -
181Y ALA* 1.3 76.3 - - - +
183Y ARG* 1.3 55.5 + - - +
185Y LEU* 3.5 8.1 + - - +
186Y THR* 3.0 17.7 + - - -
213Y LYS* 2.8 31.4 + - - -
303Y THR* 3.1 21.2 + - - -
306Y TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y SER* 2.8 36.2 + - - -
69Y TYR* 3.5 28.9 + - - +
71Y ILE 4.8 5.3 + - - -
72Y GLU* 4.6 14.1 + - - +
73Y HIS* 5.2 7.4 - - - +
157Y ASP* 2.9 48.1 + - - +
158Y GLY* 4.4 15.1 - - - -
182Y GLY* 1.3 70.9 - - - +
184Y ASP* 1.3 70.4 + - - +
186Y THR* 3.3 14.2 + - - -
187Y ASP* 3.4 24.6 + - - +
206Y ARG* 6.1 2.2 - - - +
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Residues in contact with ASP 184 (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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73Y HIS* 5.4 3.1 - - - -
157Y ASP 4.5 1.0 - - - +
158Y GLY* 4.7 4.7 - - - +
179Y ASP 3.9 12.3 - - - +
180Y LEU* 3.8 11.1 - - + +
181Y ALA* 3.2 28.6 + - - +
183Y ARG* 1.3 81.6 - - - +
185Y LEU* 1.3 62.1 + - + +
187Y ASP* 3.2 8.8 + - - +
188Y TYR* 3.1 27.5 + - - +
267Y ILE* 5.0 12.7 - - + +
269Y MET* 5.6 1.0 - - - +
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Residues in contact with LEU 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180Y LEU* 3.9 24.2 - - + -
181Y ALA 3.0 16.9 + - - +
182Y GLY 3.5 6.7 - - - +
184Y ASP* 1.3 77.6 - - + +
186Y THR* 1.3 62.9 + - - +
188Y TYR* 3.7 5.8 + - + +
189Y LEU 3.3 8.1 + - - -
213Y LYS* 4.1 2.9 - - + -
257Y CYS* 3.2 39.5 - - - +
258Y PRO* 5.1 0.2 - - + -
260Y THR* 4.3 19.7 - - + -
261Y LEU* 4.0 10.8 - - + -
303Y THR* 3.8 18.4 - - + -
306Y TYR* 3.0 41.3 - - + +
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Residues in contact with THR 186 (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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182Y GLY 3.0 8.0 + - - -
183Y ARG* 3.3 7.9 + - - -
185Y LEU* 1.3 75.1 - - - +
187Y ASP* 1.3 66.5 + - - +
189Y LEU* 3.4 5.2 + - - +
190Y MET* 3.1 25.8 + - - +
206Y ARG* 4.6 10.1 - - - +
209Y VAL* 3.6 26.0 - - + +
210Y ARG* 3.7 26.4 - - + +
213Y LYS* 2.7 37.3 + - - +
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Residues in contact with ASP 187 (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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183Y ARG* 3.4 17.8 + - - +
184Y ASP* 3.2 10.4 + - - +
186Y THR* 1.3 79.3 - - - +
188Y TYR* 1.3 64.2 + - - +
190Y MET* 3.1 19.9 - - - +
191Y LYS* 3.4 9.5 + - - +
206Y ARG* 3.4 35.4 + - - -
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Residues in contact with TYR 188 (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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184Y ASP 3.1 14.9 + - - +
185Y LEU* 4.1 6.1 - - - +
187Y ASP* 1.3 76.5 - - - +
189Y LEU* 1.3 66.4 + - - +
191Y LYS* 3.2 39.0 + - + +
192Y ILE* 3.0 45.1 + - + +
256Y ARG* 3.3 20.9 + - - +
257Y CYS* 3.8 11.4 - - + -
260Y THR* 3.2 25.1 - - + +
266Y PHE* 3.1 41.1 - + - +
267Y ILE* 3.5 25.1 - - + -
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Residues in contact with LEU 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Y LEU 3.3 13.1 + - - +
186Y THR* 3.7 6.7 - - - +
187Y ASP 3.4 0.2 - - - -
188Y TYR* 1.3 78.3 - - - +
190Y MET* 1.3 55.1 + - - +
192Y ILE* 3.0 25.9 + - + +
193Y LEU* 2.8 51.4 + - + +
209Y VAL* 3.5 33.2 - - + +
212Y ILE* 3.7 11.9 - - + -
213Y LYS* 3.5 28.5 - - + +
217Y CYS* 4.6 7.2 - - - -
250Y ILE* 5.5 2.5 - - + -
253Y GLU* 4.6 16.2 - - + +
254Y ARG 5.3 0.7 - - - +
257Y CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (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 3.1 9.0 + - - +
187Y ASP* 3.1 17.9 - - - +
189Y LEU* 1.3 78.6 - - - +
191Y LYS* 1.3 57.4 + - - +
193Y LEU* 3.3 2.9 + - - +
194Y THR* 2.9 37.4 + - + +
200Y PHE* 3.7 29.5 - - + +
206Y ARG* 3.7 43.5 - - + +
209Y VAL* 3.2 35.7 - - + -
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Residues in contact with LYS 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Y ASP 3.4 5.1 + - - +
188Y TYR* 3.2 48.7 + - + +
190Y MET* 1.3 78.6 - - - +
192Y ILE* 1.3 65.2 + - - +
193Y LEU 2.8 7.3 + - - -
194Y THR* 2.9 10.5 + - - -
195Y GLU* 2.8 55.2 + - + +
266Y PHE 5.0 3.4 + - - -
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Residues in contact with ILE 192 (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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188Y TYR* 3.0 49.9 + - + +
189Y LEU* 3.0 23.1 + - + +
191Y LYS* 1.3 89.8 - - - +
193Y LEU* 1.3 55.7 + - - +
195Y GLU* 3.5 25.4 - - - +
196Y ARG* 3.2 20.4 + - - +
253Y GLU* 3.6 39.0 - - + +
256Y ARG* 3.6 32.6 + - + +
257Y CYS* 4.0 3.6 - - + +
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Residues in contact with LEU 193 (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* 2.8 36.3 + - + +
190Y MET 3.6 4.5 - - - +
191Y LYS 2.8 0.6 + - - -
192Y ILE* 1.3 79.1 - - - +
194Y THR* 1.3 62.8 + - - +
195Y GLU 3.2 0.9 - - - -
196Y ARG* 3.3 6.9 + - + -
198Y TYR* 2.8 40.5 - - + +
200Y PHE* 3.6 28.0 - - + -
209Y VAL* 4.1 9.9 - - + -
212Y ILE* 4.2 18.4 - - + -
249Y THR 4.5 0.9 - - - +
250Y ILE* 3.3 33.7 - - + -
253Y GLU* 4.1 13.5 - - + -
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Residues in contact with THR 194 (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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190Y MET* 2.9 27.0 + - + +
191Y LYS* 3.0 14.5 + - - +
193Y LEU* 1.3 76.3 - - - +
195Y GLU* 1.3 59.2 + - - +
197Y GLY* 2.9 9.9 + - - -
198Y TYR 2.9 37.0 + - - +
199Y SER* 4.9 0.2 - - - -
200Y PHE* 3.5 26.5 - - + +
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Residues in contact with GLU 195 (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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112X PRO* 5.8 10.1 - - + +
191Y LYS* 2.8 45.4 + - + +
192Y ILE* 3.5 24.3 - - - +
194Y THR* 1.3 78.0 + - - +
196Y ARG* 1.3 55.6 + - - +
197Y GLY* 3.0 8.8 + - - -
256Y ARG* 3.7 15.2 + - - +
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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