Contacts of the helix formed by residues 182 - 198 (chain P) in PDB entry 3MQT
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 SER 182 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181P VAL* 1.3 76.6 - - - +
183P ASP* 1.3 59.3 + - - +
184P LYS* 3.4 12.5 + - - +
185P GLU* 2.8 38.4 + - - +
186P ILE* 3.0 25.5 + - - +
210P ARG* 3.6 1.8 - - - +
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Residues in contact with ASP 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P SER* 1.3 69.5 - - - +
184P LYS* 1.3 61.0 + - - +
186P ILE* 3.1 8.6 + - - +
187P VAL* 2.9 32.7 + - - +
210P ARG* 3.0 32.4 + - - +
211P TRP* 2.8 27.7 + - - -
216P LYS* 3.2 31.9 + - - +
219P TRP* 3.9 12.6 - - + -
220P THR* 3.4 18.9 + - - +
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Residues in contact with LYS 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P SER* 3.5 10.5 - - - +
183P ASP* 1.3 77.0 - - - +
185P GLU* 1.3 61.3 + - + +
187P VAL* 3.3 25.4 + - + +
188P ALA* 3.2 20.3 + - - +
191P ARG* 4.5 5.5 - - - +
219P TRP* 3.5 38.9 - - + -
223P GLN* 4.1 11.5 + - - +
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Residues in contact with GLU 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P LEU* 3.9 18.3 - - + +
180P LYS 4.9 0.9 - - - +
181P VAL* 3.6 15.1 - - + +
182P SER* 2.8 43.5 + - - +
184P LYS* 1.3 76.4 - - + +
186P ILE* 1.3 61.2 + - - +
188P ALA* 3.3 7.4 + - - +
189P TYR* 2.9 30.5 + - - +
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Residues in contact with ILE 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149P LEU* 4.4 13.9 - - + -
175P ILE* 3.8 46.0 - - + -
178P ASN* 6.2 0.2 - - + -
181P VAL* 3.6 22.2 - - + -
182P SER 3.0 17.2 + - - +
183P ASP* 3.1 10.5 + - - +
185P GLU* 1.3 75.0 - - - +
187P VAL* 1.3 57.2 + - - +
189P TYR* 3.2 8.6 - - + +
190P LEU* 2.8 40.7 + - + +
210P ARG* 3.6 23.1 - - - +
211P TRP* 4.4 10.8 - - + -
220P THR* 4.4 5.6 - - + -
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Residues in contact with VAL 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P ASP 2.9 17.9 + - - +
184P LYS* 3.3 22.4 + - + +
186P ILE* 1.3 73.6 - - - +
188P ALA* 1.3 63.3 + - - +
190P LEU* 3.2 2.4 + - - -
191P ARG* 2.9 58.8 + - - +
219P TRP* 3.9 18.2 - - + -
220P THR* 3.8 29.6 - - + +
223P GLN* 3.9 8.5 - - + -
224P LEU* 3.8 14.4 - - + +
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Residues in contact with ALA 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P LYS 3.2 11.5 + - - +
185P GLU* 3.3 8.3 + - - +
187P VAL* 1.3 76.2 - - - +
189P TYR* 1.3 65.1 + - - +
191P ARG* 3.3 7.9 + - - +
192P GLU* 2.9 27.6 + - - +
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Residues in contact with TYR 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149P LEU* 4.1 39.5 - - + -
152P ILE* 3.3 29.3 - - + +
153P VAL* 3.6 29.4 - - + -
156P TYR* 3.4 8.7 - - - -
174P CYS 2.8 28.7 + - - -
175P ILE* 4.3 12.1 - - + -
176P ILE 5.0 2.0 + - - -
185P GLU 2.9 15.0 + - - +
186P ILE* 3.2 20.0 - - + +
188P ALA* 1.3 77.4 - - - +
190P LEU* 1.3 82.6 + - + +
192P GLU* 3.2 9.3 + - - +
193P LEU* 3.1 29.9 + - + +
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Residues in contact with LEU 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173P VAL* 4.4 13.0 - - + -
174P CYS 5.5 0.2 - - - +
175P ILE* 4.3 5.6 - - + -
186P ILE* 2.8 33.0 + - + +
187P VAL 3.2 0.2 + - - -
189P TYR* 1.3 91.6 - - + +
191P ARG* 1.3 64.5 + - - +
193P LEU* 3.4 3.9 + - + -
194P ARG 3.1 16.8 + - - -
203P MET* 3.5 11.8 - - + +
205P VAL* 4.1 42.6 - - + -
221P PHE* 4.4 7.6 - - + -
224P LEU* 3.6 26.2 - - + -
227P ILE* 3.5 18.7 - - + +
229P LEU* 5.2 0.4 - - + -
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Residues in contact with ARG 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P LYS* 4.5 5.9 - - - +
187P VAL* 2.9 40.5 + - - +
188P ALA* 3.6 8.1 - - - +
190P LEU* 1.3 72.7 - - - +
192P GLU* 1.3 66.9 + - - +
194P ARG* 3.3 4.2 + - - +
195P GLU* 3.0 30.9 + - - +
223P GLN* 2.8 29.7 + - - +
224P LEU* 3.8 10.9 - - + +
226P ASP* 2.7 42.0 + - - -
227P ILE* 4.0 14.9 - - + +
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Residues in contact with GLU 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149P LEU 5.9 0.2 - - - -
150P SER* 5.2 7.3 + - - -
153P VAL* 3.6 34.0 - - + +
157P LYS* 5.5 2.3 + - - -
188P ALA* 2.9 15.4 + - + +
189P TYR* 3.3 12.9 - - - +
191P ARG* 1.3 77.4 - - - +
193P LEU* 1.3 57.5 + - - +
195P GLU* 3.0 23.0 + - - +
196P VAL* 2.9 33.8 + - - +
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Residues in contact with LEU 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P VAL* 4.3 19.3 - - + -
156P TYR* 3.9 33.9 - - + -
160P ILE* 4.3 12.6 - - + -
173P VAL* 3.8 24.7 - - + -
189P TYR* 3.1 47.7 + - + +
190P LEU* 3.8 10.1 - - + +
191P ARG 3.3 0.2 - - - -
192P GLU* 1.3 78.3 - - - +
194P ARG* 1.3 56.7 + - - +
196P VAL* 3.4 5.7 + - + +
197P ILE* 2.9 36.1 + - + +
203P MET* 4.0 10.8 - - + -
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Residues in contact with ARG 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P LEU 3.1 9.4 + - - +
191P ARG 3.7 7.0 - - - +
192P GLU 3.2 0.2 - - - -
193P LEU* 1.3 73.1 - - - +
195P GLU* 1.3 61.5 + - + +
197P ILE* 4.1 3.5 - - - +
198P GLY* 2.8 58.7 + - - -
199P TRP* 3.6 44.3 + - + +
201P MET 3.3 20.2 + - - -
202P ASP* 5.1 1.6 + - - +
203P MET* 3.7 42.7 - - - +
227P ILE* 2.8 44.3 + - + -
228P ASP* 3.2 20.6 + - - +
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Residues in contact with GLU 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191P ARG* 3.0 21.4 + - - +
192P GLU* 3.0 24.4 + - - +
194P ARG* 1.3 79.8 - - + +
196P VAL* 1.3 63.3 + - + +
198P GLY* 3.4 8.9 + - - -
199P TRP* 5.8 2.5 - - - +
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Residues in contact with VAL 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P VAL* 4.7 9.2 - - + -
157P LYS* 4.1 41.1 - - + +
160P ILE* 3.8 27.8 - - + +
164P LYS* 2.8 29.8 + - - -
192P GLU* 2.9 21.7 + - - +
193P LEU* 3.8 10.5 - - + +
194P ARG 3.2 0.2 - - - -
195P GLU* 1.3 77.3 - - + +
197P ILE* 1.3 54.3 + - - +
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Residues in contact with ILE 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P ILE* 3.9 28.3 - - + -
164P LYS* 3.1 19.2 - - - -
171P VAL* 3.9 20.0 - - + -
173P VAL* 4.2 13.9 - - + -
193P LEU* 2.9 21.9 + - + +
194P ARG* 3.9 13.7 - - - +
196P VAL* 1.3 75.9 - - - +
198P GLY* 1.3 70.9 + - - +
200P ASP* 4.9 2.8 + - - +
201P MET* 3.9 29.3 - - + +
203P MET* 3.7 35.2 - - + -
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Residues in contact with GLY 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P LYS* 4.8 3.1 - - - -
194P ARG* 2.8 38.0 + - - -
195P GLU 3.4 6.7 + - - -
196P VAL 3.3 3.0 - - - -
197P ILE* 1.3 83.3 - - - +
199P TRP* 1.3 71.6 + - - -
200P ASP 3.6 1.1 + - - -
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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