Contacts of the helix formed by residues 182 - 198 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181F VAL* 1.3 75.3 - - - +
183F ASP* 1.3 64.4 + - - +
184F LYS* 3.5 9.4 + - - +
185F GLU* 2.8 38.7 + - - +
186F ILE* 3.0 22.9 + - - +
210F ARG* 3.6 2.7 - - - +
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Residues in contact with ASP 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F SER* 1.3 74.5 - - - +
184F LYS* 1.3 57.8 + - - +
186F ILE* 3.0 8.0 + - - +
187F VAL* 2.9 31.5 + - - +
210F ARG* 2.9 33.3 + - - +
211F TRP* 2.9 25.7 + - + -
216F LYS* 3.3 32.7 - - - +
219F TRP* 4.0 12.7 - - + -
220F THR* 3.5 18.6 + - - +
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Residues in contact with LYS 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F SER* 3.3 8.6 + - - +
183F ASP* 1.3 77.5 - - - +
185F GLU* 1.3 57.5 + - + +
187F VAL* 3.4 21.5 - - + +
188F ALA* 3.2 24.1 + - + +
191F ARG* 4.6 6.1 - - - +
219F TRP* 3.4 36.2 - - + -
223F GLN* 4.4 12.5 + - - +
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Residues in contact with GLU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F LEU* 4.0 17.4 - - + +
180F LYS 4.5 1.6 - - - +
181F VAL* 3.4 16.7 - - - +
182F SER* 2.8 42.3 + - - +
184F LYS* 1.3 76.7 - - + +
186F ILE* 1.3 59.3 + - - +
188F ALA* 3.3 8.3 + - - +
189F TYR* 2.9 29.2 + - - +
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Residues in contact with ILE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F LEU* 4.4 14.8 - - + -
175F ILE* 3.5 52.0 - - + -
178F ASN* 6.1 0.4 - - + -
181F VAL* 3.7 19.7 - - + -
182F SER 3.0 17.1 + - - +
183F ASP* 3.0 11.7 + - - +
185F GLU* 1.3 72.6 - - - +
187F VAL* 1.3 60.2 + - - +
189F TYR* 3.1 7.8 + - + +
190F LEU* 2.8 40.8 + - + +
210F ARG* 3.7 21.3 - - - +
211F TRP* 4.5 9.9 - - + -
220F THR* 4.8 3.8 - - + -
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Residues in contact with VAL 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F ASP 2.9 16.2 + - - +
184F LYS* 3.4 23.3 - - + +
186F ILE* 1.3 77.2 - - - +
188F ALA* 1.3 58.6 + - - +
190F LEU 3.3 0.5 + - - -
191F ARG* 2.9 68.3 + - - +
219F TRP* 4.0 11.7 - - + -
220F THR* 3.8 32.5 - - + +
223F GLN* 4.0 10.3 - - + -
224F LEU* 3.7 13.9 - - + +
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Residues in contact with ALA 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F LYS* 3.2 12.5 + - + +
185F GLU* 3.3 10.1 + - - +
187F VAL* 1.3 79.9 - - - +
189F TYR* 1.3 62.4 + - - +
191F ARG* 3.6 8.5 + - - +
192F GLU* 3.0 25.9 + - - +
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Residues in contact with TYR 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F LEU* 3.8 37.7 - - + -
152F ILE* 3.4 33.8 - - + +
153F VAL* 3.7 25.1 - - + -
156F TYR* 3.4 8.7 - - - -
174F CYS 2.7 28.9 + - - -
175F ILE* 4.3 12.2 - - + -
176F ILE 5.0 1.5 + - - -
185F GLU 2.9 14.4 + - - +
186F ILE* 3.2 18.2 - - + +
188F ALA* 1.3 74.6 - - - +
190F LEU* 1.3 71.8 + - + +
192F GLU* 3.3 9.7 + - - +
193F LEU* 3.1 48.3 + - + +
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Residues in contact with LEU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F VAL* 4.4 2.7 - - + -
174F CYS 5.7 0.4 - - - +
175F ILE* 4.2 4.5 - - + -
186F ILE* 2.8 35.6 + - + +
187F VAL 3.9 2.7 - - - +
189F TYR* 1.3 90.3 - - + +
191F ARG* 1.3 65.7 + - - +
193F LEU* 3.2 12.1 + - + +
194F ARG* 3.0 20.8 + - - +
203F MET* 3.6 13.9 - - + +
205F VAL* 4.0 40.8 - - + -
221F PHE* 4.3 9.0 - - + -
224F LEU* 3.5 31.4 - - + -
227F ILE* 4.1 8.5 - - + -
229F LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F LYS* 4.6 6.3 - - - +
187F VAL* 2.9 42.1 + - - +
188F ALA* 3.8 7.3 - - - +
190F LEU* 1.3 75.8 - - - +
192F GLU* 1.3 63.1 + - - +
194F ARG* 3.3 4.7 + - - +
195F GLU* 3.2 28.7 + - - +
223F GLN* 2.9 31.8 + - - +
224F LEU* 3.7 10.2 - - + +
226F ASP* 2.6 39.6 + - - -
227F ILE* 4.0 14.8 - - + +
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Residues in contact with GLU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F SER* 5.3 4.7 + - - -
153F VAL* 3.4 38.3 - - + +
154F GLU* 5.5 0.7 - - - +
157F LYS* 4.5 7.4 + - - -
188F ALA 3.0 15.2 + - - +
189F TYR* 3.3 11.2 + - - +
191F ARG* 1.3 74.8 - - - +
193F LEU* 1.3 62.8 + - - +
195F GLU* 3.1 22.0 + - - +
196F VAL* 3.0 28.4 + - - +
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Residues in contact with LEU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F VAL* 4.5 20.6 - - + -
156F TYR* 4.1 29.4 - - + -
160F ILE* 4.4 11.0 - - + -
173F VAL* 3.8 28.0 - - + -
189F TYR* 3.1 52.2 + - + +
190F LEU* 3.2 11.1 + - + +
192F GLU* 1.3 75.7 - - - +
194F ARG* 1.3 51.9 + - - +
196F VAL* 3.1 7.0 + - + +
197F ILE* 2.7 43.9 + - + +
203F MET* 4.2 8.7 - - + -
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Residues in contact with ARG 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F LEU 3.0 9.9 + - - +
191F ARG 3.6 8.7 - - - +
193F LEU* 1.3 76.4 - - - +
195F GLU* 1.3 53.7 + - + +
197F ILE* 4.2 3.6 - - - +
198F GLY* 2.6 63.6 + - - -
199F TRP* 3.7 43.4 + - + +
201F MET 3.1 21.4 + - - -
202F ASP* 5.0 2.2 + - - +
203F MET* 3.5 44.1 - - - +
227F ILE* 2.9 42.7 + - + -
228F ASP* 3.2 18.6 + - - +
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LYS* 5.4 0.2 + - - -
191F ARG* 3.2 16.6 + - - +
192F GLU* 3.1 22.1 + - - +
194F ARG* 1.3 79.4 - - + +
196F VAL* 1.3 64.1 + - + +
198F GLY* 3.4 9.3 + - - -
199F TRP* 5.6 3.1 - - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F VAL* 4.8 8.7 - - + -
156F TYR* 6.1 0.2 - - + -
157F LYS* 4.2 43.5 - - + +
160F ILE* 3.8 29.4 - - + +
164F LYS* 2.9 24.3 + - - -
192F GLU* 3.0 17.9 + - - +
193F LEU* 3.6 10.5 - - + +
195F GLU* 1.3 79.1 - - + +
197F ILE* 1.3 57.4 + - - +
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Residues in contact with ILE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F ILE* 3.8 26.7 - - + -
164F LYS* 3.1 21.3 - - - -
171F VAL* 3.8 20.2 - - + -
173F VAL* 4.1 18.2 - - + -
193F LEU 2.7 24.2 + - - +
194F ARG* 3.7 13.2 - - - +
196F VAL* 1.3 73.0 - - - +
198F GLY* 1.3 69.6 + - - +
199F TRP 4.0 0.2 + - - -
200F ASP 5.0 1.4 + - - -
201F MET* 3.8 32.0 - - + +
203F MET* 3.7 30.3 - - + -
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Residues in contact with GLY 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LYS* 5.0 2.5 - - - -
194F ARG* 2.6 43.3 + - - -
195F GLU* 3.4 7.1 + - - -
196F VAL 3.3 2.8 - - - -
197F ILE* 1.3 80.9 - - - +
199F TRP* 1.3 72.9 + - - -
200F ASP 3.7 0.6 + - - -
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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