Contacts of the helix formed by residues 182 - 198 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181K VAL* 1.3 75.8 - - - +
183K ASP* 1.3 64.6 + - - +
184K LYS* 3.4 10.7 + - - +
185K GLU* 3.0 36.8 + - - +
186K ILE* 3.0 21.1 + - - +
210K ARG* 3.4 2.9 - - - +
216K LYS* 6.3 0.4 - - - +
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Residues in contact with ASP 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K SER* 1.3 74.3 - - - +
184K LYS* 1.3 57.5 + - - +
186K ILE* 3.2 6.8 + - - +
187K VAL* 2.9 32.4 + - - +
210K ARG* 2.9 31.4 + - - +
211K TRP* 2.7 28.1 + - - -
216K LYS* 3.3 35.4 + - - +
219K TRP* 3.8 12.2 - - + -
220K THR* 3.1 19.4 + - - +
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Residues in contact with LYS 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K SER* 3.2 9.5 + - - +
183K ASP* 1.3 77.4 - - - +
185K GLU* 1.3 63.1 + - + +
187K VAL* 3.4 19.9 - - + +
188K ALA* 3.2 21.4 + - + +
191K ARG* 5.4 2.2 - - - +
219K TRP* 3.6 37.3 - - + -
223K GLN* 4.3 11.9 + - - +
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Residues in contact with GLU 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LEU* 3.6 17.9 - - + +
180K LYS 4.7 1.4 - - - +
181K VAL* 3.5 16.1 - - - +
182K SER* 3.0 35.5 + - - +
184K LYS* 1.3 78.8 - - + +
186K ILE* 1.3 60.2 + - - +
188K ALA* 3.5 6.4 + - - +
189K TYR* 2.9 27.9 + - - +
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Residues in contact with ILE 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LEU* 4.4 13.2 - - + -
175K ILE* 3.7 48.7 - - + -
178K ASN* 6.0 0.7 - - + -
181K VAL* 3.7 22.0 - - + -
182K SER 3.0 17.7 + - - +
183K ASP* 3.2 8.9 + - - +
185K GLU* 1.3 73.7 - - - +
187K VAL* 1.3 55.2 + - - +
189K TYR* 3.2 8.1 + - + +
190K LEU* 2.8 45.9 + - + +
210K ARG* 3.6 24.9 - - - +
211K TRP* 4.4 10.1 - - + -
220K THR* 4.7 4.3 - - + -
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Residues in contact with VAL 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K ASP 2.9 17.3 + - - +
184K LYS* 3.4 21.8 - - + +
186K ILE* 1.3 77.3 - - - +
188K ALA* 1.3 58.3 + - - +
190K LEU 3.4 0.2 + - - -
191K ARG* 3.0 56.9 + - - +
219K TRP* 4.0 6.3 - - + -
220K THR* 3.8 22.7 - - + +
223K GLN* 3.8 26.9 - - + -
224K LEU* 3.5 18.4 - - + +
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Residues in contact with ALA 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D GLU* 6.0 2.2 - - - +
184K LYS* 3.2 11.9 + - + +
185K GLU* 3.8 9.9 - - - +
186K ILE 3.4 0.2 - - - -
187K VAL* 1.3 79.5 - - - +
189K TYR* 1.3 59.2 + - - +
191K ARG* 3.4 10.3 + - - +
192K GLU* 3.0 30.4 + - - +
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Residues in contact with TYR 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LEU* 3.9 43.5 - - + -
152K ILE* 3.4 18.8 - - + +
153K VAL* 3.6 30.5 - - + -
156K TYR* 3.4 17.7 - - - -
174K CYS 2.7 29.1 + - - -
175K ILE* 4.4 11.2 - - + -
176K ILE* 4.9 1.5 + - - +
185K GLU 2.9 18.4 + - - +
186K ILE* 3.4 13.5 - - + +
188K ALA* 1.3 76.3 - - - +
190K LEU* 1.3 84.1 + - + +
192K GLU* 3.4 8.7 + - - +
193K LEU* 3.1 33.7 + - + +
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Residues in contact with LEU 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K VAL* 4.4 12.8 - - + -
175K ILE* 4.3 7.4 - - + -
186K ILE* 2.8 34.5 + - + +
187K VAL 4.1 2.9 - - - +
189K TYR* 1.3 94.8 - - + +
191K ARG* 1.3 65.2 + - - +
193K LEU* 3.4 4.3 + - + +
194K ARG 3.0 17.3 + - - -
203K MET* 3.6 11.4 - - + +
205K VAL* 4.2 38.8 - - + -
221K PHE* 4.4 8.7 - - + -
224K LEU* 3.7 28.5 - - + -
227K ILE* 3.6 12.3 - - + +
229K LEU* 5.1 0.7 - - + -
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Residues in contact with ARG 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K LYS* 5.4 2.4 - - - +
187K VAL* 3.0 45.1 + - - +
188K ALA* 3.7 9.2 - - - +
189K TYR 3.4 0.2 - - - -
190K LEU* 1.3 72.8 - - - +
192K GLU* 1.3 67.8 + - - +
194K ARG* 3.2 3.3 + - - +
195K GLU* 3.1 24.6 + - + +
223K GLN* 2.8 31.2 + - - +
224K LEU* 3.9 7.3 - - + +
226K ASP* 2.6 35.7 + - - -
227K ILE* 4.1 18.0 - - + +
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Residues in contact with GLU 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D SER* 5.3 5.0 + - - -
192D GLU* 5.1 12.4 - - - +
150K SER* 5.2 7.0 + - - -
153K VAL* 3.7 37.1 - - + +
154K GLU* 4.4 7.6 - - - +
157K LYS* 4.5 5.7 + - - -
188K ALA 3.0 18.8 + - - +
189K TYR* 3.7 7.2 - - - +
190K LEU 3.3 0.2 - - - -
191K ARG* 1.3 75.5 - - - +
193K LEU* 1.3 62.9 + - - +
195K GLU* 3.1 26.4 + - + +
196K VAL* 3.0 25.1 + - + +
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Residues in contact with LEU 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K VAL* 4.2 22.0 - - + -
156K TYR* 3.9 35.4 - - + -
160K ILE* 4.4 10.5 - - + -
173K VAL* 3.8 24.9 - - + -
189K TYR* 3.1 52.2 + - + +
190K LEU* 3.8 6.7 - - + +
191K ARG 3.2 0.2 - - - -
192K GLU* 1.3 77.0 - - - +
194K ARG* 1.3 56.0 + - - +
196K VAL* 3.8 6.5 - - + +
197K ILE* 3.0 37.2 + - + +
203K MET* 4.0 11.2 - - + -
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Residues in contact with ARG 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K LEU 3.0 14.4 + - - +
191K ARG 3.2 7.6 + - - +
193K LEU* 1.3 75.2 - - - +
195K GLU* 1.3 60.0 + - - +
197K ILE* 3.3 3.8 + - - +
198K GLY* 2.8 59.2 + - - -
199K TRP* 3.7 42.1 + - + +
201K MET 3.3 18.6 + - - -
202K ASP* 5.0 1.8 + - - +
203K MET* 3.6 41.9 - - - +
227K ILE* 2.8 45.7 + - + -
228K ASP* 3.3 19.0 + - - +
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Residues in contact with GLU 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ALA* 4.2 20.8 - - - +
191K ARG* 3.1 13.5 + - + +
192K GLU* 3.1 28.5 + - + +
194K ARG* 1.3 76.8 - - - +
196K VAL* 1.3 66.7 + - + +
198K GLY* 3.4 9.2 + - - -
199K TRP* 5.9 3.1 - - - +
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Residues in contact with VAL 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K VAL* 4.6 9.0 - - + -
157K LYS* 3.8 44.4 - - + +
160K ILE* 4.0 29.1 - - + +
164K LYS* 2.9 25.5 + - - -
192K GLU* 3.0 19.5 + - + +
193K LEU* 3.8 11.7 - - + +
195K GLU* 1.3 78.1 - - + +
197K ILE* 1.3 58.6 + - - +
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Residues in contact with ILE 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K ILE* 4.1 26.9 - - + -
164K LYS* 3.2 19.3 + - - -
171K VAL* 3.8 21.8 - - + -
173K VAL* 4.2 13.9 - - + -
193K LEU* 3.0 23.3 + - + +
194K ARG* 3.9 13.7 - - - +
196K VAL* 1.3 76.1 - - - +
198K GLY* 1.3 70.2 + - - +
200K ASP* 4.9 1.6 + - - +
201K MET* 3.9 32.3 + - + +
203K MET* 3.7 30.7 - - + -
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Residues in contact with GLY 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K LYS* 5.0 2.5 - - - -
194K ARG* 2.8 45.1 + - - -
195K GLU 3.4 6.5 + - - -
196K VAL 3.4 2.4 - - - -
197K ILE* 1.3 84.6 - - - +
199K TRP* 1.3 67.0 + - - -
200K ASP 3.5 1.3 + - - -
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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