Contacts of the helix formed by residues 182 - 198 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H LYS 4.4 0.2 + - - -
181H VAL* 1.3 75.5 - - - +
183H ASP* 1.3 64.8 + - - +
184H LYS* 3.2 13.2 + - - +
185H GLU* 2.8 35.7 + - - +
186H ILE* 2.9 19.9 + - - +
210H ARG* 3.4 3.1 - - - +
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Residues in contact with ASP 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H SER* 1.3 73.4 - - - +
184H LYS* 1.3 52.2 + - - +
186H ILE* 3.0 6.9 + - - +
187H VAL* 2.7 37.9 + - - +
210H ARG* 2.9 33.7 + - - +
211H TRP* 2.9 25.0 + - + -
216H LYS* 3.2 34.7 - - - +
219H TRP* 4.0 13.1 - - + -
220H THR* 3.4 18.1 + - - +
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Residues in contact with LYS 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TRP 6.2 0.4 - - - -
182H SER* 3.2 9.6 + - - +
183H ASP* 1.3 77.5 - - - +
185H GLU* 1.3 62.8 + - + +
187H VAL* 3.3 13.8 + - + +
188H ALA* 3.1 21.0 + - + +
219H TRP* 3.7 38.4 - - + -
223H GLN* 4.8 7.9 + - - +
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Residues in contact with GLU 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H LEU* 3.7 8.2 - - + +
180H LYS 4.5 1.9 - - - +
181H VAL* 3.2 26.8 - - + +
182H SER* 2.8 41.1 + - - +
184H LYS* 1.3 80.5 - - + +
186H ILE* 1.3 55.9 + - - +
188H ALA* 3.4 8.3 + - - +
189H TYR* 3.0 28.2 + - - +
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Residues in contact with ILE 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H LEU* 4.1 16.2 - - + -
175H ILE* 3.6 46.7 - - + -
178H ASN* 5.9 0.2 - - + -
181H VAL* 3.7 21.3 - - + -
182H SER 2.9 11.1 + - - +
183H ASP* 3.0 9.6 + - - +
185H GLU* 1.3 70.9 - - - +
187H VAL* 1.3 66.5 + - - +
189H TYR* 3.2 7.3 + - + +
190H LEU* 2.9 35.4 + - + +
210H ARG* 3.6 30.5 - - - +
211H TRP* 4.3 10.8 - - + -
220H THR* 4.6 4.3 - - + -
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Residues in contact with VAL 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H ASP 2.7 18.6 + - - +
184H LYS* 3.3 18.1 + - + +
186H ILE* 1.3 72.8 - - - +
188H ALA* 1.3 60.5 + - - +
190H LEU 3.4 0.3 + - - -
191H ARG* 3.1 54.1 + - - +
219H TRP* 4.2 5.2 - - + -
220H THR* 3.7 37.2 - - + +
223H GLN* 3.9 17.9 - - + -
224H LEU* 3.5 16.4 - - + +
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Residues in contact with ALA 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H LYS* 3.1 13.7 + - + +
185H GLU* 3.7 9.9 - - - +
186H ILE 3.3 0.2 - - - -
187H VAL* 1.3 76.7 - - - +
189H TYR* 1.3 57.7 + - - +
191H ARG* 3.3 9.6 + - - +
192H GLU* 2.9 30.3 + - - +
195W GLU* 4.7 17.3 - - - +
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Residues in contact with TYR 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H LEU* 4.0 38.6 - - + -
152H ILE* 3.2 36.5 - - + +
153H VAL* 3.5 28.3 - - + -
156H TYR* 3.6 6.9 - - - -
174H CYS 2.7 28.9 + - - -
175H ILE* 4.4 10.4 - - + -
176H ILE 4.9 1.8 + - - -
185H GLU 3.0 17.2 + - - +
186H ILE* 3.5 12.6 - - + +
188H ALA* 1.3 75.2 - - - +
190H LEU* 1.3 75.6 + - + +
192H GLU* 3.3 10.1 + - - +
193H LEU* 3.0 44.9 + - + +
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Residues in contact with LEU 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H VAL* 4.5 4.5 - - + -
174H CYS 5.5 0.2 - - - +
175H ILE* 4.4 5.8 - - + -
186H ILE* 2.9 33.1 + - + +
187H VAL 4.1 0.2 - - - +
189H TYR* 1.3 94.3 - - + +
191H ARG* 1.3 64.9 + - - +
193H LEU* 3.3 11.7 + - + +
194H ARG 3.1 18.0 + - - -
203H MET* 3.5 10.6 - - + +
205H VAL* 4.0 42.4 - - + -
221H PHE* 4.3 10.3 - - + -
224H LEU* 3.5 31.4 - - + -
227H ILE* 3.6 12.6 - - + +
229H LEU* 4.9 1.1 - - + -
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Residues in contact with ARG 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H VAL* 3.1 31.0 + - - +
188H ALA* 3.6 10.8 - - - +
190H LEU* 1.3 72.3 - - - +
192H GLU* 1.3 65.8 + - - +
194H ARG* 3.3 3.6 + - - +
195H GLU* 3.1 26.2 + - - +
223H GLN* 2.8 36.1 + - - +
224H LEU* 3.6 10.4 - - + +
226H ASP* 2.5 39.6 + - - -
227H ILE* 3.9 17.0 - - + +
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Residues in contact with GLU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H SER* 5.3 6.7 + - - -
153H VAL* 3.6 35.5 - - + +
154H GLU* 4.5 7.3 - - - +
157H LYS* 4.6 5.7 + - - -
188H ALA 2.9 18.4 + - - +
189H TYR* 3.5 7.6 - - - +
191H ARG* 1.3 74.7 - - - +
193H LEU* 1.3 61.4 + - - +
195H GLU* 3.2 22.8 + - - +
196H VAL* 3.1 23.9 + - + +
150W SER* 5.1 5.9 + - - -
192W GLU* 5.2 13.3 - - - +
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Residues in contact with LEU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H VAL* 4.0 28.5 - - + -
156H TYR* 4.0 25.1 - - + -
160H ILE* 4.5 8.7 - - + -
173H VAL* 3.7 29.8 - - + -
189H TYR* 3.0 49.7 + - + +
190H LEU* 3.7 11.0 - - + +
191H ARG 3.3 0.6 - - - -
192H GLU* 1.3 77.2 - - - +
194H ARG* 1.3 56.7 + - - +
196H VAL* 3.2 4.8 + - + +
197H ILE* 2.8 37.2 + - + +
203H MET* 4.1 9.9 - - + -
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Residues in contact with ARG 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H LEU 3.1 8.9 + - - +
191H ARG 3.3 6.7 + - - +
193H LEU* 1.3 72.1 - - - +
195H GLU* 1.3 59.2 + - + +
197H ILE* 4.0 4.1 - - - +
198H GLY* 2.7 55.0 + - - -
199H TRP* 3.6 44.3 + - + +
201H MET 3.1 20.2 + - - -
202H ASP* 5.1 2.2 + - - +
203H MET* 3.6 47.5 - - - +
227H ILE* 2.9 44.2 + - + -
228H ASP* 3.1 19.4 + - - +
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Residues in contact with GLU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H ARG 3.1 16.4 + - - +
192H GLU* 3.3 22.9 - - + +
194H ARG* 1.3 79.1 - - + +
196H VAL* 1.3 62.8 + - + +
198H GLY* 3.6 7.4 + - - -
199H TRP* 5.6 4.3 - - - +
188W ALA* 5.0 16.0 - - - +
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Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H VAL* 4.4 11.7 - - + -
156H TYR* 6.0 0.2 - - + -
157H LYS* 3.7 45.8 - - + +
160H ILE* 3.8 30.0 - - + +
161H ALA 5.9 0.2 - - - +
164H LYS* 2.9 24.4 + - - -
192H GLU* 3.1 17.8 + - + +
193H LEU* 3.2 8.7 + - + +
194H ARG 3.2 0.2 - - - -
195H GLU* 1.3 78.2 - - + +
197H ILE* 1.3 58.9 + - - +
198H GLY 3.5 0.2 + - - -
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Residues in contact with ILE 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H ILE* 4.0 26.7 - - + -
164H LYS* 3.0 20.6 - - - -
171H VAL* 3.8 21.3 - - + -
173H VAL* 4.0 17.5 - - + -
193H LEU* 2.8 21.3 + - + +
194H ARG* 3.9 13.7 - - - +
196H VAL* 1.3 77.5 - - - +
198H GLY* 1.3 67.4 + - - +
200H ASP 5.1 0.3 + - - -
201H MET* 3.8 33.4 + - + +
203H MET* 3.8 31.0 - - + -
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Residues in contact with GLY 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H LYS* 4.7 3.4 - - - -
194H ARG* 2.7 43.2 + - - -
195H GLU* 3.6 6.5 + - - -
196H VAL 3.3 3.0 - - - -
197H ILE* 1.3 79.5 - - - +
199H TRP* 1.3 70.3 + - - -
200H ASP 3.5 2.1 + - - -
201H MET 4.1 0.3 - - - +
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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
------------------------------------------------------------
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