Contacts of the helix formed by residues 185 - 197 (chain C) in PDB entry 3HTM
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 ARG 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C PRO* 6.0 5.3 - - - +
183C GLU 4.2 9.0 - - - +
184C CYS* 1.3 75.6 - - - +
186C LEU* 1.3 62.7 + - - +
187C ALA 3.3 1.8 - - - +
188C ASP* 3.9 21.3 - - + +
189C GLU* 3.0 51.7 + - + +
221D ARG* 3.7 8.5 - - - +
283D GLU* 3.8 31.5 - - - +
284D ARG* 4.6 15.5 - - + +
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C CYS* 3.6 19.0 - - - -
185C ARG* 1.3 78.3 - - - +
187C ALA* 1.3 58.0 + - - +
189C GLU* 3.8 1.2 - - - +
190C LEU* 3.0 40.5 + - + +
186D LEU* 4.4 6.1 - - + -
187D ALA* 4.0 17.3 - - + +
190D LEU* 3.8 22.0 - - + -
217D ILE* 6.0 0.2 - - + -
221D ARG* 3.4 38.9 - - - +
258D ILE 3.8 4.5 - - - +
259D TYR* 3.6 24.2 - - - +
260D THR* 3.5 22.4 - - - +
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C CYS* 5.3 0.4 - - - -
185C ARG* 3.3 0.6 - - - -
186C LEU* 1.3 80.5 - - - +
188C ASP* 1.3 57.6 + - - +
190C LEU* 3.2 2.0 + - - +
191C GLY 2.9 24.9 + - - -
260C THR* 3.4 37.3 - - - +
262C LYS* 4.3 19.3 - - - +
186D LEU* 3.9 15.6 - - + +
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Residues in contact with ASP 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C CYS 4.8 1.7 - - - +
185C ARG* 3.6 24.9 + - + +
186C LEU 3.4 0.2 - - - -
187C ALA* 1.3 75.5 - - - +
189C GLU* 1.3 60.5 + - + +
191C GLY* 3.2 3.5 + - - -
192C GLY* 3.0 23.4 + - - -
260C THR* 5.5 0.2 - - - -
262C LYS* 3.9 17.9 + - - -
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ARG* 3.0 43.5 + - + +
186C LEU 3.9 2.5 - - - +
188C ASP* 1.3 74.4 - - + +
190C LEU* 1.3 60.8 + - + +
192C GLY* 3.2 3.4 + - - +
193C LEU 3.0 21.0 + - - -
220D ALA* 3.5 33.7 - - + +
221D ARG* 2.6 49.6 + - - +
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C LEU* 3.0 25.9 + - + +
187C ALA 3.8 1.1 - - - +
189C GLU* 1.3 74.4 - - + +
191C GLY* 1.3 66.3 + - - +
193C LEU* 3.0 32.2 + - + +
194C TRP 3.1 9.9 + - - -
217C ILE* 4.6 11.9 - - + -
259C TYR* 3.1 38.5 - - + +
186D LEU* 3.8 15.0 - - + -
190D LEU* 2.9 40.2 - - + -
217D ILE* 4.6 17.0 - - + -
220D ALA* 5.2 4.0 - - + -
221D ARG* 5.9 2.5 - - - -
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Residues in contact with GLY 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ALA 2.9 11.3 + - - -
188C ASP* 3.6 5.2 - - - -
190C LEU* 1.3 78.6 - - - +
192C GLY* 1.3 60.1 + - - +
194C TRP* 3.2 10.1 + - - +
195C GLU* 2.9 30.3 + - - +
259C TYR* 4.7 0.2 - - - -
260C THR* 3.4 23.5 - - - +
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Residues in contact with GLY 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ASP 3.0 13.6 + - - -
189C GLU* 3.2 5.3 + - - -
190C LEU 3.1 0.6 - - - -
191C GLY* 1.3 77.2 - - - +
193C LEU* 1.3 62.1 + - - +
195C GLU* 4.4 5.8 - - - -
196C ASN* 2.9 42.4 + - - +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLU 3.0 12.2 + - - +
190C LEU* 3.1 17.9 - - + +
192C GLY* 1.3 77.5 - - - +
194C TRP* 1.3 56.7 + - - +
196C ASN* 3.9 1.9 - - - +
197C SER* 3.0 25.8 + - - -
198C ARG* 3.8 22.5 + - + +
199C PHE* 5.6 0.2 - - + -
214C HIS* 3.8 10.8 - - + +
217C ILE* 3.7 28.5 - - + -
259C TYR* 4.6 1.6 - - + -
216D ALA* 3.6 49.4 - - + +
217D ILE* 4.1 4.7 - - - +
219D ALA* 6.0 0.2 - - + -
220D ALA* 3.9 14.5 - - + +
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Residues in contact with TRP 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LEU 3.1 2.9 + - - +
191C GLY* 3.2 9.4 + - - +
193C LEU* 1.3 79.0 - - - +
195C GLU* 1.3 86.4 + - - +
197C SER* 3.4 15.5 + - - -
211C PHE* 4.2 30.7 - + + -
212C GLN 3.3 24.9 - - - -
213C ALA* 4.2 10.3 - - + -
214C HIS* 4.8 2.9 - + - -
251C PHE* 4.4 0.4 - + - -
252C LYS* 4.7 15.0 + - + +
255C MSE 3.5 38.2 - - + +
256C CYS* 4.7 16.3 - - + +
259C TYR* 3.5 48.7 - + + -
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Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C GLY* 2.9 23.1 + - - +
192C GLY* 3.9 6.5 - - - +
194C TRP* 1.3 93.4 + - + +
196C ASN* 1.3 66.5 + - - +
197C SER* 4.0 3.6 + - - -
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Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLY* 2.9 33.9 + - - +
193C LEU* 4.3 1.8 - - - +
195C GLU* 1.3 80.6 - - - +
197C SER* 1.3 72.8 + - - +
198C ARG* 3.5 17.6 + - + +
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Residues in contact with SER 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU 3.0 13.6 + - - -
194C TRP* 3.4 13.8 + - - -
195C GLU 3.4 4.4 + - - -
196C ASN* 1.3 80.6 - - - +
198C ARG* 1.3 58.5 + - - +
199C PHE 4.3 0.3 + - - -
200C THR* 3.8 20.5 + - - -
212C GLN* 4.3 21.8 + - - +
214C HIS* 4.7 4.3 - - - -
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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