Contacts of the helix formed by residues 185 - 201 (chain C) in PDB entry 3N6J
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 ASP 185 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C TYR* 5.0 3.4 - - - -
182C LYS* 6.2 0.3 - - - -
184C MSE 1.3 79.7 + - - +
186C THR* 1.3 69.2 + - - +
187C GLN* 3.0 34.7 - - - +
188C ALA* 3.1 28.0 + - - +
189C VAL* 3.5 9.6 + - - +
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Residues in contact with THR 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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154C TYR* 5.3 0.6 - - - -
185C ASP* 1.3 72.0 - - - +
187C GLN* 1.3 54.8 + - - +
189C VAL* 2.6 30.8 + - - +
190C ILE* 3.2 25.4 + - + -
216C LYS 4.4 2.6 + - - -
219C ASP* 4.4 4.3 - - - +
220C THR* 2.5 52.9 + - + +
223C GLU* 3.8 19.7 - - + -
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Residues in contact with GLN 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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185C ASP* 3.0 15.7 - - - +
186C THR* 1.3 78.0 - - - +
188C ALA* 1.3 60.1 + - - +
190C ILE* 3.2 28.8 + - - +
191C GLU* 3.2 34.2 + - + +
227C HIS* 6.2 0.2 + - - -
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Residues in contact with ALA 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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178C ILE* 5.5 1.0 - - - +
182C LYS 4.5 4.3 - - - +
183C ALA* 3.6 27.5 - - + +
185C ASP* 3.1 26.2 + - - +
186C THR 2.9 1.2 + - - -
187C GLN* 1.3 79.9 - - - +
189C VAL* 1.3 61.3 + - - +
191C GLU* 3.6 11.2 - - - +
192C LEU* 3.3 26.7 + - - +
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Residues in contact with VAL 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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152C LEU* 4.4 14.0 - - + +
153C PHE 4.3 13.9 - - - +
154C TYR* 4.1 28.0 - - + -
183C ALA 4.6 5.2 - - - +
185C ASP 3.5 11.9 + - - +
186C THR 2.6 16.5 + - - +
188C ALA* 1.3 70.1 - - - +
190C ILE* 1.3 62.2 + - - -
192C LEU* 3.4 10.8 + - + +
193C ALA* 3.1 19.6 + - - +
207C LEU* 4.1 21.5 - - + -
220C THR* 4.1 16.4 - - + -
224C LEU* 4.4 10.1 - - + -
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Residues in contact with ILE 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 THR* 3.2 37.8 + - + +
187C GLN* 3.2 24.2 + - - +
189C VAL* 1.3 72.2 - - + +
191C GLU* 1.3 59.6 + - - +
192C LEU 2.8 3.1 + - - -
193C ALA* 2.8 7.6 + - - +
194C ALA* 2.7 36.2 + - + +
223C GLU* 4.1 15.3 - - + +
224C LEU* 4.4 14.1 - - + -
227C HIS* 3.9 36.3 - - + +
228C PHE* 3.8 23.8 - - + -
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Residues in contact with GLU 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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174C GLU* 4.7 12.6 - - - +
178C ILE* 4.7 23.5 - - + +
187C GLN* 3.2 36.5 + - + +
188C ALA* 3.6 11.9 - - - +
190C ILE* 1.3 78.0 - - - +
192C LEU* 1.3 60.3 + - - +
194C ALA* 3.4 12.2 - - - +
195C ALA* 3.4 21.5 + - - +
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Residues in contact with LEU 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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152C LEU* 4.2 9.4 - - + -
153C PHE 3.7 24.9 - - - +
155C VAL* 4.6 5.8 - - + -
175C TRP* 4.2 19.2 - - + -
178C ILE* 3.9 43.5 - - + +
179C ARG* 4.2 3.6 - - - -
183C ALA* 3.8 20.2 - - + -
188C ALA 3.3 16.8 - - - +
189C VAL* 3.4 14.1 + - + +
190C ILE 2.8 1.8 + - - -
191C GLU* 1.3 74.5 - - - +
193C ALA* 1.3 63.1 + - - +
194C ALA 3.1 1.3 - - - -
195C ALA* 3.1 2.9 + - - +
196C SER* 2.8 28.8 + - - -
372C TRP* 4.8 7.6 - - + -
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Residues in contact with ALA 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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152C LEU* 3.7 19.4 - - + +
189C VAL 3.1 10.0 + - - +
190C ILE 2.8 9.5 + - - +
192C LEU* 1.3 74.1 - - - +
194C ALA* 1.3 63.2 + - - +
196C SER* 3.6 7.0 - - - -
197C LYS* 3.1 25.5 + - - +
205C PHE* 3.5 20.2 - - + -
224C LEU* 4.2 5.4 - - + -
228C PHE* 3.7 23.0 - - + -
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLU* 5.9 0.9 - - - +
190C ILE* 2.7 18.9 + - + +
191C GLU* 3.4 20.6 - - - +
193C ALA* 1.3 73.7 - - - +
195C ALA* 1.3 57.9 + - + +
197C LYS* 3.6 4.2 + - - +
198C ASP* 3.1 25.0 + - - +
228C PHE* 3.8 18.1 - - + -
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Residues in contact with ALA 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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173C HIS* 3.5 6.6 + - - +
174C GLU* 3.9 19.5 - - + +
175C TRP* 4.2 28.3 - - + +
178C ILE* 4.5 3.6 - - + -
191C GLU 3.4 11.9 + - - +
192C LEU 3.1 4.2 + - - +
194C ALA* 1.3 77.4 - - - +
196C SER* 1.3 61.9 + - - +
198C ASP* 3.4 7.5 - - - +
199C ARG* 2.8 31.8 + - - +
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 4.1 7.4 - - - +
175C TRP* 4.2 22.0 - - - -
192C LEU 2.8 19.1 + - - -
193C ALA* 3.6 9.4 - - - -
195C ALA* 1.3 75.2 - - - +
197C LYS* 1.3 60.4 + - - +
200C TYR* 2.9 46.1 + - - +
202C PHE* 3.3 21.0 - - - -
205C PHE* 3.9 7.1 - - - -
371C ILE* 4.4 4.0 - - - +
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Residues in contact with LYS 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 ALA 3.1 19.8 + - - +
194C ALA* 3.7 4.0 - - - +
196C SER* 1.3 77.0 + - - +
198C ASP* 1.3 61.0 + - - +
201C GLY* 2.5 38.6 + - - +
202C PHE* 3.2 35.6 + - - +
203C LYS* 4.9 6.5 - - - +
205C PHE* 3.6 14.2 - - + -
228C PHE* 4.1 28.6 - - - +
231C ALA* 4.9 4.8 - - - +
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Residues in contact with ASP 198 (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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173C HIS* 2.6 29.7 - - + -
194C ALA 3.1 13.3 + - - +
195C ALA* 3.4 12.3 - - - +
197C LYS* 1.3 82.8 - - - +
199C ARG* 1.3 60.8 + - - +
200C TYR 5.0 0.2 - - - -
201C GLY 4.6 0.5 + - - -
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Residues in contact with ARG 199 (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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173C HIS* 3.5 36.5 - - + +
175C TRP* 4.5 4.5 - - + -
176C TYR* 2.9 25.0 + - - +
195C ALA 2.8 19.3 + - - +
198C ASP* 1.3 76.0 - - - +
200C TYR* 1.3 87.0 + - + +
374C GLU* 2.8 34.3 + - - -
385C GLU* 4.5 15.2 + - - +
386C ILE 4.3 8.4 + - - +
387C LYS* 5.7 0.5 - - - -
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Residues in contact with TYR 200 (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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175C TRP* 3.0 45.0 + + - -
176C TYR* 4.0 0.2 + - - -
179C ARG* 4.4 0.7 + - - -
196C SER* 2.9 25.3 + - - +
199C ARG* 1.3 100.0 - - + +
201C GLY* 1.3 52.1 + - - +
202C PHE* 3.5 29.2 - + + -
371C ILE* 3.8 18.6 + - + -
374C GLU* 2.8 36.9 + - + +
386C ILE* 3.5 45.5 - - + +
387C LYS* 3.3 3.6 - - - -
388C ASP 2.8 10.9 + - - -
389C GLY* 2.7 26.4 + - - -
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Residues in contact with GLY 201 (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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197C LYS* 2.5 30.9 + - - +
198C ASP 4.6 0.6 + - - -
199C ARG 3.9 0.2 - - - -
200C TYR* 1.3 71.9 - - - +
202C PHE* 1.3 66.8 + - - +
203C LYS* 3.1 10.2 + - - +
388C ASP* 3.5 26.3 - - - +
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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