Contacts of the helix formed by residues 186 - 206 (chain C) in PDB entry 5FN3
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 186 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ASP* 5.1 4.2 + - - -
181C ALA* 3.3 16.4 + - - +
184C ARG* 3.2 52.0 - - + +
185C ARG* 1.3 74.6 - - - +
187C TYR* 1.3 62.8 + - - +
188C TRP* 3.4 46.2 + - + +
189C ALA* 3.7 26.9 + - + +
190C LEU* 3.9 4.5 + - - +
227C TRP* 6.1 4.3 - - - -
231C THR* 5.9 3.2 - - - +
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Residues in contact with TYR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PHE* 6.3 3.1 - + - -
185C ARG* 3.6 50.6 + - + +
186C ARG* 1.3 71.8 - - - +
188C TRP* 1.3 61.5 + - - +
190C LEU* 3.2 24.4 - - + +
191C GLY* 2.9 25.8 + - - -
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Residues in contact with TRP 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ARG* 3.5 48.3 - - + +
187C TYR* 1.3 78.7 - - - +
189C ALA* 1.3 60.6 - - + +
191C GLY* 3.2 3.1 + - - +
192C LEU* 2.9 51.3 + - + +
227C TRP* 4.8 14.4 - + - -
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 5.4 4.5 - - + -
181C ALA* 3.8 15.9 - - + -
186C ARG* 3.7 28.4 + - + +
187C TYR 3.2 0.4 - - - -
188C TRP* 1.3 83.9 - - + +
190C LEU* 1.3 57.7 + - - +
192C LEU* 3.2 5.7 + - - +
193C VAL* 2.9 33.8 + - - +
227C TRP* 4.3 24.3 - - + -
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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
----------------------------------------------------------
88C PHE* 4.9 12.1 - - + -
178C PHE* 3.9 33.4 - - + +
181C ALA* 4.2 16.0 - - + +
182C CYS* 4.1 22.4 - - - +
186C ARG 3.9 2.1 + - - +
187C TYR* 3.2 32.4 + - + +
189C ALA* 1.3 78.3 - - - +
191C GLY* 1.3 57.8 + - - +
193C VAL* 3.2 9.7 + - - +
194C VAL* 2.9 38.8 + - + +
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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
----------------------------------------------------------
187C TYR 2.9 13.5 + - - -
188C TRP* 3.2 4.7 + - - -
190C LEU* 1.3 77.2 - - - +
192C LEU* 1.3 57.3 + - - +
194C VAL* 3.2 10.2 + - - +
195C GLY* 2.9 25.6 + - - -
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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
----------------------------------------------------------
188C TRP* 2.9 30.1 + - + +
189C ALA* 3.4 9.6 - - - +
191C GLY* 1.3 75.6 - - - +
193C VAL* 1.3 53.5 + - - +
195C GLY* 3.2 3.1 + - - -
196C SER* 2.6 47.1 + - - +
224C MET* 5.4 3.6 - - + -
227C TRP* 3.6 33.2 - - + -
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 3.6 14.8 - - - +
174C TRP* 3.6 34.7 + - + +
177C VAL* 3.7 31.2 - - + -
178C PHE* 4.6 19.7 - - + +
189C ALA 2.9 19.2 + - - +
190C LEU* 3.4 11.2 - - - +
192C LEU* 1.3 74.0 - - - +
194C VAL* 1.3 58.6 + - - +
196C SER* 3.2 10.3 + - - -
197C HIS* 2.9 27.7 + - - +
224C MET* 4.9 2.7 - - - -
227C TRP* 4.5 7.6 - - + -
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.3 15.0 - - + -
84C GLU* 3.5 33.4 - - + +
178C PHE* 5.7 2.7 - - + -
190C LEU* 2.9 29.3 + - + +
191C GLY* 3.4 10.5 - - - +
193C VAL* 1.3 76.5 - - + +
195C GLY* 1.3 56.7 + - - +
197C HIS* 3.2 2.8 + - - +
198C LEU* 2.9 53.1 + - + +
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Residues in contact with GLY 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLY 2.9 13.3 + - - -
192C LEU 3.2 4.4 + - - -
194C VAL* 1.3 76.9 - - - +
196C SER* 1.3 52.4 + - - +
198C LEU* 3.2 9.2 + - - +
199C LEU* 2.8 37.2 + - - +
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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
----------------------------------------------------------
174C TRP* 3.8 8.5 - - - -
192C LEU* 2.6 32.9 + - - +
193C VAL* 3.3 8.6 + - - -
195C GLY* 1.3 76.6 - - - +
197C HIS* 1.3 57.8 + - - +
199C LEU* 3.2 11.1 + - - +
200C THR* 2.9 32.9 + - - +
220C VAL* 4.6 7.5 - - - +
224C MET* 3.4 33.3 - - - +
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Residues in contact with HIS 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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467B ILE 3.6 17.9 - - - -
80C VAL* 3.6 20.5 - - + +
83C GLN* 2.9 34.2 + - + +
84C GLU* 3.5 36.6 - - + +
87C ARG* 4.8 0.9 - - - -
167C ILE* 5.3 1.1 - - + -
171C HIS* 3.6 8.8 - + - -
174C TRP* 3.3 43.3 - + + -
193C VAL 2.9 7.1 + - - +
194C VAL 3.4 9.4 - - - +
196C SER* 1.3 74.8 - - - +
198C LEU* 1.3 62.7 + - - +
200C THR* 2.3 27.4 + - - -
201C SER* 3.3 5.7 + - - -
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA* 5.2 11.0 - - + +
80C VAL* 3.3 28.9 - - + -
81C LEU* 4.2 21.8 - - + -
194C VAL* 2.9 43.5 + - + +
195C GLY* 3.5 11.2 - - - +
197C HIS* 1.3 76.3 - - - +
199C LEU* 1.3 56.4 + - - +
201C SER* 3.2 8.9 + - - -
202C GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C GLY 2.8 18.2 + - - +
196C SER* 3.4 10.5 - - - +
198C LEU* 1.3 76.1 - - - +
200C THR* 1.3 56.4 + - + +
202C GLY* 3.2 4.5 + - - +
203C LEU* 2.9 55.3 + - + +
220C VAL* 5.0 13.9 - - + -
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Residues in contact with THR 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 4.4 15.3 - - + +
170C LEU* 3.4 32.1 - - + -
174C TRP* 3.8 9.8 - - + -
196C SER 2.9 20.6 + - - +
197C HIS* 2.3 33.4 + - - -
199C LEU* 1.3 73.8 - - - +
201C SER* 1.3 61.8 + - - +
203C LEU* 3.2 15.3 + - + +
204C THR* 2.9 35.6 + - - +
217C ILE* 3.9 11.5 - - + +
220C VAL* 4.6 8.1 - - + -
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Residues in contact with SER 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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466B TYR 3.6 16.7 + - - -
467B ILE 4.0 7.8 + - - -
76C ALA* 5.4 2.4 - - - +
77C ALA* 6.3 0.7 - - - -
80C VAL* 3.3 29.5 - - - +
197C HIS* 3.7 5.3 + - - -
198C LEU* 3.4 8.3 - - - -
200C THR* 1.3 84.5 + - - +
202C GLY* 1.3 55.4 + - - +
204C THR* 2.3 28.7 + - - -
205C PHE* 2.9 31.2 + - - -
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Residues in contact with GLY 202 (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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198C LEU 2.9 14.1 + - - -
199C LEU* 3.2 7.6 + - - -
201C SER* 1.3 74.8 - - - +
203C LEU* 1.3 62.6 + - - +
205C PHE* 3.2 34.0 + - - +
206C LEU* 3.2 16.0 - - - +
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Residues in contact with LEU 203 (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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199C LEU* 2.9 44.4 + - + +
200C THR* 3.3 13.5 - - + +
202C GLY* 1.3 75.5 - - - +
204C THR* 1.3 64.2 + - - +
206C LEU* 3.0 31.1 + - + +
212C ALA 4.0 3.0 - - - +
213C SER* 3.7 12.4 - - - +
216C PRO* 4.0 23.6 - - + -
217C ILE* 3.4 42.2 - - + +
220C VAL* 4.4 9.6 - - + -
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Residues in contact with THR 204 (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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465B PHE* 3.3 6.5 - - - +
466B TYR* 3.1 44.8 + - + -
163C LEU* 3.8 12.8 - - + -
167C ILE* 5.6 4.3 - - + -
200C THR* 2.9 23.9 + - - +
201C SER* 2.3 30.7 + - - -
203C LEU* 1.3 75.2 - - - +
205C PHE* 1.3 64.0 + - - +
206C LEU 3.1 0.9 + - - -
207C ASN* 2.9 32.2 + - - +
213C SER* 4.5 1.3 - - - -
217C ILE* 3.7 17.7 - - + -
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Residues in contact with PHE 205 (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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463B HIS 5.6 0.3 - - - +
465B PHE* 3.3 53.5 - + + -
466B TYR 4.7 3.4 - - - -
69C TYR* 5.7 4.7 + - + +
73C ILE* 3.8 46.0 - - + -
76C ALA* 3.4 31.0 - - + -
77C ALA* 5.1 1.8 - - + -
201C SER* 2.9 24.3 + - - -
202C GLY* 3.2 20.2 + - - +
204C THR* 1.3 84.1 + - - +
206C LEU* 1.3 64.9 + - + +
207C ASN* 3.0 7.8 + - - +
208C PRO* 4.9 1.7 - - - +
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR* 5.8 3.8 - - - +
202C GLY 3.2 17.3 - - - +
203C LEU* 3.0 20.5 + - + +
205C PHE* 1.3 84.0 - - + +
207C ASN* 1.3 57.5 + - - +
208C PRO* 4.0 1.8 - - - -
209C TRP* 3.0 20.5 + - + +
212C ALA* 3.0 33.0 - - + +
213C SER* 3.5 0.9 - - - -
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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
------------------------------------------------------------
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