Contacts of the helix formed by residues 190 - 209 (chain C) in PDB entry 3SF4
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 190 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C VAL* 3.0 34.5 + - + +
188C LEU* 3.3 9.5 - - + +
189C GLY* 1.3 74.1 - - - +
191C ARG* 1.3 62.1 + - - +
192C ALA* 3.5 8.1 + - - +
193C ALA* 3.2 33.4 + - + +
194C GLN* 3.1 7.3 + - - +
196C ARG* 4.5 5.8 + - - -
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Residues in contact with ARG 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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189C GLY 3.2 8.5 + - - +
190C ASP* 1.3 70.9 + - - +
192C ALA* 1.3 65.5 + - - +
194C GLN* 2.9 37.1 + - - +
195C GLY 3.0 16.8 + - - -
198C PHE* 5.6 1.8 - - - -
220C GLN* 5.5 4.8 - - - +
223C LEU* 4.7 12.7 - - - +
224C ILE* 3.6 30.2 - - + +
227C GLU* 2.7 43.8 + - - +
228C PHE* 3.8 21.8 - - + -
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Residues in contact with ALA 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ASP* 3.5 7.4 + - - +
191C ARG* 1.3 78.4 - - - +
193C ALA* 1.3 58.1 + - - +
195C GLY* 2.8 18.6 + - - +
196C ARG* 3.0 32.5 + - - +
224C ILE* 4.8 2.2 - - - -
228C PHE* 3.8 26.6 - - + -
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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
----------------------------------------------------------
139C TYR* 5.2 0.7 - - - -
181C ASN* 4.5 3.3 + - - +
185C VAL* 3.4 24.0 - - + +
190C ASP* 3.2 31.6 + - + +
192C ALA* 1.3 78.6 - - - +
194C GLN* 1.3 62.9 + - - +
196C ARG* 3.2 24.4 + - - +
197C ALA* 3.0 24.4 + - - +
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Residues in contact with GLN 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 3.9 10.7 - - + +
185C VAL* 3.3 16.0 + - + -
186C THR* 3.3 45.0 + - + +
189C GLY* 4.0 5.5 - - - -
190C ASP 3.1 30.0 + - - +
191C ARG* 2.9 44.6 + - - +
193C ALA* 1.3 75.2 - - - +
195C GLY* 1.3 57.8 + - - +
197C ALA* 3.3 1.8 + - - +
198C PHE* 2.9 40.3 + - + -
224C ILE* 3.8 7.1 - - + +
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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
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191C ARG 3.0 7.9 + - - -
192C ALA 2.8 9.8 + - - -
194C GLN* 1.3 79.1 - - - +
196C ARG* 1.3 60.3 + - - -
198C PHE* 3.5 2.9 + - - +
199C GLY 3.1 7.3 + - - -
221C ARG* 3.0 47.0 - - - -
224C ILE* 3.7 15.7 - - - +
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C TYR* 3.5 32.0 + - + +
190C ASP* 4.5 5.1 + - - -
192C ALA* 3.0 30.2 + - - +
193C ALA* 3.2 33.4 + - - +
195C GLY* 1.3 72.5 - - - +
197C ALA* 1.3 65.5 + - - +
199C GLY 3.3 1.2 + - - -
200C ASN* 3.1 25.1 + - - +
221C ARG* 5.6 1.6 - - - +
42F GLU* 3.4 24.9 - - + +
43F CYS* 4.5 11.0 - - - +
46F VAL* 5.4 0.6 - - - +
62F LEU* 4.7 13.9 - - - +
64F LEU* 3.9 42.0 - - - +
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Residues in contact with ALA 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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139C TYR* 4.0 10.2 - - - -
178C TYR* 4.4 10.6 - - + +
181C ASN* 3.3 27.1 - - - +
182C LEU* 3.8 22.4 - - + -
193C ALA 3.0 13.5 + - - +
194C GLN 3.5 4.0 - - - +
196C ARG* 1.3 78.6 - - - +
198C PHE* 1.3 57.8 + - - +
200C ASN* 3.3 1.2 + - - +
201C LEU* 2.8 33.2 + - - +
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Residues in contact with PHE 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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182C LEU* 3.5 38.1 - - + -
186C THR* 5.6 2.7 - - + -
191C ARG* 5.6 1.6 - - - -
194C GLN* 2.9 29.4 + - + +
195C GLY 3.8 4.5 - - - +
197C ALA* 1.3 74.9 - - - +
199C GLY* 1.3 58.9 + - - +
201C LEU* 4.3 7.9 - - + -
202C GLY* 2.8 25.1 + - - -
216C ILE* 6.5 0.7 - - + -
217C ALA* 3.5 36.9 - - + +
220C GLN* 3.4 42.0 - - + -
221C ARG* 4.0 7.0 - - - +
224C ILE* 3.9 20.0 - - + -
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Residues in contact with GLY 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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195C GLY 3.1 12.1 + - - -
196C ARG 3.3 2.7 + - - -
197C ALA 3.2 0.6 - - - -
198C PHE* 1.3 76.1 - - - +
200C ASN* 1.3 58.4 + - - +
202C GLY 3.0 2.8 + - - -
203C ASN* 3.0 35.6 + - - -
218C HIS* 3.4 9.6 - - - -
221C ARG* 3.7 23.7 - - - +
240C ASN* 5.9 0.9 - - - -
42F GLU* 3.8 7.2 - - - -
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Residues in contact with ASN 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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139C TYR* 3.0 31.5 + - - -
143C ASN* 3.2 19.4 + - - -
146C HIS* 4.4 1.8 - - + -
178C TYR* 3.3 25.8 - - + +
196C ARG 3.1 11.1 + - - +
197C ALA 4.0 0.7 - - - +
199C GLY* 1.3 71.0 - - - +
201C LEU* 1.3 64.3 + - - +
203C ASN* 3.4 6.2 + - - +
204C THR* 2.8 30.9 + - - -
41F CYS* 4.2 4.3 - - - +
42F GLU* 3.1 24.5 + - - +
43F CYS 3.8 0.8 + - - -
44F MET* 3.6 17.2 - - + +
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Residues in contact with LEU 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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175C VAL* 3.9 19.1 - - + +
178C TYR* 3.9 18.5 - - + -
179C GLU* 3.9 31.9 - - + +
182C LEU* 4.6 19.3 - - + -
197C ALA 2.8 18.1 + - - +
198C PHE* 3.6 9.4 - - + +
200C ASN* 1.3 75.1 - - - +
202C GLY* 1.3 65.5 + - - +
204C THR* 3.1 3.9 + - - -
205C HIS* 3.0 53.8 + - + +
217C ALA* 4.2 14.1 - - + -
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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 PHE 2.8 14.5 + - - -
199C GLY 3.0 4.5 + - - -
201C LEU* 1.3 77.8 - - - +
203C ASN* 1.3 59.5 + - - +
205C HIS 3.6 0.2 + - - -
206C TYR* 3.1 19.6 + - - +
214C ALA* 3.5 13.1 - - - +
217C ALA* 3.7 15.7 - - - +
218C HIS* 3.3 23.8 + - - -
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Residues in contact with ASN 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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146C HIS* 4.1 10.8 - - - +
199C GLY* 3.0 24.8 + - - +
200C ASN* 4.0 5.6 - - - +
201C LEU 3.2 0.2 - - - -
202C GLY* 1.3 74.1 - - - +
204C THR* 1.3 64.9 + - - +
206C TYR* 3.4 8.2 + - - +
207C LEU* 3.1 27.2 + - - +
218C HIS* 3.4 4.8 + - - -
240C ASN* 3.3 28.5 + - - +
39F THR* 3.8 25.9 - - + +
40F GLU 3.1 23.2 + - - -
41F CYS* 3.6 16.0 - - - +
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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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146C HIS* 2.8 25.0 - - + -
171C LEU* 3.2 38.8 - - + +
174C ALA* 3.9 10.5 - - + -
175C VAL* 3.6 14.8 - - + -
178C TYR* 3.3 12.6 - - - -
200C ASN 2.8 21.1 + - - -
201C LEU 3.1 4.7 + - - -
203C ASN* 1.3 72.4 - - - +
205C HIS* 1.3 66.8 + - - +
207C LEU* 3.1 6.5 + - - +
208C LEU* 3.0 22.6 + - - +
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Residues in contact with HIS 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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172C GLN* 5.6 0.7 - - - -
175C VAL* 3.9 26.2 - - + +
179C GLU* 4.6 5.6 + - - -
201C LEU* 3.0 49.7 + - + +
202C GLY 3.8 4.5 - - - +
204C THR* 1.3 76.6 - - - +
206C TYR* 1.3 58.2 + - - +
208C LEU* 3.2 5.9 + - + +
209C GLY 2.9 9.7 + - - -
210C ASN* 2.8 63.9 + - - +
213C ASP* 3.9 38.5 + - + +
214C ALA* 3.9 5.4 - - - +
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Residues in contact with TYR 206 (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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202C GLY 3.1 12.0 + - - +
203C ASN* 3.4 12.3 - - - +
204C THR 3.2 0.2 - - - -
205C HIS* 1.3 79.1 - - - +
207C LEU* 1.3 66.6 + - + +
209C GLY* 3.3 9.4 + - - -
211C PHE* 3.6 24.4 - + - -
214C ALA* 3.9 9.1 - - + +
218C HIS* 5.1 4.0 - - - +
240C ASN* 5.0 2.2 - - + -
243C ASN* 3.5 36.5 - - + +
244C ALA* 3.7 24.5 - - + -
247C PHE* 3.2 26.5 - + - -
35F LEU* 2.7 24.3 + - - +
36F LYS* 3.7 13.8 - - - +
38F MET 3.1 24.9 - - - -
39F THR* 4.1 10.8 - - + -
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Residues in contact with LEU 207 (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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146C HIS* 3.9 19.7 - - + +
150C LYS* 3.7 38.4 - - + -
163C PHE* 3.9 16.8 - - - -
171C LEU* 4.1 20.0 - - + +
203C ASN 3.1 9.3 + - - +
204C THR* 3.6 6.7 - - - +
206C TYR* 1.3 87.8 - - + +
208C LEU* 1.3 60.6 + - - +
209C GLY 3.6 0.2 + - - -
36F LYS 3.8 21.7 - - - +
37F LEU* 4.1 23.8 - - + +
39F THR* 4.2 7.9 - - + -
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Residues in contact with LEU 208 (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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163C PHE* 4.3 15.3 - - + -
168C ARG* 3.9 29.2 - - + +
171C LEU* 3.5 35.0 - - + -
172C GLN* 3.5 29.2 - - - +
175C VAL* 3.7 28.0 - - + -
204C THR 3.0 13.3 + - - +
205C HIS* 3.5 7.0 - - - +
206C TYR 3.2 0.2 - - - -
207C LEU* 1.3 79.1 - - - +
209C GLY* 1.3 57.2 + - - +
210C ASN* 4.0 14.8 - - - +
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Residues in contact with GLY 209 (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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205C HIS 2.9 3.6 + - - -
206C TYR 3.3 4.4 + - - -
207C LEU 3.4 0.4 - - - -
208C LEU* 1.3 79.5 - - - +
210C ASN* 1.3 65.0 + - - +
211C PHE* 3.3 40.5 + - - -
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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