Contacts of the helix formed by residues 164 - 189 (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 PRO 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PHE* 5.5 3.4 - - + -
162C GLU* 3.6 18.8 - - + +
163C PHE* 1.3 88.7 - - + +
165C GLU* 1.3 60.6 + - - +
166C GLU* 4.1 11.2 - - + +
167C VAL* 2.9 49.2 + - + +
168C ARG* 3.0 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C GLU* 5.6 0.8 + - - -
163C PHE 3.4 5.1 + - - -
164C PRO* 1.3 71.2 - - - +
166C GLU* 1.3 57.7 + - + +
168C ARG* 3.9 31.5 + - - +
169C ASP* 2.8 55.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LYS* 5.7 1.2 + - - -
152C PHE* 3.6 43.6 - - + -
164C PRO* 3.0 9.5 - - + +
165C GLU* 1.3 79.3 - - + +
167C VAL* 1.3 60.6 + - - +
169C ASP* 3.9 6.0 - - - +
170C ALA* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLY 3.5 17.7 - - - +
152C PHE* 3.4 39.5 - - + -
163C PHE* 3.8 25.1 - - + -
164C PRO* 2.9 33.5 + - + +
166C GLU* 1.3 78.9 - - - +
168C ARG* 1.3 62.2 + - - +
170C ALA* 3.5 3.1 + - - +
171C LEU* 3.1 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PHE* 3.7 30.3 - - + -
164C PRO 3.0 9.4 + - - +
165C GLU* 3.7 36.0 + - - +
167C VAL* 1.3 75.3 - - - +
169C ASP* 1.3 65.8 + - - +
171C LEU* 3.3 1.9 + - - +
172C GLN* 2.8 42.3 + - + +
208C LEU* 3.9 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 6.0 0.2 - - - -
165C GLU* 2.8 44.1 + - - +
166C GLU* 3.9 5.9 - - - +
168C ARG* 1.3 81.5 + - - +
170C ALA* 1.3 64.5 + - - +
172C GLN* 3.8 4.6 - - - +
173C ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.5 35.3 - - + +
148C LYS* 4.2 21.8 - - + +
149C GLY* 3.8 14.4 - - - +
152C PHE* 5.2 1.3 - - + -
166C GLU 3.1 15.7 + - - +
167C VAL 3.7 3.8 - - - +
169C ASP* 1.3 79.7 - - - +
171C LEU* 1.3 55.9 + - - +
173C ALA* 3.1 5.7 + - - +
174C ALA 2.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C HIS* 4.1 16.8 - - + +
149C GLY* 3.8 21.3 - - - +
163C PHE* 4.1 8.7 - - + -
167C VAL* 3.1 33.7 + - + +
170C ALA* 1.3 76.8 - - - +
172C GLN* 1.3 57.3 + - - +
174C ALA* 3.1 2.8 + - - -
175C VAL* 2.8 24.8 + - - +
204C THR* 3.2 24.0 - - + +
207C LEU* 4.1 31.0 - - + +
208C LEU* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ARG* 2.8 33.7 + - + +
169C ASP* 3.9 6.1 - - - +
171C LEU* 1.3 70.2 - - - +
173C ALA* 1.3 66.2 + - - +
175C VAL* 3.2 17.4 + - - +
176C ASP* 3.0 32.1 + - - +
205C HIS* 5.6 0.7 - - - -
208C LEU* 3.5 27.0 - - + +
210C ASN* 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.7 28.7 - - + -
169C ASP 2.9 13.9 + - - +
170C ALA 3.3 9.4 - - - +
172C GLN* 1.3 77.1 - - - +
174C ALA* 1.3 63.4 + - - +
176C ASP* 3.2 11.2 + - - +
177C PHE* 2.9 33.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLY* 3.5 25.4 - - - +
145C TYR* 3.9 6.9 - - + +
146C HIS* 3.9 14.1 - - - +
170C ALA 2.9 11.8 + - - +
171C LEU 3.3 9.2 - - - +
173C ALA* 1.3 73.4 - - - +
175C VAL* 1.3 67.1 + - - +
177C PHE* 3.3 1.8 + - - +
178C TYR* 2.9 35.9 + - + -
204C THR* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU 2.8 17.6 + - - +
172C GLN* 3.5 17.5 - - - +
174C ALA* 1.3 77.9 - - - +
176C ASP* 1.3 65.8 + - - +
178C TYR* 3.3 2.6 + - - +
179C GLU* 3.0 49.9 + - - +
201C LEU* 3.9 11.6 - - + +
204C THR* 3.6 19.1 - - + -
205C HIS* 3.9 30.1 - - + +
208C LEU* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLN* 3.0 26.6 + - - +
173C ALA* 3.2 11.0 + - - +
175C VAL* 1.3 77.7 - - - +
177C PHE* 1.3 64.4 + - + +
179C GLU* 3.3 17.3 + - - +
180C GLU* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLN* 4.5 8.7 - - - -
122C LEU* 4.4 5.8 - - + -
138C LEU* 3.5 35.8 - - + +
141C LEU* 3.4 43.1 - - + -
142C GLY* 3.7 10.5 - - - +
145C TYR* 3.4 35.9 - + - -
173C ALA* 2.9 29.9 + - + +
174C ALA 3.9 0.2 - - - +
176C ASP* 1.3 78.7 - - + +
178C TYR* 1.3 57.6 + - - +
180C GLU* 3.3 15.9 + - - +
181C ASN* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C TYR* 4.0 21.5 - + - -
142C GLY* 3.3 24.5 + - - -
143C ASN* 2.5 41.3 + - - -
146C HIS* 3.8 9.3 - + - +
174C ALA* 2.9 29.7 + - + +
175C VAL* 3.8 4.0 - - - +
177C PHE* 1.3 72.9 - - - +
179C GLU* 1.3 57.6 + - - +
181C ASN* 3.4 6.3 + - - +
182C LEU* 2.8 29.3 + - - +
197C ALA* 4.4 8.0 - - - +
200C ASN* 3.3 37.8 + - + +
201C LEU* 3.9 22.9 - - + -
204C THR* 3.3 26.2 - - - -
44F MET* 4.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 3.0 43.4 + - - +
176C ASP* 3.7 14.7 - - - +
178C TYR* 1.3 75.0 - - - +
180C GLU* 1.3 59.6 + - - +
182C LEU* 3.2 10.6 + - + +
183C SER* 2.9 29.7 + - - -
201C LEU* 3.9 20.6 - - + +
205C HIS* 4.6 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ARG* 3.1 28.7 + - - -
138C LEU* 3.8 18.7 - - + +
176C ASP* 3.0 25.0 + - - +
177C PHE* 3.7 21.6 - - - +
179C GLU* 1.3 75.8 - - - +
181C ASN* 1.3 64.3 + - - +
183C SER* 3.3 7.4 + - - -
184C LEU* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 2.8 25.8 - - - +
138C LEU* 3.8 18.3 - - + +
139C TYR* 3.6 26.9 - - - +
177C PHE 2.9 17.3 + - - +
178C TYR* 3.5 6.7 + - - +
180C GLU* 1.3 77.5 - - - +
182C LEU* 1.3 56.7 + - - +
184C LEU* 3.2 3.5 + - - +
185C VAL* 2.8 45.6 + - - +
193C ALA* 4.5 3.2 + - - +
197C ALA* 3.3 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR 2.8 19.0 + - - +
179C GLU* 3.4 8.3 - - + +
181C ASN* 1.3 82.4 - - - +
183C SER* 1.3 57.4 + - - +
185C VAL* 3.8 2.3 - - - -
186C THR* 2.8 48.3 + - + +
194C GLN* 3.9 10.3 - - - +
197C ALA* 3.8 21.3 - - + -
198C PHE* 3.5 49.8 - - + -
201C LEU* 4.6 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C GLU 2.9 15.5 + - - -
180C GLU* 3.6 8.5 - - - -
182C LEU* 1.3 77.4 - - - +
184C LEU* 1.3 61.1 + - - +
186C THR* 3.2 8.9 + - - -
187C ALA* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LYS* 3.4 43.3 - - + +
134C GLU* 3.7 22.9 - - + +
135C ALA* 3.4 39.3 - - + +
138C LEU* 4.2 5.2 - - + -
180C GLU 3.0 15.3 + - - +
181C ASN* 3.8 3.4 - - - +
183C SER* 1.3 77.0 - - - +
185C VAL* 1.3 58.8 + - - +
187C ALA* 3.4 8.1 + - + +
188C LEU* 3.0 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 4.1 14.8 - - + -
181C ASN* 2.8 37.5 + - - +
182C LEU* 4.0 4.3 - - - +
184C LEU* 1.3 75.4 - - - +
186C THR* 1.3 59.1 + - - +
187C ALA 3.2 0.4 - - - -
188C LEU* 3.3 8.1 + - + +
189C GLY 3.0 21.0 + - - -
190C ASP* 3.0 35.1 + - + +
193C ALA* 3.4 26.0 - - + -
194C GLN* 3.3 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 2.8 35.2 + - + +
183C SER* 3.2 11.8 + - - -
185C VAL* 1.3 76.9 - - - +
187C ALA* 1.3 64.3 + - - +
189C GLY* 3.4 10.6 + - - -
194C GLN* 3.3 35.4 + - + +
198C PHE* 5.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C SER 3.2 14.9 + - - +
184C LEU* 3.6 12.6 - - + +
185C VAL 3.2 0.4 - - - -
186C THR* 1.3 84.2 + - - +
188C LEU* 1.3 60.2 + - + +
189C GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LYS* 4.2 38.6 - - + +
132C VAL* 4.2 22.0 - - + -
135C ALA* 4.3 11.9 - - + -
184C LEU* 3.0 29.9 + - + +
185C VAL* 3.8 10.3 - - + +
186C THR 3.2 0.2 - - - -
187C ALA* 1.3 77.9 - - + +
189C GLY* 1.3 62.1 + - - +
190C ASP* 3.5 8.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C VAL 3.0 5.7 + - - -
186C THR 3.4 8.8 + - - -
187C ALA 3.3 4.0 + - - -
188C LEU* 1.3 80.5 - - - +
190C ASP* 1.3 59.8 + - - +
191C ARG* 3.2 9.0 + - - +
194C GLN* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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