Contacts of the helix formed by residues 181 - 198 (chain C) in PDB entry 1SIW
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 ALA 181 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C PHE* 4.0 26.2 - - + -
155C GLU* 3.3 8.3 + - - +
179C GLY 3.6 2.1 + - - -
180C VAL* 1.3 81.1 - - - +
182C PHE* 1.3 64.7 + - - +
183C ILE* 4.1 3.6 - - + -
184C PHE* 3.0 39.8 + - + +
185C ARG 3.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL 3.4 2.9 + - - -
181C ALA* 1.3 70.3 - - - +
183C ILE* 1.3 56.2 + - - +
185C ARG* 2.6 57.2 + - + +
186C LEU* 3.2 41.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 3.9 15.4 - - + +
142C LEU* 3.3 51.1 - - + +
143C THR* 3.6 15.0 - - + +
146C PHE* 3.8 37.4 - - + -
181C ALA* 4.1 4.0 - - + -
182C PHE* 1.3 79.0 - - - +
184C PHE* 1.3 76.6 + - + +
186C LEU* 3.6 13.2 + - + +
187C HIS* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C THR* 3.6 33.2 - - + -
146C PHE* 4.0 11.2 - - + -
147C SER* 3.3 26.7 - - - -
155C GLU* 3.6 24.9 - - + -
159C LEU* 4.1 21.5 - - + -
180C VAL* 3.3 29.4 - - + -
181C ALA* 3.0 30.2 + - + +
183C ILE* 1.3 75.8 - - + +
185C ARG* 1.3 66.2 + - - +
187C HIS* 3.5 6.7 + - + +
188C LEU* 3.0 31.5 + - - +
807C HEM 4.0 23.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASN* 2.5 33.0 + - - +
9C PHE* 3.6 33.9 - - + -
174C SER 4.8 0.8 + - - -
177C LEU* 3.3 42.9 + - - +
178C ASP* 4.5 2.6 + - - +
179C GLY 4.4 6.3 - - - +
180C VAL* 3.8 16.3 + - + +
181C ALA 4.2 2.7 - - - +
182C PHE* 2.6 50.2 + - + +
184C PHE* 1.3 71.5 - - - +
186C LEU* 1.3 62.3 + - + +
188C LEU* 3.0 7.0 + - - +
189C VAL* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 4.2 26.7 - - + -
182C PHE* 3.2 44.5 + - + +
183C ILE* 3.7 13.7 - - + +
185C ARG* 1.3 79.1 - - + +
187C HIS* 1.3 63.1 + - - +
189C VAL* 3.1 8.2 + - + +
190C LEU* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLN* 2.8 68.9 + - - -
139C LEU* 3.8 8.2 - - + +
140C GLY* 3.5 15.4 + - - -
143C THR* 4.6 7.2 - - + -
183C ILE 3.2 14.7 + - - +
184C PHE* 3.7 7.2 - - + +
185C ARG 3.3 0.2 - - - -
186C LEU* 1.3 77.6 - - - +
188C LEU* 1.3 58.3 + - + +
191C GLY* 2.9 11.6 + - - -
807C HEM 2.0 91.3 + + + -
----------------------------------------------------------
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
----------------------------------------------------------
9C PHE* 3.8 24.0 - - + -
70C MET* 5.8 0.2 - - - -
159C LEU* 3.8 28.3 - - + -
162C TRP* 3.6 24.7 - - + -
177C LEU* 3.9 13.9 - - + -
184C PHE 3.0 22.3 + - - +
185C ARG* 3.0 8.1 + - - +
187C HIS* 1.3 78.4 - - + +
189C VAL* 1.3 57.7 + - - +
191C GLY* 3.4 0.9 + - - -
192C MET* 3.0 35.4 + - - +
807C HEM 3.4 47.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE* 3.8 43.1 - - + -
9C PHE* 3.9 20.6 - - + -
12C TYR* 4.0 4.1 - - + -
185C ARG* 3.0 16.5 + - + +
186C LEU* 3.7 9.9 - - + +
188C LEU* 1.3 72.4 - - - +
190C LEU* 1.3 63.2 + - - +
192C MET* 3.2 11.2 + - + +
193C THR* 2.8 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 4.0 34.1 - - + +
135C ILE* 3.7 19.5 - - + -
136C GLN* 3.3 48.0 - - + +
139C LEU* 3.8 9.9 - - + -
186C LEU 2.9 13.6 + - - +
189C VAL* 1.3 79.5 - - - +
191C GLY* 1.3 63.4 + - - +
193C THR* 3.3 10.7 + - + -
194C LEU* 3.1 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLN* 3.1 21.7 - - - +
187C HIS 2.9 13.6 + - - -
188C LEU 3.8 0.2 - - - -
190C LEU* 1.3 78.4 - - - +
192C MET* 1.3 57.7 + - - +
194C LEU* 3.5 14.9 + - - +
195C PHE* 3.1 22.2 - - - -
807C HEM 3.2 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE 3.2 24.7 - - - +
9C PHE* 4.5 3.1 - - + -
12C TYR* 3.9 15.7 - - + -
13C PRO* 3.5 35.7 - - + -
16C ALA* 3.6 14.3 - - + +
162C TRP* 3.8 23.6 - - + -
188C LEU 3.0 25.3 + - - +
189C VAL* 3.2 18.1 + - + +
191C GLY* 1.3 74.1 - - - +
193C THR* 1.3 66.2 + - - +
195C PHE* 3.0 20.5 + - + +
196C LEU 3.2 7.4 + - - -
807C HEM 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 2.7 27.9 + - - +
132C LEU* 5.1 3.8 - - + -
189C VAL* 2.8 22.3 + - - +
190C LEU* 3.3 20.1 + - + -
192C MET* 1.3 78.7 - - - +
194C LEU* 1.3 56.3 + - - +
196C LEU* 2.9 25.4 + - + +
197C LEU* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 4.4 23.6 - - + -
132C LEU* 3.8 36.1 - - + +
133C LEU* 3.7 25.8 - - + -
136C GLN* 4.2 22.0 - - + -
190C LEU* 3.1 20.4 + - + +
191C GLY* 3.6 10.1 - - - +
192C MET 3.1 0.4 - - - -
193C THR* 1.3 76.6 - - - +
195C PHE* 1.3 60.4 + - + +
197C LEU* 3.9 6.2 - - + +
198C PHE* 2.9 26.3 + - - +
203C LEU* 4.4 10.8 - - + +
807C HEM 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 4.2 7.4 - - + +
17C GLY* 5.8 0.7 - - - -
20C PHE* 3.3 58.6 - + + +
63C PHE* 6.6 0.4 - + - -
191C GLY 3.1 21.3 - - - -
192C MET* 3.0 11.9 + - + +
194C LEU* 1.3 78.4 - - + +
196C LEU* 1.3 64.6 + - - +
198C PHE* 3.3 20.8 - + + +
199C PRO* 3.5 2.1 - - - +
807C HEM 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 4.0 21.1 - - + +
15C ILE* 4.4 8.7 - - + +
16C ALA* 3.6 36.7 - - + +
19C VAL* 3.7 29.1 - - + +
192C MET 3.2 4.0 + - - +
193C THR* 2.9 15.9 + - + +
195C PHE* 1.3 79.9 - - - +
197C LEU* 1.3 73.1 + - + +
199C PRO* 3.4 10.9 - - - +
200C PHE* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 4.3 19.1 - - + -
129C ILE* 5.7 6.5 - - + -
132C LEU* 3.9 28.5 - - + -
193C THR* 3.0 26.8 + - + +
194C LEU* 4.3 7.9 - - + +
196C LEU* 1.3 90.1 - - + +
198C PHE* 1.3 67.2 + - - +
199C PRO* 3.4 1.1 - - - -
200C PHE* 2.9 25.9 + - + +
201C SER* 3.4 14.1 + - - -
203C LEU* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.3 27.4 - + + -
24C SER* 3.9 5.6 - - - -
194C LEU 2.9 15.2 + - - +
195C PHE* 3.3 16.6 - + - +
197C LEU* 1.3 74.8 - - - +
199C PRO* 1.3 68.2 - - + +
200C PHE 3.1 3.5 + - - -
201C SER* 3.0 27.4 + - - +
203C LEU* 3.1 52.1 - - + +
204C ILE* 4.0 8.1 - - + +
206C ILE* 3.6 21.3 - - + -
207C TRP* 3.2 39.5 - + - -
----------------------------------------------------------
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