Contacts of the helix formed by residues 153 - 165 (chain C) in PDB entry 3IO6
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 GLU 153 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ASN* 3.4 23.0 + - - +
151C LEU 3.3 1.5 - - - +
152C GLN* 1.3 88.4 - - - +
154C PRO* 1.3 71.9 - - + +
155C TYR* 4.1 8.3 - - + +
156C PHE* 3.5 27.8 + - + -
157C THR* 3.1 26.8 + - - +
344C ARG* 2.9 41.6 + - - -
347C VAL* 5.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C GLU* 1.3 94.3 - - - +
155C TYR* 1.3 63.0 + - + +
156C PHE 3.1 0.7 - - - -
157C THR* 3.5 8.5 - - - +
158C TRP* 2.8 36.4 + - + +
339C PHE* 5.7 0.4 - - + -
340C TRP* 3.7 30.5 - - + +
343C VAL* 3.9 27.1 - - + +
344C ARG* 3.8 39.0 - - + +
347C VAL* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 4.5 6.1 + - - +
112C ALA* 4.8 0.2 - - - -
113C LEU* 3.4 50.4 + - + +
153C GLU* 3.2 6.2 - - + +
154C PRO* 1.3 82.2 - - + +
156C PHE* 1.3 77.4 + + + +
158C TRP* 4.4 1.8 - - - +
159C PRO* 3.5 10.0 - - - +
230C TRP* 4.0 20.0 - + - -
258C PHE* 3.5 44.5 + - + -
260C GLY* 5.5 1.2 + - - -
330C MET* 3.7 17.2 - - + +
340C TRP* 3.8 28.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.7 36.2 - - + +
149C PHE* 4.0 17.0 - + + -
150C ASN* 3.3 44.6 - - + +
153C GLU* 3.5 25.5 + - + +
154C PRO 3.1 0.6 - - - -
155C TYR* 1.3 88.8 - + + +
157C THR* 1.3 58.8 + - - +
158C TRP 3.3 0.4 - - - -
159C PRO* 3.2 19.1 - - - +
160C LEU 5.2 0.2 + - - -
210C TYR* 3.8 26.5 - + - -
226C ILE* 4.1 27.7 - - + +
227C ASN* 4.3 8.7 - - - -
230C TRP* 4.4 8.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PHE* 3.8 12.3 - - + -
150C ASN 3.9 1.1 - - - +
151C LEU* 3.8 42.8 - - + +
153C GLU 3.1 19.1 + - - +
154C PRO* 3.5 9.5 - - - +
156C PHE* 1.3 74.7 - - - +
158C TRP* 1.3 64.7 + - - +
159C PRO 3.4 0.2 - - - -
160C LEU* 3.3 14.8 + - - +
161C ILE* 3.3 21.6 + - - +
195C LEU* 4.3 8.8 - - + +
347C VAL* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 2.8 20.8 + - + +
155C TYR 4.4 2.0 - - - +
157C THR* 1.3 75.9 + - - +
159C PRO* 1.4 64.2 - - + +
161C ILE* 3.0 27.6 + - + -
162C ALA* 2.7 49.3 + - + +
166C GLY* 3.7 8.7 - - - -
167C TYR* 3.5 43.6 - - - +
168C ALA 3.9 2.7 - - - -
182C GLY 4.4 2.0 - - - -
183C VAL* 4.3 18.2 - - + -
188C ALA* 5.4 0.2 - - + -
256C LYS 4.0 10.4 + - - -
258C PHE* 3.2 41.4 - + + -
328C GLU* 5.1 3.8 + - - +
339C PHE* 3.8 32.5 - + - -
340C TRP* 5.4 0.7 - - + -
343C VAL* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 4.3 7.0 - - + -
129C TRP* 6.0 2.5 - - + -
155C TYR 3.5 13.0 - - - +
156C PHE 3.2 18.8 - - - +
158C TRP* 1.4 95.2 - - + +
160C LEU* 1.3 56.6 + - - +
162C ALA 4.1 0.2 - - - -
163C ALA* 3.1 25.8 + - - +
226C ILE* 5.8 2.2 - - + -
247C LEU* 4.4 11.7 - - + -
255C SER* 3.5 18.7 + - - +
256C LYS 3.4 21.6 + - - +
257C PRO* 3.8 26.7 - - + -
258C PHE* 5.4 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C TRP* 3.8 44.6 - - + -
149C PHE* 6.2 0.4 - - + -
157C THR* 3.3 10.8 + - - +
158C TRP 3.1 0.8 - - - -
159C PRO* 1.3 77.7 - - - +
161C ILE* 1.3 67.5 + - + +
163C ALA* 3.2 18.5 - - - +
164C ASP 4.4 0.2 + - - -
191C GLY* 4.0 17.8 - - - +
194C PHE* 4.5 5.6 - - + -
195C LEU* 3.8 44.2 - - + +
198C LEU* 5.2 0.4 - - + -
250C PHE* 3.8 37.4 - - + -
255C SER* 4.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C THR* 3.3 26.5 - - - +
158C TRP* 3.0 28.6 + - + +
160C LEU* 1.3 77.4 - - + +
162C ALA* 1.3 62.1 + - - +
163C ALA 3.4 0.7 + - - -
164C ASP 4.1 0.3 + - - -
166C GLY 3.9 0.6 + - - -
187C GLY 3.4 19.9 - - - +
188C ALA* 3.4 37.6 + - + +
191C GLY* 4.2 8.1 - - - -
192C LEU* 4.3 25.6 - - + +
195C LEU* 5.4 3.4 - - + -
343C VAL* 4.9 2.2 - - + -
347C VAL* 3.8 29.4 - - + -
361C LEU* 5.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C TRP* 2.7 43.7 + - + +
159C PRO 4.2 0.4 - - - +
161C ILE* 1.3 73.4 - - - +
163C ALA* 1.3 65.8 + - - +
164C ASP 3.3 0.2 - - - -
165C GLY* 3.0 14.4 + - - -
166C GLY* 3.2 29.7 + - - +
256C LYS* 4.0 26.4 - - + +
328C GLU* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C PRO 3.1 17.3 + - - +
160C LEU* 3.2 17.3 - - - +
161C ILE 3.2 1.0 - - - -
162C ALA* 1.3 75.4 - - - +
164C ASP* 1.3 62.3 + - - +
165C GLY* 4.8 0.2 - - - -
250C PHE* 4.0 23.1 - - + -
253C GLN* 3.4 19.4 - - - +
254C PRO 3.9 15.0 - - - +
255C SER* 4.0 14.1 - - - +
256C LYS* 4.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LEU 4.4 0.6 + - - -
161C ILE 4.1 2.8 + - - -
162C ALA 3.3 0.6 - - - -
163C ALA* 1.3 79.6 - - - +
165C GLY* 1.3 57.1 + - - +
186C ALA* 4.2 4.0 - - - +
187C GLY* 3.4 31.6 + - - +
190C ALA* 5.1 0.8 - - + +
250C PHE* 4.3 15.3 - - + -
251C LYS* 3.4 38.1 - - + +
253C GLN* 3.9 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ALA 3.0 4.6 + - - -
164C ASP* 1.3 79.8 - - - +
166C GLY* 1.3 68.8 + - - +
167C TYR* 3.2 20.3 - - - -
185C ASN* 3.3 11.7 + - - -
187C GLY* 3.6 8.9 - - - -
256C LYS* 6.3 0.4 - - - -
----------------------------------------------------------
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