Contacts of the helix formed by residues 176 - 187 (chain A) in PDB entry 3NY5
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 THR 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY 4.0 0.4 + - - -
175A VAL* 1.3 74.9 - - - +
177A VAL* 1.3 59.3 + - - +
178A ARG* 3.6 5.6 - - - +
179A ASP* 2.9 35.5 + - - +
180A SER* 2.9 31.5 + - - -
210A TRP 3.7 11.2 - - - -
211A ASP* 3.6 24.5 - - + +
212A THR 3.3 7.2 - - - -
214A ILE* 4.5 0.2 - - - -
233B THR* 3.5 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 1.3 71.8 - - - +
178A ARG* 1.3 64.5 + - - +
180A SER* 3.2 8.6 + - - -
181A LEU* 3.0 36.9 + - + +
197A VAL* 4.3 18.2 - - + -
208A ILE* 4.1 3.8 - - + -
209A GLY 4.4 0.7 - - - +
210A TRP* 3.4 30.5 + - + +
212A THR* 3.1 30.5 + - - +
214A ILE* 4.2 13.9 - - + -
217A LEU* 4.0 20.9 - - + -
222A LEU* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 3.6 8.3 + - - +
177A VAL* 1.3 77.4 - - - +
179A ASP* 1.3 66.1 + - - +
181A LEU* 3.7 0.9 - - - +
182A LYS* 2.9 33.4 + - + +
192A PRO* 3.7 26.4 - - + +
193A GLU* 3.0 33.2 + - - +
210A TRP* 3.1 44.7 + - + +
211A ASP* 3.1 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 4.1 13.6 - - + -
176A THR* 2.9 27.5 + - - +
178A ARG* 1.3 83.8 - - - +
180A SER* 1.3 66.6 + - - +
181A LEU 3.3 0.5 + - - -
182A LYS* 3.0 44.9 + - - +
183A LYS* 5.0 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 3.4 28.2 - - - +
170A PRO* 4.2 4.4 + - - -
175A VAL* 3.3 10.9 - - - +
176A THR 2.9 23.9 + - - -
177A VAL 3.5 5.6 - - - -
179A ASP* 1.3 73.9 - - - +
181A LEU* 1.3 61.1 + - - +
183A LYS* 5.2 2.3 + - - +
184A ALA* 5.5 1.4 + - - +
214A ILE* 3.3 40.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.7 39.9 - - + -
161A LEU* 4.9 2.9 - - + -
167A THR* 4.0 9.9 - - + -
169A VAL* 3.9 16.4 - - + -
177A VAL* 3.0 34.4 + - + +
178A ARG 4.3 1.1 - - - +
180A SER* 1.3 79.5 - - - +
182A LYS* 1.3 66.1 + - - +
183A LYS 3.2 3.0 + - - -
184A ALA* 3.2 9.0 + - + +
185A LEU* 3.0 35.1 + - + +
197A VAL* 4.8 3.6 - - + -
210A TRP* 4.1 6.3 - - + -
214A ILE* 5.8 0.7 - - + -
222A LEU* 5.2 2.2 - - + -
224A VAL* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 2.9 17.8 + - + +
179A ASP* 3.0 43.7 + - - +
180A SER 3.6 1.2 - - - -
181A LEU* 1.3 75.2 - - - +
183A LYS* 1.3 65.3 + - + +
185A LEU* 3.4 5.3 + - - +
186A MSE 2.9 33.7 + - + +
192A PRO* 5.0 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP 5.0 2.1 + - - +
180A SER 5.2 1.8 + - - +
181A LEU 3.3 1.2 - - - -
182A LYS* 1.3 83.2 - - + +
184A ALA* 1.3 67.9 + - - +
186A MSE 3.3 5.4 + - - +
187A MSE 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.4 4.3 - - + -
167A THR* 4.0 28.9 - - + +
169A VAL* 5.6 1.8 - - + -
180A SER 5.5 1.3 + - - +
181A LEU* 3.2 16.3 + - + +
183A LYS* 1.3 78.6 - - - +
185A LEU* 1.3 65.7 - - + +
187A MSE 3.6 12.9 + - + +
188A ARG* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.9 27.8 - - + -
181A LEU* 3.0 27.4 + - + +
182A LYS* 3.6 4.5 - - - +
184A ALA* 1.3 76.8 - - + +
186A MSE 1.3 60.7 + - - +
188A ARG* 2.8 17.0 + - - +
190A LEU* 2.8 53.1 + - + +
191A ILE* 4.2 2.0 - - - -
192A PRO* 3.8 29.6 - - + -
195A CYS* 4.8 1.8 - - - -
210A TRP* 3.9 25.4 - - + -
224A VAL* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LYS* 2.9 21.4 + - + +
183A LYS* 3.8 6.1 - - - +
185A LEU* 1.3 71.0 - - - +
187A MSE 1.3 64.1 + - - +
188A ARG 2.9 4.9 - - - -
189A GLY* 2.9 24.1 + - - -
190A LEU 3.4 24.1 + - - +
191A ILE* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 2.9 25.1 + - - +
184A ALA* 3.7 9.0 - - + +
185A LEU 3.2 0.2 - - - -
186A MSE 1.3 75.0 - - - +
188A ARG* 1.3 89.3 + - + +
189A GLY 3.3 1.1 + - - -
----------------------------------------------------------
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