Contacts of the helix formed by residues 184 - 192 (chain A) in PDB entry 3N2N
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 ASN 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP 4.8 0.8 + - - -
151A GLY* 5.9 1.2 - - - -
182A ASP 3.8 0.8 + - - +
183A PHE* 1.3 73.2 - - - +
185A GLU* 1.3 62.4 + - - +
186A THR* 3.0 27.9 + - - +
187A GLN* 3.1 32.2 + - + +
188A LEU* 3.1 24.3 + - - +
210C GLY* 3.0 31.3 + - - +
213C HIS* 3.4 21.5 - - + -
214C SER* 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.8 23.4 + - + -
184A ASN* 1.3 72.7 - - - +
186A THR* 1.3 58.0 + - - +
188A LEU* 3.3 2.4 + - - +
189A ALA* 2.9 27.8 + - - +
195A LYS* 4.0 22.2 - - + +
198A VAL* 3.8 28.3 - - + +
200A PRO* 5.3 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASN* 3.0 12.2 + - - +
185A GLU* 1.3 78.4 - - - +
187A GLN* 1.3 61.4 + - - +
189A ALA* 3.3 18.7 + - + +
190A ARG* 3.6 21.2 + - - +
207C ALA 4.9 0.7 + - - -
210C GLY* 4.1 0.7 - - - -
211C ILE* 3.4 37.7 + - + +
214C SER* 3.6 22.9 - - - +
215C ILE* 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLY* 5.3 2.7 - - - +
158A PHE* 3.4 55.8 - - + -
184A ASN* 3.1 37.3 - - + +
186A THR* 1.3 75.6 - - - +
188A LEU* 1.3 64.5 + - + +
190A ARG* 3.1 24.2 + - - +
191A ILE 3.9 0.5 + - - -
213C HIS* 5.1 3.7 + - + -
214C SER* 2.9 29.6 + - - +
217C LYS* 3.9 26.9 - - - +
218C LYS* 5.1 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 5.4 1.6 - - + -
149A THR* 3.8 19.1 - - + +
151A GLY* 3.7 27.4 - - - -
158A PHE* 4.8 6.7 - - + -
177A ALA* 4.1 18.0 - - + +
179A GLY* 3.9 19.7 - - - +
183A PHE* 3.5 29.2 - - + -
184A ASN 3.1 14.2 + - - +
185A GLU 3.3 0.4 + - - +
187A GLN* 1.3 80.6 - - + +
189A ALA* 1.3 57.7 + - - +
191A ILE* 3.1 13.7 + - + +
192A ALA* 2.9 29.5 + - - +
198A VAL* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU 2.9 16.5 + - - +
186A THR* 3.4 14.1 - - + +
187A GLN 3.1 0.6 - - - -
188A LEU* 1.3 76.2 - - - +
190A ARG* 1.3 57.8 + - - +
192A ALA 3.0 18.2 - - - +
193A ASP 4.5 0.9 - - - +
194A SER* 4.3 9.2 + - - -
195A LYS* 3.9 30.7 - - + +
198A VAL* 3.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 4.7 8.1 - - + -
162A GLU* 3.4 48.0 + - + +
166A ASN* 4.8 0.2 - - - +
169A ARG* 3.8 9.4 + - - -
186A THR* 3.7 21.7 - - - +
187A GLN* 3.1 17.1 + - - +
189A ALA* 1.3 77.1 - - - +
191A ILE* 1.3 62.9 + - - +
192A ALA 4.0 1.1 - - - +
40C TYR* 3.8 15.2 + - - -
214C SER* 3.4 24.0 + - - -
215C ILE* 5.5 4.8 - - - +
218C LYS* 3.4 45.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 3.8 16.6 - - + -
124A PHE* 3.5 36.3 - - + -
147A ALA* 5.3 3.6 - - + -
158A PHE* 3.7 32.5 - - + -
161A SER* 3.7 13.5 - - - -
162A GLU* 3.6 31.0 - - + +
165A ALA* 3.5 9.7 - - + +
169A ARG* 2.8 25.5 + - - -
175A VAL* 3.7 4.6 - - + +
177A ALA* 5.3 4.5 - - + -
187A GLN 4.2 3.4 - - - +
188A LEU* 3.1 12.5 + - + +
190A ARG* 1.3 76.7 - - - +
192A ALA* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG* 3.4 6.1 + - - -
175A VAL* 3.4 20.4 - - - +
177A ALA* 3.9 9.4 - - + +
188A LEU 2.9 15.9 + - - +
189A ALA* 3.0 13.5 - - - +
190A ARG 4.0 2.1 - - - -
191A ILE* 1.3 81.7 - - - +
193A ASP* 1.3 67.1 + - - +
194A SER 3.2 5.8 - - - +
197A HIS* 3.8 11.0 - - + +
198A VAL* 3.7 20.2 - - + -
----------------------------------------------------------
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