Contacts of the helix formed by residues 203 - 217 (chain A) in PDB entry 3N4E
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 SER 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A CYS* 3.4 12.6 - - - -
171A ASP* 2.7 30.3 + - - -
202A TYR* 1.3 76.2 - - - +
204A VAL* 1.3 61.0 + - - +
205A GLY* 3.8 3.1 + - - -
206A GLY 3.1 12.1 + - - -
207A ALA* 2.8 26.7 + - - +
226A VAL* 3.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 1.3 75.9 - - - +
205A GLY* 1.3 64.3 + - - +
207A ALA* 3.1 3.3 + - - +
208A ILE* 3.0 26.7 + - + +
226A VAL* 4.1 2.6 - - + +
233A ALA* 3.6 31.6 - - + -
236A GLU* 3.8 23.3 - - + +
237A VAL* 3.9 22.2 - - + +
240A ARG* 3.9 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 3.4 3.9 + - - -
204A VAL* 1.3 79.0 - - - +
206A GLY* 1.3 56.8 + - - +
208A ILE* 3.3 11.4 + - - +
209A ARG* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP* 3.8 13.7 + - - -
174A ILE* 4.0 15.7 - - - -
202A TYR* 3.8 6.7 - - - -
203A SER* 3.1 17.4 + - - -
205A GLY* 1.3 74.2 - - - +
207A ALA* 1.3 57.4 + - - +
209A ARG* 3.4 4.6 + - - +
210A VAL* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.5 16.1 - - + +
203A SER 2.8 19.9 + - - +
204A VAL 3.1 5.6 + - - +
206A GLY* 1.3 72.4 - - - +
208A ILE* 1.3 54.9 + - - +
210A VAL 3.4 0.2 + - - -
211A GLY* 2.8 30.0 + - - -
222A PHE* 3.2 11.7 - - - -
225A PRO* 3.8 26.9 - - + -
226A VAL* 4.1 6.3 - - + -
237A VAL* 3.9 13.9 - - + -
241A LEU* 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.0 27.6 + - + +
205A GLY* 3.7 10.1 - - - +
207A ALA* 1.3 71.7 - - - +
209A ARG* 1.3 68.4 + - - +
211A GLY* 3.3 0.3 + - - -
212A ARG* 2.9 41.4 + - + +
237A VAL* 4.9 6.5 - - + -
240A ARG* 3.3 56.5 - - + +
241A LEU* 4.1 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 4.1 29.9 - - + +
178A ILE* 4.7 7.0 - - + +
205A GLY 3.0 17.0 + - - +
206A GLY* 3.6 6.7 - - - +
208A ILE* 1.3 81.2 - - - +
210A VAL* 1.3 60.9 + - - +
212A ARG* 3.5 6.1 + - - +
213A ALA* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 3.8 25.8 - - + +
177A ASP* 5.4 0.9 - - + -
178A ILE* 4.6 11.4 - - + +
196A PHE* 4.4 7.0 - - + -
202A TYR* 3.8 31.6 - - + +
206A GLY 3.0 20.3 + - - +
207A ALA 3.9 2.9 - - - +
209A ARG* 1.3 71.7 - - - +
211A GLY* 1.3 61.3 + - - +
213A ALA* 3.0 9.4 + - - +
214A LEU* 2.8 46.1 + - + +
222A PHE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ALA 2.8 21.7 + - - -
208A ILE 3.6 1.3 - - - -
210A VAL* 1.3 72.6 - - - +
212A ARG* 1.3 56.2 + - - +
214A LEU* 3.1 5.8 + - - +
215A GLU* 2.9 31.8 + - - +
222A PHE* 3.7 18.1 - - - -
241A LEU* 4.0 16.8 - - - -
243A ILE* 4.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 2.9 34.9 + - + +
209A ARG* 3.8 6.3 - - - +
210A VAL 3.2 0.2 - - - -
211A GLY* 1.3 71.7 - - - +
213A ALA* 1.3 62.1 + - - +
215A GLU* 2.8 44.9 + - - +
216A ASP* 3.1 29.1 + - - +
240A ARG 3.2 20.9 + - - -
241A LEU* 3.8 9.2 - - - +
242A ASP* 3.7 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE* 3.7 44.4 - - + -
182A ARG* 5.2 4.1 + - - +
209A ARG 3.3 6.7 + - - +
210A VAL 3.0 9.2 + - - +
212A ARG* 1.3 78.0 - - - +
214A LEU* 1.3 61.6 + - + +
216A ASP* 3.4 12.2 + - - +
217A LEU* 3.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE* 6.0 2.2 - - + -
181A ALA* 3.8 19.3 - - + -
196A PHE* 3.7 41.3 - - + -
210A VAL* 2.8 28.7 + - + +
211A GLY 3.5 5.6 - - - +
213A ALA* 1.3 76.2 - - + +
215A GLU* 1.3 62.9 + - - +
217A LEU* 3.1 10.5 + - + +
219A TYR* 3.0 37.7 + - + +
222A PHE* 3.6 38.8 - - + -
243A ILE* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLY 2.9 16.5 + - - +
212A ARG* 2.8 41.4 + - - +
214A LEU* 1.3 75.8 - - - +
216A ASP* 1.3 65.5 + - - +
218A GLY* 3.1 13.3 + - - +
219A TYR 4.9 2.7 - - - +
241A LEU* 3.4 9.9 - - - +
242A ASP* 2.7 38.2 + - + +
243A ILE* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 5.9 3.8 - - - +
212A ARG* 3.1 18.9 + - - +
213A ALA* 3.5 13.9 - - - +
214A LEU 3.2 0.4 - - - -
215A GLU* 1.3 78.2 - - - +
217A LEU* 1.3 61.6 + - + +
218A GLY 3.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE* 4.4 5.8 - - + +
181A ALA* 4.0 15.0 - - + -
182A ARG* 3.7 64.6 - - + +
185A ARG* 2.8 47.8 + - + -
186A GLU* 5.6 3.1 - - - +
213A ALA 3.3 17.9 + - - +
214A LEU* 3.1 9.1 + - + +
216A ASP* 1.3 78.5 - - + +
218A GLY* 1.3 55.6 + - - +
219A TYR* 3.3 15.0 + - + -
----------------------------------------------------------
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