Contacts of the helix formed by residues 198 - 212 (chain A) in PDB entry 2EZT
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 ASP 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU 3.6 3.6 + - - -
197A PRO* 1.3 68.8 - - - +
199A VAL* 1.3 63.1 + - - +
200A GLN* 2.8 31.6 + - - +
201A ALA* 3.2 32.1 + - + +
202A VAL* 3.1 25.3 + - - +
204A ARG* 4.8 3.6 + - - -
322A VAL* 4.9 4.4 - - + +
190B GLN* 5.9 2.7 - - - +
193B LEU* 3.6 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO 4.3 7.0 - - - +
198A ASP* 1.3 73.6 + - - +
200A GLN* 1.3 80.0 + - + +
202A VAL* 3.3 7.3 + - - +
203A THR* 2.9 33.6 + - - +
336A GLN* 5.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 2.8 31.6 + - - +
199A VAL* 1.3 93.8 - - + +
201A ALA* 1.3 57.2 + - - +
203A THR* 3.4 7.1 + - - -
204A ARG* 2.9 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 3.2 30.8 + - + +
199A VAL 3.3 0.6 - - - -
200A GLN* 1.3 75.6 - - - +
202A VAL* 1.3 56.4 + - - +
204A ARG* 3.3 24.0 + - - +
205A LEU* 2.8 29.7 + - - +
320A ILE* 3.8 10.0 - - + +
321A ALA 5.0 4.0 - - - +
322A VAL* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 3.5 27.4 - - + -
198A ASP 3.1 17.7 + - - +
199A VAL* 3.3 6.3 + - - +
201A ALA* 1.3 73.0 - - - +
203A THR* 1.3 54.1 + - - +
205A LEU* 3.6 6.3 - - - +
206A THR* 2.6 41.8 + - - -
322A VAL* 4.6 7.6 - - + -
329A THR* 3.9 13.9 - - + -
332A ALA* 4.1 7.9 - - + -
333A ILE* 3.7 29.2 - - + +
336A GLN* 3.3 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 2.9 19.7 + - - +
200A GLN* 3.7 8.3 - - - -
202A VAL* 1.3 76.2 - - - +
204A ARG* 1.3 58.4 + - + +
206A THR* 3.4 1.6 + - - -
207A GLN* 3.0 39.5 + - + +
336A GLN* 3.2 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 4.8 2.8 + - - -
200A GLN* 2.9 40.5 + - + +
201A ALA* 3.7 29.1 - - - +
203A THR* 1.3 76.0 - - + +
205A LEU* 1.3 62.1 + - - +
207A GLN* 3.3 4.9 + - - +
208A THR* 3.1 27.4 + - - -
320A ILE* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA 2.8 20.0 + - - +
202A VAL* 3.6 4.9 - - - +
204A ARG* 1.3 69.9 - - - +
206A THR* 1.3 71.4 + - - +
208A THR* 3.3 3.6 + - - -
209A LEU* 2.9 23.8 + - + +
281A LEU* 3.9 28.5 - - + -
303A LEU* 3.7 23.0 - - + +
304A GLN 4.9 2.2 - - - +
305A ILE* 4.0 12.8 - - + -
320A ILE* 3.5 20.5 - - + +
322A VAL* 4.0 23.3 - - + -
329A THR* 5.1 2.0 - - + -
333A ILE* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL 2.6 29.3 + - - -
203A THR 3.7 4.5 - - - -
204A ARG 3.4 0.2 - - - -
205A LEU* 1.3 77.6 - - - +
207A GLN* 1.3 64.0 + - - +
209A LEU* 3.2 5.8 + - + +
210A LEU* 2.9 38.9 + - + +
237A LEU* 5.8 0.9 - - + -
333A ILE* 3.5 26.1 - - + +
336A GLN* 3.8 17.7 - - + +
337A VAL* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.0 27.4 + - + +
204A ARG* 4.0 5.2 - - - +
206A THR* 1.3 84.6 - - - +
208A THR* 1.3 58.6 + - - +
210A LEU* 3.4 31.1 + - - +
211A ALA* 3.0 31.1 + - - +
336A GLN* 5.5 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG 3.1 15.0 + - - -
205A LEU 3.7 7.0 - - - -
207A GLN* 1.3 77.2 - - - +
209A LEU* 1.3 60.2 + - - +
211A ALA* 3.5 6.9 + - - +
212A ALA* 3.4 19.2 + - - +
279A VAL* 4.2 4.9 - - + +
301A TYR* 3.9 42.1 - - + -
303A LEU* 4.0 19.5 - - + -
319A ASP* 5.9 0.7 - - + -
320A ILE* 3.8 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 2.9 22.3 + - + +
206A THR* 3.6 5.4 - - + +
208A THR* 1.3 77.7 - - - +
210A LEU* 1.3 62.3 + - + +
212A ALA* 3.4 18.0 - - - +
215A PRO* 3.9 25.9 - - + +
216A LEU 4.6 7.0 - - - +
217A ILE* 4.7 7.9 - - + -
233A LEU* 5.7 1.1 - - + -
237A LEU* 4.5 13.0 - - + -
239A ILE* 3.8 22.5 - - + +
279A VAL* 4.4 14.6 - - + -
281A LEU* 4.0 37.5 - - + -
303A LEU* 4.1 7.3 - - + +
333A ILE* 5.0 9.9 - - + -
340A ARG* 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 2.9 30.2 + - + +
207A GLN* 3.6 35.0 - - - +
209A LEU* 1.3 74.5 - - + +
211A ALA* 1.3 61.3 + - - +
212A ALA 3.5 2.9 + - - +
237A LEU* 3.5 39.3 - - + -
336A GLN 5.9 0.2 - - - +
337A VAL* 4.2 9.2 - - + -
340A ARG* 3.0 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLN 3.0 18.6 + - - +
208A THR* 3.9 6.7 - - - +
209A LEU 3.4 0.6 - - - -
210A LEU* 1.3 74.3 - - - +
212A ALA* 1.3 63.9 + - - +
213A GLU* 3.6 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A THR 3.4 6.0 + - - +
209A LEU 3.4 15.9 - - - +
210A LEU 3.3 7.5 - - - +
211A ALA* 1.3 78.8 - - - +
213A GLU* 1.3 61.9 + - - +
215A PRO* 3.8 19.5 - - + +
278A ASP* 3.5 13.5 - - - +
279A VAL* 3.4 34.8 - - + -
340A ARG* 4.9 3.6 + - - -
----------------------------------------------------------
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