Contacts of the helix formed by residues 201 - 216 (chain A) in PDB entry 3I58
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 LEU 201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TRP* 5.0 19.1 - - + +
137A GLY* 6.3 2.7 - - - -
200A ASP* 1.3 89.7 + - - +
202A GLN* 1.3 67.6 + - + +
203A GLY 3.3 2.1 + - - +
204A PRO* 3.3 9.9 - - + +
205A ALA* 3.1 15.6 + - - +
225A VAL* 4.8 1.8 - - - -
226A GLY 4.4 6.3 - - - +
227A SER* 4.7 6.3 - - - -
401A SAH 3.6 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLY 5.7 1.4 - - - +
201A LEU* 1.3 75.5 - - + +
203A GLY* 1.3 66.5 + - - +
205A ALA* 4.1 0.2 - - - +
206A SER* 3.1 26.3 + - - -
225A VAL* 3.6 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 4.7 8.5 - - - -
147A ASP* 4.3 5.3 - - - +
201A LEU* 4.6 1.2 - - - +
202A GLN* 1.3 87.7 - - - +
204A PRO* 1.3 71.4 - - - +
206A SER* 3.1 17.1 + - - -
207A ALA* 3.1 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 4.4 10.3 - - - +
146A PHE* 6.4 1.1 - - + -
147A ASP* 3.3 32.3 - - - +
179A GLY* 3.4 26.2 - - - +
200A ASP* 3.4 22.2 - - - +
201A LEU* 3.3 16.8 - - + +
203A GLY* 1.3 88.6 - - - +
205A ALA* 1.3 49.4 + - - +
207A ALA* 2.9 5.1 + - + +
208A ALA 2.7 31.7 + - - -
401A SAH 3.7 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 4.5 1.8 - - - -
198A VAL* 5.1 2.0 - - - +
200A ASP* 3.9 18.3 - - + +
201A LEU 3.1 20.0 + - - +
202A GLN 4.1 0.4 - - - +
204A PRO* 1.3 77.0 - - - +
206A SER* 1.3 57.8 + - - +
208A ALA* 3.2 9.3 + - - +
209A HIS* 2.9 23.2 + - - +
223A VAL* 3.5 22.7 - - + +
224A VAL 4.6 2.7 - - - +
225A VAL* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN 3.1 17.5 + - - -
203A GLY* 3.1 10.4 + - - -
205A ALA* 1.3 77.8 - - - +
207A ALA* 1.3 60.8 + - - +
209A HIS* 3.4 8.6 + - - +
210A ARG* 3.0 26.9 + - - +
223A VAL* 5.5 0.4 - - - -
225A VAL* 5.5 0.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
147A ASP* 4.4 8.5 - - + +
180A SER* 4.1 20.6 - - - +
203A GLY 3.1 7.8 + - - +
204A PRO* 2.9 13.2 + - + +
206A SER* 1.3 79.7 + - - +
208A ALA* 1.3 65.3 + - - +
210A ARG* 3.4 11.1 + - - +
211A ARG* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 3.4 22.4 - - - +
180A SER 3.1 19.5 + - - +
181A GLY 3.9 2.2 - - - +
198A VAL* 4.1 11.0 - - + -
204A PRO 2.7 5.4 + - - +
205A ALA 3.2 10.7 + - - +
207A ALA* 1.3 78.3 - - - +
209A HIS* 1.3 56.5 + - - +
211A ARG* 3.2 3.6 + - - +
212A PHE* 3.0 42.2 + - + -
223A VAL* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ALA 2.9 13.7 + - - +
206A SER* 3.5 12.6 - - - +
207A ALA 3.2 0.2 - - - -
208A ALA* 1.3 73.6 - - - +
210A ARG* 1.3 68.1 + - - +
211A ARG 3.1 0.2 + - - -
212A PHE* 3.2 6.3 + - - +
213A LEU* 3.0 57.3 + - + +
218A SER* 6.1 2.2 - - - -
222A GLN* 6.0 1.0 - - - -
223A VAL* 3.5 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER 3.0 16.7 + - - +
207A ALA* 3.7 10.1 + - - +
209A HIS* 1.3 78.3 - - - +
211A ARG* 1.3 83.2 + - - +
213A LEU* 3.6 5.9 - - - +
214A ASP* 3.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 3.4 22.2 + - - -
180A SER* 3.0 29.1 + - - +
181A GLY 4.2 1.8 - - - -
182A GLY* 2.6 46.7 - - - +
185A SER* 4.0 20.9 - - - +
207A ALA 3.1 12.9 + - - +
208A ALA 3.4 8.1 - - - +
209A HIS 3.0 0.6 - - - -
210A ARG* 1.3 91.7 - - - +
212A PHE* 1.3 63.2 + - + +
214A ASP* 3.3 2.1 + - - +
215A THR* 2.7 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 3.9 23.1 - - - -
184A LEU* 3.8 10.8 - - + -
185A SER* 4.2 14.4 - - - -
198A VAL* 3.5 33.7 - - + -
208A ALA* 3.0 20.6 + - + +
209A HIS* 3.9 4.9 - - - +
211A ARG* 1.3 81.3 - - + +
213A LEU* 1.3 64.5 - - + +
215A THR* 4.3 3.8 - - - -
216A GLY 2.9 3.5 + - - -
217A LEU* 2.9 37.8 + - + -
218A SER* 3.5 21.8 + - - +
221A ALA* 3.7 31.4 - - + +
222A GLN 4.3 4.5 - - - -
223A VAL* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A HIS* 3.0 59.6 + - + +
210A ARG* 3.6 8.5 - - - +
212A PHE* 1.3 81.5 - - + +
214A ASP* 1.3 65.0 + - - +
216A GLY* 3.2 9.4 + - - -
218A SER* 4.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG* 3.3 48.5 + - - +
211A ARG* 3.3 3.0 + - - +
213A LEU* 1.3 84.2 - - - +
215A THR* 1.3 62.1 + - - +
216A GLY* 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 4.4 8.3 + - - +
189A THR* 5.2 3.6 - - - +
211A ARG* 2.7 33.9 + - - +
212A PHE* 4.0 1.6 - - - -
214A ASP* 1.3 74.0 - - - +
216A GLY* 1.3 58.6 + - - +
217A LEU* 3.2 41.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE 2.9 5.7 + - - -
213A LEU 3.2 7.6 + - - -
214A ASP 3.1 5.0 - - - -
215A THR* 1.3 79.7 - - - +
217A LEU* 1.3 63.4 + - - +
218A SER* 3.6 4.7 - - - -
219A GLY 5.1 1.3 + - - -
----------------------------------------------------------
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