Contacts of the helix formed by residues 209 - 225 (chain A) in PDB entry 1W45
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 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.1 13.0 - - - -
170A VAL* 3.8 32.0 - - - +
172A SER* 3.8 24.0 - - - -
173A PHE 6.1 0.2 - - - -
208A ARG* 1.3 77.7 - - - +
210A ALA* 1.3 59.2 + - - +
211A THR 3.5 3.2 + - - -
212A HIS* 3.1 25.3 + - - +
213A LEU* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.1 28.0 + - + +
209A SER* 1.3 71.5 - - - +
211A THR* 1.3 62.3 + - - +
213A LEU* 3.4 3.0 + - - -
214A LEU* 3.0 37.4 + - + +
251A THR* 3.5 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 3.7 28.9 + - - +
174A VAL* 3.4 23.9 - - + +
209A SER* 3.4 3.9 + - - -
210A ALA* 1.3 75.6 - - - +
212A HIS* 1.3 66.4 + - - +
214A LEU* 3.6 15.3 + - + +
215A ARG* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 6.1 1.1 - - + -
173A PHE 6.2 0.2 - - - -
174A VAL* 3.7 17.8 - - + +
175A ASP* 4.1 20.4 + - + -
178A LEU* 3.9 12.1 - - + +
179A ALA* 3.5 22.1 + - + -
182A ASP* 2.7 30.9 + - - -
208A ARG* 3.5 25.7 - - + +
209A SER* 3.1 26.1 + - - +
211A THR* 1.3 74.4 - - - +
213A LEU* 1.3 66.1 + - - +
215A ARG* 3.0 16.1 + - - +
216A VAL* 3.1 27.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
167A ARG* 6.2 3.4 - - + -
204A ILE* 3.4 35.0 - - + +
205A LEU* 3.7 29.4 - - + +
208A ARG* 4.0 15.5 - - + +
209A SER 2.8 26.5 + - - +
210A ALA* 3.6 5.8 - - - +
212A HIS* 1.3 74.7 + - - +
214A LEU* 1.3 63.0 + - - +
216A VAL* 3.2 6.9 + - + +
217A PHE* 3.1 48.1 + - + -
247A VAL* 4.7 2.9 - - + -
251A THR* 4.0 24.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
210A ALA* 3.0 24.9 + - + +
211A THR* 3.8 17.0 - - + +
212A HIS 3.3 0.4 - - - -
213A LEU* 1.3 74.8 - - - +
215A ARG* 1.3 61.6 + - - +
217A PHE* 3.4 10.5 + - + +
218A GLU* 3.2 21.2 + - - +
251A THR* 3.6 30.3 - - + +
252A GLN* 4.0 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 3.9 29.7 + - + +
176A PRO* 3.5 27.5 + - - +
179A ALA* 3.7 20.4 - - + +
211A THR 3.5 5.8 + - - +
212A HIS 3.0 10.6 + - - +
214A LEU* 1.3 75.0 - - - +
216A VAL* 1.3 64.2 + - - +
218A GLU* 3.0 22.4 + - - +
219A GLU* 2.9 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 3.7 20.2 - - - +
182A ASP* 3.8 12.1 - - + +
183A ALA* 3.8 24.5 - - + +
186A LEU* 4.2 17.5 - - + -
204A ILE* 4.8 4.7 - - + -
212A HIS* 3.1 40.5 + - + +
213A LEU* 3.2 13.7 + - + +
215A ARG* 1.3 73.2 - - - +
217A PHE* 1.3 60.4 + - + +
219A GLU* 3.1 2.9 + - - +
220A TYR* 2.7 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 5.7 1.3 - - + -
204A ILE* 6.4 0.2 - - + -
205A LEU* 4.3 18.2 - - + -
213A LEU* 3.1 39.4 + - + -
214A LEU* 3.5 13.0 - - + +
215A ARG 3.2 0.2 - - - -
216A VAL* 1.3 80.5 - - + +
218A GLU* 1.3 61.8 + - - +
220A TYR* 3.6 5.4 + - - +
221A GLU* 3.2 29.2 + - - +
228A ILE* 3.5 40.7 + - + +
248A VAL* 4.0 29.2 - - + -
251A THR* 4.2 20.2 - - + -
252A GLN* 4.6 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU 3.2 12.0 + - - +
215A ARG* 3.0 25.6 + - - +
217A PHE* 1.3 74.5 - - - +
219A GLU* 1.3 65.8 - - - +
221A GLU* 3.4 6.7 + - + +
222A LYS* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO 5.8 0.9 - - - +
179A ALA 4.0 15.9 - - - +
180A LEU* 3.5 33.2 - - + +
183A ALA* 3.6 19.7 - - + -
215A ARG* 2.9 51.0 + - + +
216A VAL 3.7 1.8 - - - +
218A GLU* 1.3 72.7 - - - +
220A TYR* 1.3 58.4 + - - +
222A LYS* 3.0 40.3 + - - +
223A ILE* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA* 3.6 24.7 - - + +
186A LEU* 3.7 19.1 + - + -
187A TYR* 3.4 35.3 - - + -
190A GLY* 5.8 3.3 - - - -
216A VAL* 2.7 22.8 + - + +
217A PHE* 3.9 7.0 - - - +
219A GLU* 1.3 72.2 - - - +
221A GLU* 1.3 57.8 + - - +
223A ILE* 3.3 3.2 + - - +
224A ALA* 2.8 41.0 + - + +
226A LYS* 3.5 31.5 + - + -
227A SER 3.9 10.8 - - - -
228A ILE* 4.3 13.7 - - + -
231A SER* 2.9 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 3.2 18.0 + - - +
218A GLU* 3.8 5.6 - - - +
219A GLU 3.3 0.2 - - - -
220A TYR* 1.3 77.3 - - - +
222A LYS* 1.3 64.6 + - - +
225A ASN* 3.2 23.8 + - - +
226A LYS 3.8 19.5 - - - +
227A SER* 4.2 25.3 + - - -
228A ILE 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 5.8 0.2 - - - +
218A GLU* 3.1 24.8 + - + +
219A GLU* 3.0 49.7 + - - +
221A GLU* 1.3 76.5 - - - +
223A ILE* 1.3 64.8 + - + +
225A ASN* 4.6 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.3 20.0 - - + -
183A ALA* 4.1 21.5 - - + -
184A GLN* 4.2 21.5 - - - +
187A TYR* 3.3 45.6 + - + -
219A GLU* 2.8 20.3 + - + +
220A TYR* 3.6 4.0 - - - +
222A LYS* 1.3 82.0 - - + +
224A ALA* 1.3 60.5 + - + +
225A ASN* 4.8 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 3.5 34.8 - - + -
220A TYR* 2.8 35.4 + - + +
223A ILE* 1.3 73.7 - - + +
225A ASN* 1.3 72.1 + - - +
226A LYS* 3.1 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 3.2 18.1 + - - +
222A LYS 4.6 7.8 - - - +
223A ILE 4.8 4.5 + - - -
224A ALA* 1.3 80.4 + - - +
226A LYS* 1.3 58.3 + - - +
----------------------------------------------------------
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