Contacts of the helix formed by residues 182 - 195 (chain D) in PDB entry 1A4Y
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 182 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER* 6.1 0.4 - - - -
155D ALA* 5.2 4.9 - - - +
180D ASP* 3.3 33.4 + - - +
181D ILE* 1.3 85.9 + - - +
183D GLU* 1.3 67.7 + - + +
184D ALA* 4.5 4.3 - - + +
186D VAL* 2.9 22.0 + - - +
208D CYS 3.0 15.7 + - - +
209D GLY* 3.7 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ASN* 1.3 77.0 - - + +
184D ALA* 1.3 52.0 + - - +
186D VAL 3.3 0.7 + - - -
187D ARG* 2.8 57.7 + - - +
209D GLY 3.5 5.2 + - - -
211D THR* 3.7 23.7 + - + +
213D ASP* 3.4 25.4 - - - +
214D ASN* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ALA* 4.5 12.3 - - + -
181D ILE 4.7 0.9 - - - +
182D ASN* 4.5 2.6 - - + +
183D GLU* 1.3 79.6 - - - +
185D GLY* 1.3 65.2 + - - +
187D ARG* 2.9 18.8 + - - +
188D VAL* 2.9 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ALA* 3.9 7.4 - - - +
158D CYS* 3.4 33.3 - - - +
181D ILE* 3.0 22.0 + - - -
184D ALA* 1.3 76.4 - - - +
186D VAL* 1.3 63.8 + - - +
188D VAL* 3.3 2.8 + - - -
189D LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D ILE* 3.4 24.4 - - + +
182D ASN 2.9 28.9 + - - +
183D GLU 3.5 4.9 - - - +
185D GLY* 1.3 74.4 - - - +
187D ARG* 1.3 56.7 + - - +
189D LEU* 3.7 5.2 - - - +
190D CYS* 3.1 38.1 + - - -
205D LEU* 4.4 11.9 - - + -
208D CYS* 4.7 0.4 - - + -
210D VAL* 3.6 32.1 - - + +
214D ASN* 3.5 29.2 - - + +
218D LEU* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D GLU* 2.8 49.1 + - - +
184D ALA* 2.9 13.0 + - - +
186D VAL* 1.3 74.7 - - - +
188D VAL* 1.3 67.7 + - + +
190D CYS* 3.2 4.1 + - - +
191D GLN* 3.1 41.3 + - - +
213D ASP* 3.7 25.2 + - - -
214D ASN* 3.6 8.8 - - - +
217D ASP* 2.9 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ALA* 5.3 2.9 - - + +
158D CYS* 3.7 21.8 - - + +
159D GLU* 3.6 37.9 - - + +
162D ALA* 4.3 3.3 - - + +
166D ARG* 5.3 0.8 + - - +
184D ALA* 2.9 18.8 + - + +
185D GLY* 3.6 8.1 - - - +
187D ARG* 1.3 74.8 - - + +
189D LEU* 1.3 57.0 + - - +
191D GLN* 2.8 32.6 + - + +
192D GLY* 3.0 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D CYS* 3.5 35.0 - - + +
161D LEU* 3.9 21.8 - - + -
162D ALA* 4.2 6.7 - - - +
165D LEU* 4.4 9.4 - - + +
174D LEU* 4.8 13.5 - - + -
176D VAL* 4.3 18.6 - - + -
181D ILE* 3.9 27.4 - - + -
185D GLY 3.0 8.3 + - - +
186D VAL* 3.7 6.1 - - - +
188D VAL* 1.3 79.9 - - - +
190D CYS* 1.3 64.1 + - - +
191D GLN 3.2 0.2 + - - -
192D GLY* 3.3 2.5 + - - +
193D LEU* 3.0 27.1 + - + +
203D LEU* 5.9 2.0 - - + -
205D LEU* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D VAL* 3.1 33.0 + - - +
187D ARG 3.2 4.5 + - - +
189D LEU* 1.3 77.4 - - - +
191D GLN* 1.3 57.0 + - - +
193D LEU* 3.8 8.3 - - - -
194D LYS* 2.9 30.1 + - - +
203D LEU* 5.9 1.3 - - - -
205D LEU* 5.6 1.8 - - - -
217D ASP* 3.6 34.3 - - + +
218D LEU* 3.8 30.1 - - - -
221D ILE* 3.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 4.2 7.0 - - - +
187D ARG* 3.1 36.0 + - - +
188D VAL* 2.8 18.5 + - + +
190D CYS* 1.3 75.3 - - - +
192D GLY* 1.3 64.3 + - - +
193D LEU 3.0 2.0 + - - -
194D LYS* 3.2 14.3 + - + +
195D ASP* 3.1 24.9 + - - +
217D ASP* 5.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ALA* 4.1 15.7 - - - -
165D LEU* 4.7 6.3 - - - -
166D ARG* 3.5 30.2 + - - +
188D VAL 3.0 11.1 + - - -
189D LEU 3.3 3.3 + - - -
191D GLN* 1.3 75.3 - - - +
193D LEU* 1.3 56.0 + - - +
195D ASP* 3.1 2.6 - - - +
196D SER* 3.1 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 3.9 25.3 - - + +
189D LEU* 3.0 15.6 + - + +
190D CYS* 3.7 7.9 - - - +
191D GLN 3.0 0.4 - - - -
192D GLY* 1.3 74.0 - - - +
194D LYS* 1.3 66.4 + - - +
195D ASP 2.9 3.6 + - - -
196D SER* 3.2 9.9 + - - -
198D CYS* 4.2 21.3 - - - -
200D LEU* 3.6 37.2 - - + -
203D LEU* 3.6 23.6 - - + -
221D ILE* 3.7 25.6 - - + -
225D LYS* 3.2 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D CYS 2.9 19.0 + - - +
191D GLN* 3.2 8.0 + - + +
193D LEU* 1.3 76.3 - - - +
195D ASP* 1.3 59.5 + - + +
196D SER 4.7 1.0 - - - +
220D GLY 5.9 0.4 - - - -
221D ILE* 3.5 17.9 - - + +
224D SER* 5.0 9.9 + - - +
225D LYS* 5.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 3.2 32.0 + - - +
191D GLN* 3.1 16.6 - - - +
192D GLY 3.1 13.7 - - - +
193D LEU 3.0 0.2 - - - -
194D LYS* 1.3 80.8 - - + +
196D SER* 1.3 66.0 + - - +
197D PRO* 3.7 2.1 - - - +
----------------------------------------------------------
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