Contacts of the helix formed by residues 194 - 213 (chain D) in PDB entry 1U5D
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 194 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D SER* 3.1 10.9 + - - -
192D ALA* 3.3 5.9 - - - +
193D THR* 1.3 81.0 + - - +
195D PRO* 1.3 76.5 - - - +
196D ALA* 3.4 8.0 + - - +
197D GLU* 3.0 28.1 + - - +
198D ALA 3.0 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MET* 4.2 4.1 - - + +
175D GLU* 3.4 40.8 - - + +
176D SER* 3.1 8.9 - - - +
194D SER* 1.3 87.8 - - - +
196D ALA* 1.3 58.5 + - - +
198D ALA* 3.2 2.3 + - - +
199D ARG* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D SER* 3.2 7.9 + - - +
195D PRO* 1.3 80.5 - - - +
197D GLU* 1.3 61.0 + - + +
199D ARG* 3.3 8.0 + - - +
200D ASP* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LYS* 2.9 33.8 + - - -
192D ALA* 4.2 7.4 - - + -
193D THR* 3.6 20.4 - - - +
194D SER* 3.0 23.7 + - - +
196D ALA* 1.3 77.7 - - + +
198D ALA* 1.3 65.8 + - - +
200D ASP* 3.1 5.7 + - - +
201D TRP* 3.0 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MET* 3.9 16.6 - - + -
176D SER* 3.3 35.0 - - - +
177D CYS 4.4 0.4 - - - +
178D PHE* 4.0 14.1 - - + -
192D ALA* 3.6 8.6 - - + +
194D SER 3.0 9.8 + - - +
195D PRO 3.7 7.4 - - - +
197D GLU* 1.3 74.8 - - - +
199D ARG* 1.3 63.8 + - - +
201D TRP* 3.2 3.5 + - - +
202D VAL* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MET* 3.5 46.2 - - - +
195D PRO 2.9 16.6 + - - +
196D ALA* 3.5 8.7 - - - +
197D GLU 3.2 0.2 - - - -
198D ALA* 1.3 76.4 - - - +
200D ASP* 1.3 58.8 + - - +
202D VAL* 3.5 6.1 + - - +
203D ASP* 2.9 54.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LYS* 2.7 34.3 + - - +
196D ALA 3.0 16.7 + - - +
197D GLU* 3.1 8.0 + - - +
199D ARG* 1.3 76.0 - - - +
201D TRP* 1.3 64.9 + - - +
203D ASP* 4.5 4.2 - - - +
204D GLN* 3.0 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LYS* 3.3 39.3 - - + +
111D GLN* 3.9 4.5 - - - -
112D GLY* 3.8 24.3 - - - -
113D TYR 5.1 1.8 + - - -
114D LEU* 3.6 30.4 - - + +
133D CYS* 3.6 26.9 - - + -
135D VAL* 4.0 24.0 - - + -
140D PHE* 4.1 15.7 - + - -
178D PHE* 3.5 27.4 - + + -
192D ALA* 4.7 0.9 - - + -
197D GLU* 3.0 34.7 + - + +
198D ALA 3.6 5.2 - - - +
200D ASP* 1.3 76.8 - - - +
202D VAL* 1.3 56.9 + - - +
204D GLN* 4.0 1.0 - - - +
205D ILE* 2.9 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D VAL* 3.7 22.6 - - + +
163D ARG* 4.0 6.3 - - - -
164D MET* 3.7 32.3 - - + +
178D PHE* 3.4 34.8 - - + -
198D ALA 2.9 20.0 + - - +
199D ARG* 3.8 7.6 - - - +
201D TRP* 1.3 75.2 - - - +
203D ASP* 1.3 68.3 + - - +
206D SER* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ARG* 2.9 41.4 + - - +
200D ASP* 4.0 5.5 - - - +
202D VAL* 1.3 83.7 - - - +
204D GLN* 1.3 69.8 + - - +
206D SER* 3.4 6.4 + - - -
207D PHE* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 3.5 30.6 - - + +
110D LYS* 4.7 10.8 - - + -
135D VAL* 5.6 0.9 - - + -
200D ASP* 3.0 43.4 + - - +
201D TRP* 4.0 3.1 - - - +
203D ASP* 1.3 81.2 - - - +
205D ILE* 1.3 64.1 + - + +
207D PHE* 3.3 8.6 + - - +
208D LEU* 3.2 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D VAL* 4.2 22.2 - - + -
140D PHE* 4.3 15.0 - - + -
157D ILE* 4.8 8.3 - - + -
162D VAL* 4.0 9.2 - - + -
178D PHE* 4.4 5.2 - - + -
180D LEU* 4.0 34.1 - - + -
201D TRP* 2.9 44.3 + - + +
202D VAL 3.9 2.0 - - - +
204D GLN* 1.3 74.5 - - + +
206D SER* 1.3 64.1 + - - +
208D LEU* 3.1 9.1 + - - +
209D LEU* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D VAL* 3.7 17.6 - - - +
202D VAL* 2.8 21.7 + - - -
203D ASP* 3.7 7.9 - - - -
205D ILE* 1.3 77.1 - - - +
207D PHE* 1.3 56.6 + - - +
209D LEU* 3.2 6.0 + - - +
210D LYS* 2.8 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ASP 3.1 13.6 + - - +
204D GLN* 3.6 12.8 - - - +
205D ILE 3.2 0.2 - - - -
206D SER* 1.3 75.6 - - - +
208D LEU* 1.3 75.6 + - + +
210D LYS* 3.3 7.6 + - + +
211D ASP* 3.1 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE* 4.1 33.2 - - + -
135D VAL* 3.8 28.9 - - + -
136D SER 4.0 11.7 - - - +
137D ARG* 4.3 17.9 - - + -
138D GLY 5.2 1.1 - - - +
157D ILE* 3.8 15.5 - - + -
204D GLN 3.2 15.5 + - - +
205D ILE* 3.1 10.6 + - - +
207D PHE* 1.3 88.6 - - + +
209D LEU* 1.3 57.8 + - - +
211D ASP* 3.2 10.1 + - + +
212D LEU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D ILE* 3.1 45.1 - - + +
158D LYS* 4.6 4.0 - - - +
159D GLY 4.7 1.3 - - - +
160D TYR* 3.4 35.2 - - + +
161D SER* 4.2 1.3 - - - -
162D VAL* 3.9 22.4 - - + +
180D LEU* 4.9 0.2 - - + -
205D ILE* 2.9 36.1 + - + +
206D SER* 3.2 6.9 + - - +
208D LEU* 1.3 72.4 - - - +
210D LYS* 1.3 66.8 + - + +
212D LEU* 3.3 6.8 + - + +
213D SER* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D SER* 2.8 41.5 + - - +
207D PHE* 3.9 6.3 - - - +
209D LEU* 1.3 78.3 - - + +
211D ASP* 1.3 63.6 + - - +
213D SER* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ARG* 6.1 1.0 - - - -
207D PHE* 3.1 30.0 + - + +
208D LEU* 3.5 13.9 - - - +
210D LYS* 1.3 77.0 - - - +
212D LEU* 1.3 63.0 + - + +
213D SER* 3.3 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D GLY* 4.1 17.3 - - - +
157D ILE* 3.8 33.4 - - + -
158D LYS* 3.6 59.2 + - + +
159D GLY 5.8 0.2 - - - +
208D LEU* 2.9 21.4 + - + +
209D LEU* 3.6 7.6 - - - +
210D LYS 3.2 0.2 - - - -
211D ASP* 1.3 75.1 - - + +
213D SER* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ARG* 3.8 54.7 + - - +
171A ASP* 5.4 2.0 - - - -
158D LYS* 5.6 2.0 + - - +
209D LEU 3.1 14.6 + - - -
210D LYS* 3.0 22.5 + - - +
211D ASP 3.5 6.6 - - - +
212D LEU* 1.3 79.6 - - - +
----------------------------------------------------------
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