Contacts of the helix formed by residues 194 - 213 (chain D) in PDB entry 5HP1
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 GLU 194 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ASP 3.8 0.4 + - - -
193D LEU* 1.3 74.9 - - - +
195D ILE* 1.3 80.8 + - + +
196D GLY* 2.8 35.8 + - - -
197D GLN* 3.0 43.9 + - - +
198D HIS 2.9 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D SER* 4.7 13.7 - - - +
193D LEU 3.8 1.7 + - - -
194D GLU* 1.3 83.6 - - + +
196D GLY* 1.3 69.5 + - - +
198D HIS* 3.0 13.7 + - + +
199D ARG* 3.0 62.1 + - + +
233D GLU* 3.6 17.9 - - + +
235D HIS* 5.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D GLU* 2.8 23.0 + - - -
195D ILE* 1.3 77.0 - - - +
197D GLN* 1.3 57.7 + - - -
199D ARG* 3.4 7.2 + - - +
200D THR* 3.0 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D LEU* 4.1 17.7 - - + +
194D GLU* 3.0 46.0 + - - +
196D GLY* 1.3 73.0 - - - +
198D HIS* 1.3 60.4 + - - +
200D THR* 3.4 11.0 - - + -
201D LYS* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D SER* 3.4 42.0 - - - -
107D THR* 2.5 33.0 + - - -
189D VAL* 3.5 15.9 - - + -
190D GLY 4.4 0.2 - - - -
191D SER* 2.6 32.4 + - - +
193D LEU* 4.2 4.4 - - + +
194D GLU 2.9 12.1 + - - +
195D ILE* 3.0 18.8 + - + +
197D GLN* 1.3 73.4 - - - +
199D ARG* 1.3 66.8 + - + +
201D LYS* 3.0 8.6 + - - +
202D ILE* 2.8 40.0 + - + +
233D GLU* 5.4 4.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
195D ILE* 3.0 36.6 + - + +
196D GLY* 3.8 7.2 - - - +
198D HIS* 1.3 77.2 - - + +
200D THR* 1.3 62.7 + - - +
202D ILE* 3.2 10.5 + - - +
203D GLU* 3.0 22.7 + - - +
233D GLU* 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D GLY 3.0 16.0 + - - -
197D GLN* 3.4 15.5 - - + +
199D ARG* 1.3 76.4 - - - +
201D LYS* 1.3 66.6 + - + +
203D GLU* 3.1 10.3 + - - +
204D GLU* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D PHE* 3.7 10.0 - - + -
175D ASN* 2.7 38.3 + - - +
178D ILE* 3.8 28.3 - - + -
193D LEU* 3.9 17.7 - - + -
197D GLN* 2.9 25.8 + - + +
198D HIS* 3.0 6.3 + - - +
200D THR* 1.3 78.6 - - + +
202D ILE* 1.3 64.6 + - + +
204D GLU* 3.3 32.1 + - - +
205D LEU 3.0 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D THR* 3.7 38.8 - - + +
109D LEU* 4.1 21.0 - - + +
171D PHE* 6.4 0.2 - - + -
189D VAL* 3.7 34.8 - - + -
198D HIS* 2.8 27.3 + - + +
199D ARG* 3.5 10.3 - - - +
201D LYS* 1.3 73.3 - - + +
203D GLU* 1.3 61.6 + - - +
205D LEU* 3.2 6.0 + - + +
206D ARG* 2.8 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ARG 3.0 12.2 + - - +
200D THR* 3.1 11.9 + - - +
202D ILE* 1.3 74.2 - - - +
204D GLU* 1.3 65.5 + - - +
206D ARG* 3.1 38.0 + - - +
207D GLN* 2.8 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D PHE* 3.9 9.9 - - + -
174D GLN* 5.1 6.8 - - - +
175D ASN* 4.2 6.1 + - - -
200D THR* 3.1 23.6 + - + +
201D LYS* 3.3 45.7 + - - +
203D GLU* 1.3 77.4 - - - +
205D LEU* 1.3 57.5 + - - +
207D GLN* 3.3 8.1 + - - +
208D HIS* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 3.9 16.2 - - + -
168D LEU* 3.6 24.2 - - + -
171D PHE* 3.3 43.4 - - + -
180D ILE* 4.1 3.8 - - + -
187D LEU* 4.0 14.6 - - + -
189D VAL* 3.6 33.4 - - + -
201D LYS 3.0 13.4 + - - +
202D ILE* 3.2 8.9 + - + +
204D GLU* 1.3 76.3 - - - +
206D ARG* 1.3 57.5 + - - +
208D HIS* 3.3 7.5 + - + +
209D LEU* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 4.0 9.8 - - + +
202D ILE* 2.8 37.3 + - - +
203D GLU* 3.1 32.9 + - - +
205D LEU* 1.3 77.0 - - - +
207D GLN* 1.3 59.0 + - + +
209D LEU* 3.2 8.4 + - - +
210D LEU* 2.9 28.2 + - + +
228D LEU* 3.5 34.6 + - + +
229D TRP* 2.7 50.0 + - - +
230D MET 4.0 8.5 + - - -
231D GLY* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D GLU* 2.8 48.9 + - - +
204D GLU* 4.1 5.5 - - - +
206D ARG* 1.3 77.2 - - + +
208D HIS* 1.3 52.1 + - - +
210D LEU* 3.0 21.6 + - + +
211D ARG* 2.7 60.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 2.6 37.5 + - + +
168D LEU* 4.8 1.6 - - + -
170D PRO* 3.4 35.3 - - + +
171D PHE* 4.0 20.2 + - + +
174D GLN* 6.3 0.2 - - - -
204D GLU 2.9 18.8 + - - +
205D LEU* 3.5 12.6 - - + +
207D GLN* 1.3 77.8 - - - +
209D LEU* 1.3 62.9 + - + +
211D ARG* 3.4 24.0 + - - +
212D TRP* 3.6 10.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
109D LEU* 5.4 2.0 - - + -
111D VAL* 3.7 31.2 - - + -
114D ALA* 5.9 7.0 - - + -
160D PHE* 6.2 0.2 - - + -
164D MET* 4.1 16.4 - - + -
167D ILE* 3.8 33.0 - - + -
168D LEU* 5.1 4.0 - - + -
187D LEU* 4.2 16.6 - - + -
205D LEU* 2.9 21.8 + - + +
206D ARG* 3.5 9.6 - - - +
208D HIS* 1.3 76.1 - - + +
210D LEU* 1.3 61.7 + - - +
211D ARG 3.5 0.2 + - - -
212D TRP* 3.5 9.9 + - + +
213D GLY* 3.1 17.7 + - - -
228D LEU* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ARG* 2.9 14.9 + - + +
207D GLN* 3.0 25.8 + - + +
209D LEU* 1.3 75.8 - - - +
211D ARG* 1.3 63.1 + - + +
213D GLY* 2.9 29.7 + - - +
228D LEU* 4.4 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GLN* 2.7 41.8 + - + +
208D HIS* 3.7 16.9 - - - +
209D LEU 3.3 0.6 - - - -
210D LEU* 1.3 75.9 - - + +
212D TRP* 1.3 61.6 + - - +
213D GLY 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ALA* 4.6 13.9 - - + -
117D SER* 3.8 28.3 - - - -
160D PHE* 4.3 18.8 - + - -
163D SER* 5.6 4.2 - - - -
167D ILE* 3.5 45.3 - - + +
208D HIS 3.6 4.3 + - - +
209D LEU* 3.5 13.5 + - + +
210D LEU 3.3 0.2 - - - -
211D ARG* 1.3 79.3 - - - +
213D GLY* 1.3 83.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D LEU 3.1 10.9 + - - -
210D LEU* 2.9 25.3 + - - +
211D ARG 4.6 1.3 - - - -
212D TRP* 1.3 97.3 - - - +
----------------------------------------------------------
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