Contacts of the helix formed by residues 166 - 179 (chain D) in PDB entry 1URP
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 ARG 166 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ASP* 1.3 72.4 + - - +
167D ILE* 1.3 67.9 + - + +
169D GLY 3.3 0.3 + - - -
170D LEU* 2.9 26.4 + - + +
192D GLU* 3.1 63.8 + - - +
195D LEU* 3.9 24.4 - - - +
196D GLY* 3.4 20.4 - - - +
199D ARG* 6.3 1.6 - - - -
219D ASP* 3.3 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ASP* 2.9 11.5 + - - +
166D ARG* 1.3 82.0 - - + +
168D LYS* 1.3 59.7 + - + +
170D LEU* 3.3 17.6 + - + +
171D ASN* 3.0 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ALA* 3.4 22.7 - - - +
163D ASP* 2.8 37.5 + - + +
165D ASP* 2.7 26.9 + - - +
167D ILE* 1.3 74.1 - - + +
169D GLY* 1.3 55.1 + - - +
171D ASN* 4.5 6.1 - - - +
172D VAL* 2.7 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.9 6.6 - - - +
162D ALA* 3.7 16.1 - - - +
165D ASP 2.9 19.5 + - - -
166D ARG 3.6 2.0 - - - -
167D ILE 3.2 0.4 - - - -
168D LYS* 1.3 76.7 - - - +
170D LEU* 1.3 54.5 + - - +
173D MET* 3.0 33.3 + - - +
193D MET* 4.2 13.9 - - - -
196D GLY 4.0 6.3 - - - -
197D ALA 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 2.9 13.1 + - + +
167D ILE* 3.3 24.5 - - + +
169D GLY* 1.3 76.5 - - - +
171D ASN* 1.3 68.3 + - - +
174D GLN* 2.9 45.5 + - - +
196D GLY* 3.4 15.3 - - - +
199D ARG* 4.1 21.3 - - + -
200D ALA* 3.4 37.0 - - + +
203D THR* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLN* 5.0 9.0 - - - +
203A THR* 3.6 31.3 + - + +
167D ILE* 3.0 37.8 + - - +
168D LYS* 4.0 5.4 - - - +
170D LEU* 1.3 81.3 - - - +
172D VAL* 1.3 63.9 + - + +
174D GLN* 3.3 19.5 + - - +
175D ASN* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.8 11.9 - - + -
160D GLN* 4.1 14.4 - - + +
161D PRO 3.7 24.2 - - - +
162D ALA* 4.1 7.0 - - + -
168D LYS* 2.7 32.9 + - + +
169D GLY 4.2 1.6 - - - +
171D ASN* 1.3 72.2 - - + +
173D MET* 1.3 57.3 + - - +
175D ASN* 3.2 11.7 + - + +
176D LEU* 2.9 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 4.0 31.4 - - + -
129D LEU* 4.4 6.9 - - + +
169D GLY 3.0 20.6 + - - +
170D LEU 3.8 2.2 - - - +
172D VAL* 1.3 76.4 - - - +
174D GLN* 1.3 54.3 + - - +
176D LEU* 3.7 2.6 - - + +
177D LEU* 2.7 56.3 + - + +
183D VAL* 4.6 3.8 - - + -
186D VAL* 3.7 36.6 - - + -
197D ALA* 3.7 35.9 - - + +
200D ALA* 3.8 6.5 - - + -
201D LEU* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 6.4 1.8 - - + -
171A ASN* 4.8 1.1 - - - -
170D LEU* 2.9 33.6 + - - +
171D ASN* 3.3 25.5 - - - +
173D MET* 1.3 77.6 - - - +
175D ASN* 1.3 60.8 + - - +
177D LEU* 3.5 7.0 - - + +
178D THR* 3.1 31.7 + - + +
200D ALA* 3.9 15.2 + - + +
203D THR* 4.0 25.3 - - - +
204D ALA* 6.3 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 3.9 19.8 - - - +
174A GLN* 4.2 27.0 + - - +
175A ASN* 3.7 27.4 + - - +
153B LYS* 5.3 4.4 - - - +
160D GLN* 4.8 11.1 + - - -
171D ASN 3.0 10.0 + - - +
172D VAL* 3.3 14.9 + - - +
174D GLN* 1.3 79.9 - - - +
176D LEU* 1.3 62.4 - - - +
178D THR* 3.3 16.5 + - - -
179D ALA* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 5.7 3.6 - - + -
127D ILE* 3.8 37.5 - - + -
129D LEU* 4.0 9.4 - - + -
158D ALA* 3.7 23.8 - - + -
160D GLN* 3.3 33.2 - - + +
172D VAL* 2.9 38.7 + - + +
173D MET* 3.9 4.7 - - + +
175D ASN* 1.3 75.3 - - + +
177D LEU* 1.3 54.4 + - - +
179D ALA* 3.3 5.4 + - + -
180D HIS* 2.7 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D MET* 2.7 36.4 + - + +
174D GLN* 3.5 8.5 - - + +
176D LEU* 1.3 72.7 - - - +
178D THR* 1.3 64.7 + - + +
180D HIS 3.2 3.5 - - - +
181D PRO* 3.2 31.0 - - + +
183D VAL* 4.2 16.8 - - + -
200D ALA 4.1 5.6 - - - +
201D LEU* 3.8 38.6 - - + +
204D ALA* 3.8 27.4 - - + -
206D LYS* 4.3 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.3 13.2 - - + -
171A ASN* 2.5 42.6 + - - +
174D GLN* 3.1 19.4 + - + +
175D ASN 3.3 4.2 + - - -
176D LEU 3.4 0.2 - - - -
177D LEU* 1.3 77.1 - - + +
179D ALA* 1.3 64.6 + - - +
180D HIS 3.6 0.2 + - - -
181D PRO* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 6.5 0.4 - - + -
175A ASN* 6.1 3.4 - - - +
175D ASN* 3.4 15.6 + - - +
176D LEU* 3.3 7.5 + - + +
177D LEU 3.3 0.2 - - - -
178D THR* 1.3 83.6 + - - +
180D HIS* 1.3 78.5 + - + +
181D PRO* 3.6 5.5 - - - +
----------------------------------------------------------
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