Contacts of the helix formed by residues 166 - 187 (chain D) in PDB entry 4CQM
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 GLN 166 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 3.7 0.7 + - - -
107D THR* 4.2 8.7 - - - +
109D ASP* 3.3 37.0 + - - +
156D OAS 5.1 1.8 + - - +
158D VAL* 3.4 12.7 - - + +
163D ASN* 2.8 46.1 + - + +
164D VAL 4.1 4.0 - - - +
165D GLY* 1.3 78.8 - - - +
167D THR* 1.3 58.5 + - - +
168D ASN* 3.3 8.3 - - - -
169D TYR* 3.6 33.8 - - + -
170D ALA* 2.8 29.0 + - - +
201D PHE* 5.3 5.5 - - - -
206D MET* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 4.0 27.8 - - + -
179A LEU* 4.0 29.2 - - + +
182A THR* 3.2 23.2 - - + +
183A ALA* 5.1 0.8 + - + +
186A GLU* 4.1 3.8 + - - -
110D GLU 4.8 0.2 + - - -
112D LEU* 3.9 27.5 + - + +
115D MET* 3.8 14.2 - - - +
120D TRP* 4.0 0.6 - - + -
165D GLY 3.6 1.8 - - - -
166D GLN* 1.3 75.4 - - - +
168D ASN* 1.3 63.6 + - - +
170D ALA* 4.1 1.4 - - - +
171D ALA* 3.3 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLN 3.2 25.0 + - - +
115D MET* 3.3 20.3 - - - +
119D ASP 2.4 39.2 + - - +
120D TRP* 3.7 30.1 - - + +
123D VAL* 3.3 22.2 - - + +
124D ILE* 3.7 5.4 - - - +
165D GLY 4.3 0.2 - - - +
166D GLN* 3.8 5.2 - - - -
167D THR* 1.3 79.1 + - - +
169D TYR* 1.3 66.0 + - - +
171D ALA* 4.2 0.2 - - - +
172D SER* 3.2 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D GLY 6.0 0.7 - - - -
106D ILE 3.6 2.9 - - - -
107D THR* 3.5 28.0 - - + -
108D GLN 5.9 0.4 - - - +
109D ASP* 5.0 1.6 - - - +
123D VAL* 3.9 5.4 - - + -
127D ASN* 3.5 18.4 - - - -
155D SER 4.6 1.2 - - - -
156D OAS 2.6 43.4 + - - -
158D VAL* 3.9 10.3 - - + -
166D GLN* 3.6 41.3 - - + +
167D THR 3.3 0.8 - - - -
168D ASN* 1.3 84.5 + - - +
170D ALA* 1.3 59.0 + - - +
172D SER* 2.7 17.2 + - - -
173D LYS* 3.1 51.3 + - + +
206D MET* 3.5 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLY* 3.4 14.5 - - - +
182A THR* 3.3 19.7 - - - +
158D VAL* 3.7 32.3 - - + +
159D GLY* 3.9 2.6 - - - -
162D GLY* 4.1 0.4 - - - -
166D GLN 2.8 18.8 + - - +
167D THR 4.1 1.6 - - - +
169D TYR* 1.3 75.4 - - - +
171D ALA* 1.3 60.3 + - - +
173D LYS* 3.4 0.9 + - - -
174D ALA* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.1 7.8 - - + +
175A GLY* 3.2 37.5 - - - +
178A GLY 4.4 0.6 - - - -
179A LEU* 4.2 4.7 - - + +
120D TRP* 3.8 26.0 - - + -
124D ILE* 4.5 3.4 - - + -
128D LEU* 4.7 0.2 - - - +
167D THR 3.3 16.2 + - - +
168D ASN 4.2 2.2 - - - +
170D ALA* 1.3 79.0 - - - +
172D SER* 1.3 57.6 + - - +
175D GLY* 2.9 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D VAL 4.1 4.3 - - - -
124D ILE* 3.8 17.8 - - - +
127D ASN* 3.7 32.8 + - - +
128D LEU* 3.6 12.1 - - - +
168D ASN 3.2 16.0 + - - -
169D TYR* 2.7 24.3 + - - -
171D ALA* 1.3 79.8 - - - +
173D LYS* 1.3 58.5 + - - +
175D GLY* 3.2 2.1 + - - -
176D VAL* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ALA 5.2 2.8 + - - -
105D GLY* 5.0 8.3 - - - -
127D ASN* 3.8 27.0 + - - +
131D THR* 5.7 0.8 + - - -
154D ILE* 3.1 21.2 + - - +
155D SER* 3.7 20.5 + - - +
156D OAS 4.1 8.1 - - - +
159D GLY* 3.8 21.3 - - - +
169D TYR* 3.1 60.1 + - + +
172D SER* 1.3 78.2 + - - +
174D ALA* 1.3 64.8 + - - +
176D VAL* 3.4 10.7 + - + +
177D ILE* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 3.2 33.9 - - + +
175A GLY* 4.2 0.2 - - - -
177A ILE* 5.8 0.4 - - + -
178A GLY* 4.2 10.5 - - - -
159D GLY* 3.3 24.1 - - - +
170D ALA 2.9 19.1 + - - +
171D ALA 3.9 1.6 - - - +
173D LYS* 1.3 75.6 - - - +
175D GLY* 1.3 64.1 + - - +
177D ILE* 3.3 8.3 + - - +
178D GLY 3.1 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 3.2 35.8 - - - +
174A ALA* 4.2 0.4 - - - -
175A GLY 4.0 1.5 - - - +
128D LEU* 3.4 11.7 - - - -
171D ALA 2.9 15.4 + - - -
172D SER 3.6 3.6 - - - -
174D ALA* 1.3 74.7 - - - +
176D VAL* 1.3 63.8 + - - +
178D GLY 3.1 0.7 + - - -
179D LEU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASN 3.4 26.2 - - - +
128D LEU* 4.2 4.3 - - + -
131D THR* 4.0 13.7 - - + +
153D ASN* 3.7 26.5 - - + -
154D ILE 4.8 2.2 - - - +
155D SER* 3.4 21.8 - - - +
172D SER 2.9 21.9 + - - +
173D LYS* 3.5 19.7 - - + +
174D ALA 3.3 0.4 - - - -
175D GLY* 1.3 77.3 - - - +
177D ILE* 1.3 56.9 + - - +
179D LEU* 3.5 9.3 - - - +
180D THR* 2.5 34.2 + - - +
196D SER* 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 5.8 0.2 - - + -
155D SER* 3.5 14.4 - - - +
159D GLY 3.5 25.8 - - - +
160D LYS* 5.2 1.3 - - + -
173D LYS 3.3 14.4 - - - +
174D ALA* 3.3 7.6 + - - +
176D VAL* 1.3 76.0 - - - +
178D GLY* 1.3 62.8 + - - +
180D THR* 3.4 1.7 + - - -
181D GLN* 3.1 48.1 + - + +
196D SER* 3.8 9.6 - - - +
198D LEU* 4.0 29.6 - - + -
252D SER* 3.6 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 5.4 2.0 - - - -
162A GLY* 4.3 1.5 - - - -
170A ALA* 3.9 16.7 - - - +
171A ALA 4.4 0.2 - - - -
174A ALA* 4.1 14.6 - - - +
174D ALA 3.1 9.8 + - - -
175D GLY 3.1 6.9 + - - -
177D ILE* 1.3 78.2 - - - +
179D LEU* 1.3 60.1 + - - +
180D THR 3.4 0.2 + - - -
181D GLN* 3.4 12.6 + - - +
182D THR* 3.2 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 6.1 0.9 - - + -
120A TRP* 3.9 13.9 - - + -
167A THR* 3.8 26.3 - - + +
171A ALA* 4.0 8.4 - - + +
128D LEU* 3.6 30.3 - - + +
131D THR* 4.4 3.8 - - + -
132D PHE* 4.1 21.5 - - + +
135D THR* 4.2 19.7 - - + +
153D ASN* 4.3 9.0 - - - +
175D GLY 3.0 18.8 + - - +
176D VAL* 3.5 13.0 - - - +
178D GLY* 1.3 73.9 - - - +
180D THR* 1.3 62.0 + - - +
182D THR* 3.7 7.4 - - - -
183D ALA* 2.9 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ASN* 2.7 29.1 + - - +
176D VAL 2.5 23.3 + - - -
177D ILE 3.6 3.1 - - - -
179D LEU* 1.3 77.9 - - - +
181D GLN* 1.3 61.2 + - + +
183D ALA* 3.5 3.5 + - - -
184D ALA* 3.0 27.9 + - - +
194D CYS* 3.6 8.5 - - + +
195D ASN* 3.5 33.9 - - - +
196D SER* 3.1 23.4 + - - +
250D GLY* 5.5 0.9 - - - -
251D THR 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 5.1 0.2 - - - -
160A LYS* 2.9 36.4 + - - +
161A VAL* 3.3 21.2 - - - +
162A GLY 3.6 1.4 + - - -
234C GLN* 5.7 2.6 - - - +
235C LEU* 3.3 31.7 - - + +
177D ILE* 3.1 38.7 + - + +
178D GLY* 3.8 10.3 - - - +
180D THR* 1.3 73.3 - - + +
182D THR* 1.3 66.5 + - - +
184D ALA* 3.4 3.1 + - - -
185D ARG* 3.3 17.7 + - - +
250D GLY* 4.5 15.3 + - - +
252D SER* 5.0 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY* 3.4 1.0 - - - -
163A ASN 3.2 42.8 + - - +
166A GLN 3.7 0.2 + - - -
167A THR* 3.3 34.3 - - - +
170A ALA* 3.3 13.7 - - - +
178D GLY 3.2 13.1 + - - -
179D LEU 3.7 7.4 - - - -
180D THR 3.3 0.2 - - - -
181D GLN* 1.3 76.2 - - - +
183D ALA* 1.3 64.7 + - - +
185D ARG* 3.1 15.4 + - - +
186D GLU* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.7 30.7 - - + -
167A THR* 5.0 0.4 + - - +
135D THR* 4.4 9.9 - - + -
179D LEU* 2.9 19.4 + - + +
180D THR* 3.8 4.9 - - - +
182D THR* 1.3 77.6 - - - +
184D ALA* 1.3 53.6 + - - +
186D GLU* 3.1 4.6 + - - +
187D LEU* 2.7 40.4 + - + +
194D CYS* 3.8 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
199C PRO* 3.9 8.9 - - - +
232C GLY* 6.2 0.2 - - - -
235C LEU* 4.6 3.4 - - + -
180D THR 3.0 18.6 + - - +
181D GLN 3.6 6.5 - - - +
182D THR 3.2 0.2 - - - -
183D ALA* 1.3 76.4 - - - +
185D ARG* 1.3 61.4 + - - +
187D LEU 4.1 0.2 - - - -
188D GLY* 3.3 20.8 + - - -
192D ILE 4.7 1.5 - - - +
194D CYS* 3.6 13.4 - - - +
249D THR* 3.4 26.1 + - + +
250D GLY* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL 4.7 5.6 - - - -
162A GLY 4.4 3.0 + - - -
163A ASN* 3.5 29.2 + - - +
164A VAL* 3.3 38.6 - - + +
260A PHE* 5.0 9.7 - - - -
199C PRO* 4.4 21.2 - - + +
235C LEU* 3.7 51.0 + - + -
236C ILE* 5.0 10.0 - - - +
181D GLN 3.3 3.8 + - - +
182D THR* 3.1 11.1 + - - +
184D ALA* 1.3 79.7 - - - +
186D GLU* 1.3 62.4 + - - +
188D GLY* 4.1 3.8 + - - -
189D ARG* 5.1 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 3.8 12.0 - - + +
112A LEU* 2.9 36.9 + - + +
113A LEU* 6.0 0.3 - - - +
164A VAL* 4.4 18.4 - - + -
165A GLY* 2.8 30.8 + - - -
167A THR* 4.0 3.3 + - - -
182D THR* 3.2 26.0 + - - +
183D ALA* 3.1 7.3 + - - +
185D ARG* 1.3 76.8 - - - +
187D LEU* 1.3 65.8 + - + +
188D GLY 3.3 2.0 - - - -
189D ARG* 3.5 14.3 - - - +
190D HIS* 3.4 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.2 16.6 - - + -
113A LEU* 4.4 15.5 - - + -
139D ALA* 3.6 33.2 - - + -
143D VAL* 4.7 1.6 - - + -
151D ILE* 3.8 9.4 - - + -
183D ALA* 2.7 18.9 + - + +
186D GLU* 1.3 79.0 - - + +
188D GLY* 1.3 62.7 + - - +
189D ARG 3.3 2.2 - - - -
190D HIS* 3.2 15.7 + - + -
191D GLY 3.2 4.2 + - - -
192D ILE* 2.8 58.2 + - + +
194D CYS* 3.6 23.6 - - - -
----------------------------------------------------------
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