Contacts of the helix formed by residues 144 - 165 (chain B) in PDB entry 5Z7R
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 GLY 144 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASN* 3.3 12.1 + - - -
114B GLU* 4.4 0.9 - - - -
143B PHE* 1.3 72.2 - - - +
145B GLY* 1.3 49.6 + - - -
147B GLN* 2.6 27.2 + - - +
148B ARG* 3.0 20.1 + - - +
226C LEU* 3.6 13.9 - - - -
229C GLU* 2.6 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.9 29.1 + - - -
117B MET* 4.1 12.1 - - - -
132B GLN* 4.4 2.7 - - - -
141B PRO* 3.7 10.3 - - - -
143B PHE 3.5 0.4 - - - -
144B GLY* 1.3 77.0 - - - +
146B THR* 1.3 58.1 + - - +
147B GLN 3.1 4.2 + - - -
149B LEU* 3.5 24.9 + - - +
162B ILE* 3.5 9.0 - - - +
229C GLU* 2.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 4.3 6.7 - - - -
141B PRO* 3.7 32.5 - - + +
145B GLY* 1.3 78.2 - - - +
147B GLN* 1.3 76.3 + - - +
150B SER* 3.9 7.3 + - - -
162B ILE* 4.2 9.0 - - + -
210C SER* 4.5 9.4 - - - +
213C ALA* 3.8 23.8 - - + +
214C ILE* 3.5 22.6 - - + +
229C GLU* 2.6 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY 2.6 9.7 + - - +
145B GLY 3.0 0.2 - - - -
146B THR* 1.3 105.7 + - - +
148B ARG* 1.3 60.6 + - - +
149B LEU 3.5 1.3 - - - -
150B SER* 3.5 8.4 + - - -
151B ARG* 2.8 58.7 + - - +
213C ALA* 2.9 29.5 + - - +
214C ILE 5.1 0.2 - - - +
217C GLY* 3.1 20.3 - - - -
218C MET* 3.7 0.9 + - - +
222C ILE* 3.8 13.7 - - + -
225C ALA* 3.2 29.1 + - + +
226C LEU* 4.0 13.2 - - + -
228C PHE* 5.4 0.4 - - - +
229C GLU* 4.5 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASN* 4.3 2.0 + - - -
90B PHE* 4.2 5.1 + - - +
91B ARG* 3.9 17.0 - - - +
94B GLU* 2.6 43.3 + - - +
114B GLU 4.6 1.5 + - - -
117B MET* 3.4 44.0 - - + -
118B SER* 3.2 19.2 + - - +
143B PHE 3.7 18.8 + - - -
144B GLY* 3.0 19.4 + - - +
147B GLN* 1.3 76.4 - - + +
149B LEU* 1.3 59.6 - - - +
151B ARG* 3.3 6.9 + - - +
152B LEU* 2.8 37.1 + - + +
222C ILE* 4.8 9.9 - - + +
226C LEU* 3.6 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B CYS* 5.3 3.1 - - - -
117B MET* 3.4 26.4 - - + -
132B GLN* 4.4 12.3 - - + +
145B GLY 3.5 15.2 + - - +
147B GLN 3.5 0.2 - - - -
148B ARG* 1.3 75.2 - - - +
150B SER* 1.3 66.6 + - - +
152B LEU* 3.0 2.1 + - - -
153B VAL* 2.8 49.4 + - + +
158B ALA* 3.7 26.7 - - + +
161B LEU* 4.2 21.1 - - + -
162B ILE* 3.9 23.6 - - + -
178B LEU* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLY 4.8 1.0 + - - -
146B THR 3.9 13.5 + - - -
147B GLN 3.5 8.2 + - - -
149B LEU* 1.3 76.8 - - - +
151B ARG* 1.3 57.5 + - - +
154B GLY* 2.7 34.6 + - - -
155B MET* 4.2 12.1 - - - -
158B ALA* 3.4 21.7 - - - +
162B ILE* 5.9 0.2 - - - +
214C ILE* 4.4 9.8 + - - +
218C MET* 3.2 33.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY* 5.4 4.0 - - - -
155A MET* 5.4 6.5 + - + +
147B GLN* 2.8 54.0 + - - +
148B ARG* 3.3 8.4 + - - +
149B LEU 3.2 0.6 - - - -
150B SER* 1.3 77.7 + - - +
152B LEU* 1.3 68.1 + - + +
154B GLY 4.8 0.5 + - - -
219B GLN* 4.7 6.9 + - - +
217C GLY 2.8 14.3 + - - -
218C MET* 4.0 30.9 + - + +
220C CYS 2.8 29.7 + - - -
222C ILE* 3.6 29.2 - - - +
225C ALA* 3.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY* 5.4 6.4 - - - -
155A MET* 4.1 30.7 - - + +
156A GLY 4.6 3.8 - - - +
117B MET* 3.8 40.8 - - + +
122B ARG* 3.5 31.9 - - - +
148B ARG* 2.8 24.3 + - + +
149B LEU* 3.7 3.8 - - - +
151B ARG* 1.3 87.2 - - + +
153B VAL* 1.3 68.9 + - + +
154B GLY 3.8 0.2 - - - -
176B ILE 4.4 1.9 - - - +
177B GLY* 4.3 10.9 - - - +
178B LEU* 4.6 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 2.8 33.3 + - + +
152B LEU* 1.3 79.1 - - + +
154B GLY* 1.3 63.9 + - - +
157B MET* 3.7 30.3 + - + +
158B ALA 3.9 2.9 - - - +
161B LEU* 5.1 0.7 - - + -
176B ILE* 3.6 36.6 - - + +
178B LEU* 3.8 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER* 2.7 25.6 + - - -
151B ARG 4.6 0.4 - - - -
152B LEU 3.8 0.6 - - - -
153B VAL* 1.3 73.5 - - - +
155B MET* 1.3 64.2 + - - -
156B GLY 3.3 2.9 - - - -
157B MET 4.2 0.4 - - - -
158B ALA* 3.1 24.9 + - - +
151C ARG 5.5 5.4 - - - -
152C LEU* 5.6 5.6 - - - -
218C MET* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER* 4.1 18.8 + - - -
154B GLY* 1.3 70.3 - - - -
156B GLY* 1.3 61.0 + - - +
159B LYS* 2.9 69.5 + - + +
94C GLU* 4.6 14.6 - - - +
120C ASP 4.6 0.4 - - - +
151C ARG* 5.5 6.5 + - + +
152C LEU* 4.2 24.4 - - + +
214C ILE* 3.9 14.4 - - + +
215C ASN* 4.3 9.2 - - - +
218C MET* 4.4 26.0 - - + +
219C GLN* 5.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY* 3.3 1.2 - - - -
155B MET* 1.3 80.0 - - - +
157B MET* 1.3 60.4 + - - +
160B GLN* 3.4 11.4 + - - +
120C ASP 3.8 18.4 - - - +
121C ILE* 4.0 1.6 - - - +
122C ARG* 4.1 16.5 - - - +
152C LEU* 4.6 3.4 - - - +
177C GLY 5.6 3.8 - - - -
180C ASN* 3.0 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.7 25.0 + - + +
154B GLY 3.6 2.4 + - - -
155B MET 3.4 0.2 - - - -
156B GLY* 1.3 72.7 - - - +
158B ALA* 1.3 67.9 + - - +
160B GLN* 3.1 11.1 + - - +
161B LEU* 3.0 64.8 + - + +
168B ILE* 4.7 7.2 - - + -
172B GLU* 4.2 11.4 - - + +
175B ARG* 4.6 5.8 - - - +
176B ILE* 3.7 39.7 - - + -
180C ASN* 3.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.7 22.7 - - + -
150B SER* 3.4 34.8 - - - +
153B VAL* 3.9 1.2 - - - +
154B GLY 3.1 18.0 + - - +
155B MET 4.0 1.8 - - - +
157B MET* 1.3 77.7 - - - +
159B LYS* 1.3 65.0 + - + +
161B LEU* 3.3 0.7 + - - +
162B ILE* 2.9 33.8 + - + +
214C ILE* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B MET* 2.9 37.8 + - + +
156B GLY 4.1 0.2 - - - +
158B ALA* 1.3 77.0 - - - +
160B GLN* 1.3 57.9 + - - +
162B ILE* 4.7 0.2 - - - -
163B PHE* 2.8 60.9 + - + -
94C GLU* 4.8 6.3 + - - +
119C CYS 5.2 1.6 + - - -
120C ASP* 2.9 55.7 + - + +
121C ILE* 4.3 1.3 - - + -
211C LYS* 4.7 1.3 - - - +
214C ILE* 3.8 32.8 - - + -
215C ASN* 2.7 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLY 3.4 3.2 + - - +
157B MET* 3.1 15.3 + - - +
159B LYS* 1.3 80.6 - - - +
161B LEU* 1.3 61.1 + - + +
164B THR* 2.7 55.8 + - + +
121C ILE* 3.4 29.5 - - + +
123C ILE* 3.5 9.0 - - - +
180C ASN* 2.8 45.8 + - - +
181C LYS* 5.9 3.2 - - - +
195C ILE* 4.0 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE 6.3 0.2 - - - -
131B GLY* 5.7 5.6 - - - -
132B GLN* 3.9 12.4 + - + +
149B LEU* 4.2 25.1 - - + -
157B MET* 3.0 55.1 + - + +
158B ALA 3.9 2.9 - - - +
160B GLN* 1.3 86.5 - - + +
162B ILE* 1.3 58.9 + - - +
164B THR* 3.6 3.3 + - - +
165B ALA* 3.0 28.1 + - - -
166B GLN 3.9 14.6 + - - +
168B ILE* 4.0 26.0 - - + -
176B ILE* 4.4 12.8 - - + -
178B LEU* 5.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 4.0 22.4 - - + +
135B VAL* 3.5 20.1 - - + +
141B PRO* 4.1 14.8 - - + -
145B GLY 3.5 29.8 - - - +
146B THR* 4.2 4.0 - - + -
149B LEU* 3.9 17.7 - - + -
150B SER 5.9 0.2 - - - +
158B ALA* 2.9 21.6 + - + +
159B LYS 4.1 1.3 - - - +
161B LEU* 1.3 79.6 - - - +
163B PHE* 1.3 63.0 + - + +
164B THR 3.6 0.2 + - - -
165B ALA 3.8 1.6 + - - -
210C SER* 3.8 32.3 - - - +
214C ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.7 6.2 - - - +
159B LYS* 2.8 53.1 + - + +
160B GLN 4.4 0.7 - - - +
162B ILE* 1.3 78.1 - - + +
164B THR* 1.3 58.0 + - - +
99C PRO* 3.7 28.5 - - + -
120C ASP* 4.0 13.2 - - + -
121C ILE* 4.0 9.9 - - + -
199C ILE* 3.7 30.3 - - + +
202C ASN* 3.0 19.4 + - - +
207C VAL* 4.0 17.2 - - + +
210C SER* 4.4 2.7 - - - -
211C LYS* 3.7 46.0 - - + -
214C ILE* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN* 2.7 41.6 + - + +
161B LEU* 3.6 3.8 + - - +
163B PHE* 1.3 76.9 - - - +
165B ALA* 1.3 70.1 + - - +
166B GLN* 3.2 25.5 + - - +
195C ILE* 4.3 16.2 - - + +
198C LYS* 3.3 32.5 - - + +
199C ILE* 3.9 18.2 - - + -
202C ASN* 3.2 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN 3.3 27.5 - - - +
133B PRO* 3.7 29.4 - - + +
135B VAL* 4.1 8.1 - - + -
136B GLY* 5.1 0.7 - - - -
161B LEU 3.0 9.8 + - - -
162B ILE 3.8 0.6 + - - -
163B PHE 3.6 1.6 - - - -
164B THR* 1.3 78.7 - - - +
166B GLN* 1.3 61.4 + - - +
167B ASN* 3.9 7.3 + - - +
198C LYS* 5.8 0.4 - - - -
202C ASN* 4.0 13.7 - - - +
----------------------------------------------------------
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