Contacts of the helix formed by residues 133 - 156 (chain D) in PDB entry 5DQZ
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 133 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ARG* 4.3 5.2 - - - +
131D ARG 4.1 0.8 + - - -
132D ARG* 1.3 82.3 - - - +
134D VAL* 1.3 61.3 + - - +
135D GLU* 2.9 21.0 + - - +
136D GLN* 2.7 30.2 + - - +
137D LEU* 3.2 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ASP* 3.9 32.8 - - + +
112D ARG* 5.5 4.0 - - - +
113D LEU* 4.1 22.9 - - + -
116D VAL* 3.8 30.7 - - + -
117D ARG* 3.9 20.0 - - - +
120D PHE* 4.4 6.7 - - + -
133D SER* 1.3 68.9 - - - +
135D GLU* 1.3 65.5 + - - +
136D GLN 3.1 2.2 - - - -
137D LEU* 3.1 10.4 + - + +
138D ARG* 2.9 33.4 + - + +
207D VAL* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLU 4.5 4.4 - - - +
285C ASP* 3.1 35.2 - - - +
133D SER* 2.9 18.5 + - - +
134D VAL* 1.3 81.2 + - - +
136D GLN* 1.3 55.3 + - + +
138D ARG* 3.2 36.6 + - - +
139D GLY* 3.0 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ARG* 3.1 55.3 + - - +
133D SER* 2.7 33.4 + - - +
135D GLU* 1.3 78.4 - - + +
137D LEU* 1.3 63.1 + - - +
139D GLY* 3.1 4.6 + - - +
140D ILE* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 5.4 0.2 - - + -
117D ARG* 4.6 22.2 - - + +
120D PHE* 3.8 37.3 - - + -
124D PHE* 4.1 10.7 - - + -
128D ALA* 3.8 27.4 - - + -
129D PRO* 4.4 17.9 - - + +
132D ARG* 4.2 13.0 - - + +
133D SER 3.2 16.3 + - - +
134D VAL* 3.1 16.5 + - + +
136D GLN* 1.3 76.9 - - - +
138D ARG* 1.3 59.0 + - - +
140D ILE* 3.2 10.8 + - + +
141D GLU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLU 4.7 2.0 + - - -
285C ASP 2.7 37.0 + - - -
286C ALA 3.4 10.3 + - - -
287C GLN* 2.6 42.2 + - - +
288C PRO* 3.8 15.8 - - - +
120D PHE* 4.1 17.7 - - + -
134D VAL* 2.9 24.8 + - + +
135D GLU* 3.2 31.3 + - - +
136D GLN 3.2 0.2 - - - -
137D LEU* 1.3 75.4 - - - +
139D GLY* 1.3 62.6 + - - +
141D GLU* 3.3 3.4 + - - +
142D GLY* 2.9 20.6 + - - -
207D VAL* 4.8 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU 3.0 13.4 + - - -
136D GLN* 3.1 5.3 + - - -
138D ARG* 1.3 76.5 - - - +
140D ILE* 1.3 62.7 + - - +
142D GLY* 3.1 3.7 + - - -
143D SER* 3.0 24.3 + - - -
146D ARG* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PHE* 3.8 22.0 - - + -
129D PRO* 4.3 21.8 - - + -
132D ARG* 3.2 33.4 - - - +
136D GLN 3.0 14.7 + - - +
137D LEU* 3.2 15.0 + - + +
139D GLY* 1.3 74.0 - - - +
141D GLU* 1.3 59.8 + - - +
143D SER* 3.2 9.1 + - - -
144D ARG* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D PHE* 3.7 14.6 - - + -
123D ARG* 3.1 40.5 + - - +
124D PHE* 3.4 13.5 - - + -
137D LEU 2.9 16.8 + - - +
138D ARG* 3.7 5.4 - - - +
140D ILE* 1.3 73.7 - - - +
142D GLY* 1.3 61.4 + - - +
144D ARG* 2.5 38.5 + - - -
145D VAL* 2.9 51.5 + - + +
221D ASP 5.0 2.6 - - - +
225D PHE* 5.3 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ARG 2.9 13.6 + - - -
139D GLY* 3.1 4.4 + - - -
141D GLU* 1.3 76.9 - - - +
143D SER* 1.3 63.2 + - - +
145D VAL* 3.1 7.5 + - - +
146D ARG* 3.0 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D GLY 3.0 12.8 + - - -
140D ILE* 3.4 11.6 - - - -
142D GLY* 1.3 76.1 - - - +
144D ARG* 1.3 63.6 + - - +
146D ARG* 3.3 17.1 + - - +
147D ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ARG* 3.0 40.7 + - - +
124D PHE* 4.2 14.8 - - + +
140D ILE* 2.9 19.7 + - + +
141D GLU* 2.5 45.9 + - - +
143D SER* 1.3 75.8 - - - +
145D VAL* 1.3 59.6 + - - +
147D ALA* 3.3 8.2 + - - +
148D THR* 2.8 42.1 + - - +
221D ASP 4.9 6.5 + - - -
222D ILE 5.0 5.1 + - - -
225D PHE* 4.2 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ARG* 5.6 0.4 - - - +
141D GLU* 2.9 49.7 + - + +
142D GLY* 3.5 6.3 - - - +
144D ARG* 1.3 78.5 - - - +
146D ARG* 1.3 66.8 + - + +
148D THR* 3.1 8.6 + - - -
149D TYR* 3.0 47.6 + - + +
224D LYS* 5.9 3.6 - - - +
225D PHE* 3.8 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D GLY 4.8 1.6 + - - -
142D GLY* 3.0 43.0 + - - +
143D SER* 3.3 14.7 + - - +
145D VAL* 1.3 77.3 - - + +
147D ALA* 1.3 61.6 + - - +
149D TYR* 3.2 16.1 + - + +
150D ALA* 3.0 22.4 + - - +
160D TRP* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D SER 3.0 14.6 + - - +
144D ARG* 3.4 13.7 - - - +
146D ARG* 1.3 77.1 - - - +
148D THR* 1.3 56.1 + - - +
150D ALA* 3.3 8.5 + - - +
151D LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ARG* 2.8 32.7 + - - +
145D VAL* 3.1 9.5 + - - -
147D ALA* 1.3 73.5 - - - +
149D TYR* 1.3 66.8 + - - +
151D LEU* 3.2 10.8 + - + +
152D LEU* 2.9 35.9 + - + +
225D PHE* 3.5 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D VAL* 3.0 41.1 + - + +
146D ARG* 3.3 15.9 - - + +
148D THR* 1.3 76.4 - - - +
150D ALA* 1.3 56.6 + - - +
152D LEU* 3.6 0.8 + - - -
153D ALA* 2.9 30.4 + - - +
160D TRP* 3.6 34.3 + + + +
163D ARG* 3.8 35.8 + - + +
180D ILE* 4.1 25.6 - - + +
184D THR* 6.0 0.7 - - - +
224D LYS* 5.0 8.5 + - - -
225D PHE* 3.9 21.9 - + - -
229D VAL* 4.5 7.1 - - + +
233D PHE* 3.7 16.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ARG 3.0 12.7 + - - +
147D ALA* 3.5 11.9 - - - +
149D TYR* 1.3 78.3 - - - +
151D LEU* 1.3 56.4 + - - +
153D ALA* 3.3 8.1 + - - +
154D LYS* 3.0 30.1 + - - +
160D TRP* 4.5 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ALA 2.9 17.2 + - - +
148D THR* 3.2 12.5 + - + +
150D ALA* 1.3 76.9 - - - +
152D LEU* 1.3 59.9 + - + +
154D LYS* 3.2 21.0 + - + +
155D GLN* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 2.9 34.7 + - + +
149D TYR* 4.0 0.4 - - - +
151D LEU* 1.3 80.7 - - + +
153D ALA* 1.3 62.7 + - - +
155D GLN* 4.3 13.5 - - - +
156D TYR* 3.0 52.0 + - + +
225D PHE* 4.3 6.5 - - + +
229D VAL* 3.9 27.4 - - + -
230D PRO* 4.0 25.4 - - + -
233D PHE* 3.8 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D TYR 2.9 20.5 + - - +
150D ALA* 3.4 7.6 - - - +
152D LEU* 1.3 77.0 - - - +
154D LYS* 1.3 55.9 + - - +
157D GLY* 3.1 5.4 + - - -
158D VAL 2.9 32.5 + - - +
160D TRP* 3.6 31.4 - - + -
233D PHE* 3.6 17.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ALA 3.0 15.9 + - - +
151D LEU* 3.8 18.1 - - + +
153D ALA* 1.3 74.4 - - - +
155D GLN* 1.3 66.6 + - - +
156D TYR 3.4 0.2 - - - -
157D GLY* 3.6 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 2.9 25.2 + - + +
152D LEU* 3.3 14.6 + - - +
154D LYS* 1.3 80.5 - - - +
156D TYR* 1.3 88.8 + - + +
157D GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU* 3.0 41.6 + - + +
155D GLN* 1.3 101.1 + - + +
157D GLY* 1.3 65.5 + - - +
158D VAL* 4.4 3.6 - - + -
230D PRO* 3.6 27.3 + - + +
233D PHE* 3.9 24.5 - - + +
234D GLU* 3.6 42.1 + - + +
237D ARG* 3.3 28.2 + - + +
----------------------------------------------------------
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