Contacts of the helix formed by residues 148 - 165 (chain D) in PDB entry 3E5X
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 ASN 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D THR 4.3 0.6 + - - -
147D TYR* 1.3 75.2 - - - +
149D PRO* 1.3 76.7 - - + +
150D THR* 3.0 14.7 + - - -
151D ILE* 2.8 35.3 + - - +
152D ARG* 2.9 19.8 + - - +
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Residues in contact with PRO 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D TYR 4.6 0.2 - - - +
148D ASN* 1.3 89.4 - - + +
150D THR* 1.3 63.0 + - + +
152D ARG* 3.2 19.4 + - - +
153D ILE* 3.2 27.9 + - - +
189D VAL* 3.6 35.9 - - + +
193D THR* 4.4 7.6 - - + +
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Residues in contact with THR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ASN* 3.0 18.9 + - - +
149D PRO* 1.3 77.7 - - + +
151D ILE* 1.3 66.9 + - - +
153D ILE* 3.4 6.0 + - - +
154D LEU* 3.1 29.8 + - - +
193D THR* 3.7 15.0 - - + -
196D ARG* 4.6 9.2 - - - +
197D VAL* 3.5 32.8 - - + +
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D TYR* 3.7 33.9 - - + -
148D ASN* 2.8 33.3 + - - +
150D THR* 1.3 82.6 + - - +
152D ARG* 1.3 56.1 + - - +
154D LEU* 3.2 11.7 + - + +
155D ARG* 2.9 31.6 + - - +
225D LEU 3.5 25.1 - - - +
226D SER 3.6 19.7 - - - +
228D GLN 3.9 20.2 - - - +
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ASN* 5.4 0.6 + - - -
140D GLN* 4.5 1.0 - - - +
143D GLU* 3.4 38.6 - - + +
144D MET* 3.8 32.9 + - - +
147D TYR* 3.3 29.2 + - + +
148D ASN 2.9 14.3 + - - +
149D PRO* 3.2 26.7 + - - +
151D ILE* 1.3 76.9 - - - +
153D ILE* 1.3 57.1 + - - +
155D ARG* 3.4 7.9 + - - +
156D LEU* 2.9 28.6 + - - +
187D THR* 2.3 45.1 + - + +
188D GLY 5.3 1.6 - - - -
189D VAL* 3.6 15.8 - - - +
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Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PRO 3.2 16.4 + - - +
150D THR* 3.7 5.4 - - - +
151D ILE 3.4 0.2 - - - -
152D ARG* 1.3 75.5 - - - +
154D LEU* 1.3 62.3 + - - +
156D LEU* 3.2 4.9 + - + +
157D PHE* 3.1 48.5 + - + -
183D ILE* 4.2 13.2 - - + -
187D THR* 4.1 24.9 - - + +
189D VAL* 3.8 22.2 - - + -
193D THR* 4.3 0.9 - - + -
194D VAL* 4.0 23.1 - - + -
197D VAL* 4.0 28.9 - - + -
198D LEU* 5.4 2.7 - - + -
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D THR* 3.1 20.7 + - - +
151D ILE* 3.2 13.2 + - + +
153D ILE* 1.3 74.6 - - - +
155D ARG* 1.3 60.4 + - - +
157D PHE* 3.4 3.4 + - - +
158D TYR* 2.9 28.9 + - - +
197D VAL* 4.3 9.9 - - + -
201D LEU* 3.4 43.3 - - + -
222D LEU* 3.9 14.4 - - + +
225D LEU* 3.7 34.3 - - + +
226D SER* 3.7 15.6 - - - +
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Residues in contact with ARG 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 3.7 16.4 - - - -
68C GLU* 2.7 38.2 + - - -
139D ARG* 5.5 3.6 - - - +
143D GLU* 3.1 25.5 + - - +
147D TYR* 3.6 38.2 + - - -
151D ILE* 2.9 34.2 + - + +
152D ARG 3.7 4.7 - - - +
154D LEU* 1.3 73.7 - - - +
156D LEU* 1.3 58.8 + - - +
158D TYR* 3.4 4.6 + - - +
159D GLU* 2.9 54.8 + - - +
226D SER* 3.9 18.3 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 3.7 29.8 - - + +
15D ILE* 4.2 9.9 - - + -
152D ARG 2.9 13.9 + - - +
153D ILE* 3.4 10.1 - - - +
154D LEU 3.2 0.2 - - - -
155D ARG* 1.3 77.2 - - - +
157D PHE* 1.3 60.9 - - + +
159D GLU* 3.7 7.8 + - - +
160D LEU* 2.9 45.0 + - + +
178D LEU* 4.6 4.7 - - + -
183D ILE* 4.6 24.7 - - + -
186D ILE* 4.3 17.3 - - + -
187D THR* 3.9 22.4 - - + -
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE* 3.1 35.8 + - + -
154D LEU* 3.8 6.1 - - - +
155D ARG 3.4 0.2 - - - -
156D LEU* 1.3 82.7 - - + +
158D TYR* 1.3 63.4 + - - +
160D LEU* 3.4 6.4 + - + +
161D CYS* 2.9 25.1 + - - +
174D ILE* 4.3 3.4 - - + +
178D LEU* 4.1 15.0 - - + -
183D ILE* 3.9 26.2 - - + -
198D LEU* 3.3 35.9 - - + -
201D LEU* 3.7 14.6 - - + -
207D LEU* 3.5 33.8 - - + +
209D LYS* 4.4 3.6 - - + -
214D ILE* 4.1 20.2 - - + -
222D LEU* 3.9 6.2 - - + +
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Residues in contact with TYR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LEU 2.9 17.8 + - - +
155D ARG* 3.6 6.5 - - - +
157D PHE* 1.3 75.7 - - - +
159D GLU* 1.3 61.4 + - + +
161D CYS* 3.4 2.6 + - - +
162D SER* 2.8 60.0 + - - -
219D LEU* 3.9 22.6 - - + +
222D LEU* 3.7 11.0 - - + +
223D LYS* 3.0 65.6 + - + +
226D SER* 4.2 15.0 - - - +
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 3.5 29.9 - - + +
139D ARG* 3.8 22.6 + - - -
143D GLU* 4.3 1.6 - - - +
155D ARG* 2.9 54.8 + - - +
156D LEU* 3.7 9.9 + - - +
158D TYR* 1.3 78.0 - - + +
160D LEU* 1.3 60.2 + - - +
162D SER* 3.4 5.4 + - - -
163D SER* 3.0 31.5 + - - -
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 4.1 20.6 - - + +
15D ILE* 4.6 7.0 - - + -
156D LEU* 2.9 39.6 + - + +
157D PHE* 3.8 9.9 - - + +
159D GLU* 1.3 77.5 - - - +
161D CYS* 1.3 56.5 + - - +
163D SER* 4.2 3.8 - - - -
164D GLN* 2.9 49.0 + - - +
165D GLY 3.5 0.7 + - - -
174D ILE* 3.8 13.4 - - + +
176D MET* 3.6 29.4 - - + -
178D LEU* 3.8 30.1 - - + -
214D ILE* 4.9 1.6 - - + -
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Residues in contact with CYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D PHE 2.9 17.6 + - - +
158D TYR* 3.7 3.8 - - - +
160D LEU* 1.3 72.5 - - - +
162D SER* 1.3 62.8 + - - +
165D GLY* 2.9 29.5 + - - +
172D TYR* 3.5 42.1 - - - -
174D ILE* 3.5 13.8 - - + +
216D VAL* 3.9 15.3 - - + -
219D LEU* 3.7 26.8 - - + +
222D LEU* 4.8 0.7 - - + -
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D TYR* 2.8 53.3 + - - -
159D GLU* 3.9 5.8 - - - -
161D CYS* 1.3 72.5 - - - +
163D SER* 1.3 61.4 + - - +
165D GLY 5.6 0.5 - - - +
219D LEU* 5.1 5.8 - - - +
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Residues in contact with SER 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 3.5 21.9 - - - +
159D GLU 3.0 19.4 + - - -
160D LEU* 3.6 4.3 - - - -
162D SER* 1.3 80.3 - - - +
164D GLN* 1.3 67.3 + - - +
165D GLY 3.8 0.7 - - - -
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 6.0 0.2 - - - +
160D LEU* 2.9 31.1 + - - +
163D SER* 1.3 82.8 + - - +
165D GLY* 1.3 64.7 + - - +
166D LYS* 3.4 28.5 + - - +
173D GLU 3.9 3.8 - - - +
174D ILE* 3.8 22.5 - - + +
175D THR 3.8 21.4 + - - +
176D MET* 4.2 12.4 - - - +
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Residues in contact with GLY 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LEU 3.5 2.8 + - - -
161D CYS* 2.9 27.3 + - - +
162D SER 5.6 0.3 - - - +
164D GLN* 1.3 75.6 - - - +
166D LYS* 1.3 61.7 + - - -
167D ARG 4.0 0.9 + - - -
172D TYR* 3.8 15.2 - - - -
173D GLU 3.7 8.5 - - - -
174D ILE* 3.9 12.8 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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