Contacts of the helix formed by residues 183 - 195 (chain D) in PDB entry 3O9Z
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 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D LEU 3.2 0.4 + - - -
179D ALA 2.2 27.6 + - - -
182D ILE* 1.3 75.4 - - - +
184D ILE* 1.3 62.3 + - - -
186D PHE* 2.8 19.9 + - - +
187D PHE* 3.1 17.6 + - - -
225D LEU* 3.3 25.6 - - - +
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Residues in contact with ILE 184 (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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101D LYS* 3.3 40.4 - - + -
102D PRO* 4.1 26.9 - - + -
179D ALA 3.1 1.4 + - - -
180D THR* 3.1 22.3 + - + +
182D ILE 2.7 8.8 + - - +
183D GLY* 1.3 72.0 - - - +
185D HIS* 1.3 63.4 + - - +
187D PHE* 3.8 6.5 - - + -
188D ASP* 2.9 25.8 + - + +
285D ALA* 3.6 37.7 - - + +
286D ILE* 4.2 7.9 - - + +
289D ALA* 3.7 17.7 - - + -
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Residues in contact with HIS 185 (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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101D LYS* 3.5 29.5 - - + +
128D LEU* 6.5 0.7 - - - -
129D GLN* 4.2 15.8 + - - -
130D LEU* 3.7 23.8 - - + +
182D ILE 3.6 20.0 - - - +
184D ILE* 1.3 77.8 - - - +
186D PHE* 1.3 70.3 + + + +
188D ASP* 3.7 5.7 + - - +
189D LEU* 3.0 24.8 + - - +
260D PHE* 4.0 11.7 - + + -
311D NAD 3.7 17.2 + - - -
312D AKG 2.5 46.0 + - + +
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Residues in contact with PHE 186 (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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130D LEU* 3.7 23.6 - - + -
154D LEU* 4.1 23.8 - - + -
156D TYR* 3.4 45.1 - + + -
182D ILE 5.1 2.2 - - - -
183D GLY* 2.8 14.8 + - - +
185D HIS* 1.3 84.4 - - + +
187D PHE* 1.3 62.9 + - + +
188D ASP 3.2 0.2 - - - -
189D LEU* 3.1 4.1 + - + +
190D LEU* 2.8 35.6 + - - +
225D LEU* 4.8 5.6 - - + -
245D ARG* 3.0 34.3 - - + -
246D SER 5.7 0.2 - - - -
247D ILE* 4.1 28.7 - - + -
256D PHE* 4.4 8.1 - + + -
260D PHE* 4.6 7.9 - + - -
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Residues in contact with PHE 187 (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* 6.2 2.0 - - + -
179D ALA* 3.8 6.3 - - + -
183D GLY* 3.1 43.4 + - - -
184D ILE* 4.1 6.7 - - - +
186D PHE* 1.3 77.1 - - + +
188D ASP* 1.3 57.3 + - - +
190D LEU* 3.8 11.6 - - + +
191D ALA* 3.0 29.1 + - - +
214D LEU* 4.1 23.8 - - + -
223D TRP* 3.9 39.5 - + + -
225D LEU* 3.8 8.1 - - + -
285D ALA* 3.8 15.8 - - + +
288D VAL* 4.5 15.3 - - + +
289D ALA* 5.3 4.5 - - + -
292D LEU* 3.4 35.0 - - + -
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Residues in contact with ASP 188 (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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128D LEU* 3.6 29.3 - - + +
130D LEU* 6.1 0.9 - - - +
131D ARG* 2.8 46.9 + - - +
184D ILE* 2.9 21.2 + - + +
185D HIS* 3.7 5.9 - - - +
187D PHE* 1.3 73.7 - - - +
189D LEU* 1.3 58.9 + - - +
191D ALA* 3.2 3.7 + - - +
192D TRP* 2.9 28.8 + - - +
281D GLU 3.9 5.7 - - - +
282D ALA* 4.6 2.9 - - - -
285D ALA* 3.4 20.2 + - + +
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Residues in contact with LEU 189 (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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130D LEU* 4.3 9.2 - - + -
131D ARG* 5.9 0.4 - - + -
136D LEU* 3.5 35.0 - - + -
139D LEU* 5.9 0.4 - - + -
154D LEU* 5.5 0.2 - - + -
185D HIS 3.0 17.6 + - - +
186D PHE* 3.1 15.0 + - + +
188D ASP* 1.3 76.0 + - - +
190D LEU* 1.3 60.5 + - + +
192D TRP* 3.3 34.8 + - + +
193D LEU* 2.9 50.8 + - + +
247D ILE* 3.1 37.2 - - + -
256D PHE* 3.7 2.2 - - + -
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Residues in contact with LEU 190 (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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152D VAL* 4.3 13.0 - - + -
154D LEU* 4.5 20.4 - - + -
186D PHE 2.8 24.8 + - - +
187D PHE* 3.8 15.0 - - + +
189D LEU* 1.3 76.3 - - + +
191D ALA* 1.3 56.1 + - - +
193D LEU* 3.4 3.1 + - + -
194D PHE* 2.8 58.9 + - + +
214D LEU* 4.2 16.8 - - + -
216D LEU* 3.6 14.1 - - + +
221D VAL* 3.8 31.9 - - + -
223D TRP* 5.6 0.2 - - + -
247D ILE* 4.9 4.7 - - + -
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Residues in contact with ALA 191 (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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131D ARG* 5.4 2.5 - - - +
187D PHE 3.0 18.6 + - - +
188D ASP* 3.7 8.3 - - - +
190D LEU* 1.3 75.5 - - - +
192D TRP* 1.3 61.4 + - - +
195D GLY* 2.9 35.8 + - - +
216D LEU* 4.2 2.0 - - + +
281D GLU 6.1 0.4 - - - +
284D GLU* 3.6 35.0 - - + -
285D ALA* 4.5 4.0 - - - +
288D VAL* 6.1 0.9 - - + -
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Residues in contact with TRP 192 (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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130D LEU 4.2 3.4 - - - -
131D ARG* 3.4 84.3 - - + +
136D LEU 4.2 12.1 - - - -
137D LEU* 4.0 22.4 - - + -
140D LYS* 3.3 55.3 + - + +
188D ASP 2.9 16.9 + - - +
189D LEU* 3.4 30.7 - - + +
191D ALA* 1.3 78.5 - - - +
193D LEU* 1.3 70.0 + - + +
195D GLY 4.9 0.2 + - - -
277D PHE* 6.0 0.8 - - - -
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Residues in contact with LEU 193 (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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136D LEU 4.9 0.4 - - - +
139D LEU* 4.2 24.0 - - + -
140D LYS* 3.7 44.5 + - + +
143D LEU* 4.4 8.2 - - + +
189D LEU* 2.9 40.9 + - + +
190D LEU* 5.1 2.0 - - + -
192D TRP* 1.3 94.0 - - + +
194D PHE* 1.3 95.1 + - + +
195D GLY 3.9 0.4 - - - -
247D ILE* 5.9 3.8 - - + -
249D VAL* 6.0 0.4 - - + -
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Residues in contact with PHE 194 (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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143D LEU* 4.0 25.8 - - + -
150D LYS* 3.8 23.6 - - + -
152D VAL* 3.9 26.9 - - + -
190D LEU* 2.8 42.6 + - + +
193D LEU* 1.3 98.7 - - + +
195D GLY* 1.3 62.0 + - - +
216D LEU* 3.5 10.0 - - + +
217D GLU* 3.5 5.9 + - - +
218D GLY* 2.9 34.7 + - - -
219D ALA* 3.6 24.5 - - + -
221D VAL* 5.1 0.4 - - + -
247D ILE* 6.0 0.7 - - + -
249D VAL* 4.6 6.7 - - + -
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Residues in contact with GLY 195 (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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191D ALA* 2.9 28.1 + - - +
192D TRP 4.9 0.2 + - - -
193D LEU 3.9 0.4 - - - -
194D PHE* 1.3 77.3 - - - +
196D ARG* 1.3 64.4 + - - -
197D ALA 3.8 0.7 + - - -
216D LEU* 3.3 15.9 - - - +
217D GLU* 3.5 9.9 - - - -
284D GLU* 4.3 3.6 - - - +
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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