Contacts of the helix formed by residues 199 - 217 (chain A) in PDB entry 4LGD
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ILE* 4.2 11.7 - - - +
191A GLU* 4.4 11.5 + - - +
195A GLU* 3.3 27.3 + - - -
198A TYR* 1.3 79.7 - - - +
200A CYS* 1.3 69.5 + - - +
201A VAL* 3.1 17.7 - - + -
202A ALA* 2.7 23.3 + - - +
203A ASP 4.0 0.7 + - - -
263A PRO* 5.7 2.8 - - - +
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Residues in contact with CYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS* 3.2 56.5 + - + +
141A ARG* 5.1 6.5 - - - -
142A LYS 4.2 17.3 - - - -
143A ILE* 4.2 13.1 - - - +
199A ASN* 1.3 74.1 - - - +
201A VAL* 1.3 65.0 + - + +
202A ALA 3.0 1.4 + - - -
203A ASP* 3.0 12.9 + - - +
204A ILE 4.0 0.2 + - - -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 4.2 3.6 - - - +
199A ASN* 4.1 14.1 - - + -
200A CYS* 1.3 76.2 - - + +
202A ALA* 1.3 61.6 + - - +
203A ASP 3.1 0.4 - - - -
204A ILE* 3.1 22.1 + - + +
205A TRP 3.3 2.8 + - - -
263A PRO* 3.6 44.2 - - + +
266A ARG* 2.7 43.0 + - - +
267A ALA 4.8 2.9 - - - +
268A THR* 4.8 14.6 - - + -
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 4.1 3.2 + - + +
191A GLU* 3.7 12.6 - - - +
192A VAL* 3.9 22.0 - - + -
198A TYR* 4.1 13.2 - - + -
199A ASN 2.7 30.2 + - - +
201A VAL* 1.3 75.0 - - - +
203A ASP* 1.3 60.4 + - - +
205A TRP* 3.2 6.2 + - - +
206A SER* 3.1 24.3 + - - -
266A ARG* 3.5 9.4 - - - +
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.6 21.2 - - + +
138A HIS* 3.0 19.3 + - - +
143A ILE* 3.4 11.3 - - - +
144A HIS* 3.1 30.8 + - - +
145A ARG* 3.0 25.3 + - - -
146A ASN 4.0 3.5 + - - -
147A ILE* 4.0 7.9 + - + +
198A TYR* 5.3 0.5 - - - -
200A CYS 3.0 9.0 + - - +
202A ALA* 1.3 75.5 - - - +
204A ILE* 1.3 55.5 + - - +
206A SER* 3.3 8.6 + - - -
207A LEU* 2.7 34.4 + - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.7 0.7 - - + -
134A LEU* 4.4 15.0 - - + -
138A HIS* 4.5 5.6 - - + -
200A CYS 4.5 2.7 - - - +
201A VAL* 3.1 21.9 + - - +
203A ASP* 1.3 75.5 - - - +
205A TRP* 1.3 59.9 + - - +
207A LEU* 3.1 5.7 + - + +
208A GLY 2.8 24.3 + - - -
258A CYS* 3.7 19.0 - - - +
266A ARG* 4.1 6.7 - - + -
267A ALA 3.4 25.6 - - - +
268A THR* 4.5 1.8 - - - -
269A ALA* 3.7 36.1 - - + +
272A LEU* 3.6 25.1 - - + -
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Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PHE 5.1 0.8 + - - -
187A TRP 3.8 4.7 - - - -
188A MET 3.2 26.0 + - - -
189A ALA* 3.5 10.3 - - + -
190A PRO* 3.9 24.7 - - + -
201A VAL 3.3 2.6 + - - -
202A ALA 3.2 5.7 + - - +
204A ILE* 1.3 78.5 - - - +
206A SER* 1.3 65.7 + - - +
208A GLY* 2.9 12.2 + - - +
209A ILE* 2.9 26.8 + - + +
233A ILE* 4.6 14.1 - - + +
238A PRO* 4.1 18.2 - - + -
239A PRO* 4.4 10.5 - - + -
258A CYS 4.0 9.6 - - - -
259A LEU* 3.3 54.5 - - + +
260A VAL 3.6 19.7 - - - -
261A LYS* 3.9 9.0 - - + -
266A ARG* 3.2 23.4 - - - +
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG 6.0 0.5 - - - -
146A ASN* 5.6 1.2 + - - -
147A ILE* 3.7 31.7 + - - -
187A TRP* 2.7 29.4 + - - +
188A MET* 4.8 1.0 - - - -
189A ALA 4.9 0.3 + - - -
198A TYR* 6.0 1.7 - - - -
202A ALA 3.1 11.8 + - - -
203A ASP* 3.4 12.4 + - - -
205A TRP* 1.3 78.3 - - - +
207A LEU* 1.3 53.8 + - - +
209A ILE* 3.3 4.5 + - - +
210A THR* 2.7 37.4 + - - -
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.0 19.5 - - + +
130A THR* 3.3 33.4 - - + -
131A LEU* 3.7 36.3 - - + -
134A LEU* 3.8 14.8 - - + -
147A ILE* 4.1 9.4 - - + +
152A ILE* 5.1 1.6 - - + -
203A ASP 2.7 17.0 + - - +
204A ILE* 3.3 10.8 - - + +
206A SER* 1.3 73.2 - - - +
208A GLY* 1.3 56.9 + - - +
210A THR* 3.1 9.5 + - - -
211A SER* 2.8 32.9 + - - +
254A PHE* 4.6 8.1 - - + -
258A CYS* 5.0 0.7 - - - -
272A LEU* 4.4 12.6 - - + -
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE 2.8 11.5 + - - -
205A TRP 2.9 4.6 + - - -
207A LEU* 1.3 76.1 - - - +
209A ILE* 1.3 61.0 + - - +
211A SER* 3.1 23.6 + - - -
212A ILE* 3.4 10.0 + - - +
255A VAL* 4.7 4.5 - - - +
258A CYS* 3.6 25.1 - - - +
259A LEU* 3.7 12.8 - - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PHE 3.6 24.2 - - - +
187A TRP* 3.7 12.8 - - + -
205A TRP* 2.9 39.4 + - + +
206A SER 3.6 6.5 - - - +
208A GLY* 1.3 75.3 - - - +
210A THR* 1.3 57.7 + - - +
212A ILE* 3.1 9.8 + - + +
213A GLU* 2.9 23.9 + - - +
219A PRO* 3.7 23.8 - - + -
220A PRO* 3.8 10.0 - - + +
239A PRO* 3.8 25.1 - - + -
259A LEU* 3.7 15.7 - - + -
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.8 3.3 - - + +
148A LYS* 3.4 22.5 - - - +
149A ALA* 3.6 28.3 - - + +
152A ILE* 4.4 13.2 - - + -
187A TRP* 3.6 3.5 - - - +
206A SER 2.7 25.4 + - - -
207A LEU* 3.1 13.2 + - + -
209A ILE* 1.3 76.8 - - - +
211A SER* 1.3 60.1 + - - +
213A GLU* 3.2 10.6 + - - +
214A MET* 3.1 36.2 + - + +
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 4.4 1.4 - - - +
127A LEU* 3.9 21.2 - - - +
207A LEU 2.8 23.2 + - - -
208A GLY* 3.1 15.1 + - - -
210A THR* 1.3 78.4 - - - +
212A ILE* 1.3 58.6 + - - +
214A MET* 3.4 21.2 + - - +
215A ALA* 3.4 13.7 + - - +
251A PHE* 4.1 15.8 - - - -
254A PHE* 4.0 8.7 - - - -
255A VAL* 4.1 19.1 - - - -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLY 3.4 8.0 + - - +
209A ILE* 3.1 9.0 + - - +
211A SER* 1.3 73.9 - - - +
213A GLU* 1.3 59.8 + - - +
215A ALA* 4.5 4.5 - - - +
216A GLU* 2.9 59.6 + - + +
218A LYS 4.3 3.1 - - - +
220A PRO* 4.0 30.3 - - + -
239A PRO 4.1 12.1 - - - +
240A THR* 3.7 28.5 - - - +
241A PHE* 4.4 15.9 - - + -
255A VAL* 4.5 9.0 - - + -
259A LEU* 4.3 11.0 - - + -
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A SER* 4.6 6.8 + - - -
111A ILE* 4.4 4.3 - - + +
148A LYS* 5.0 1.6 - - - +
149A ALA* 3.1 40.3 + - + +
150A GLY 4.5 2.3 + - - -
187A TRP* 2.8 42.7 + - - +
209A ILE 2.9 12.6 + - - +
210A THR* 3.2 11.3 + - - +
212A ILE* 1.3 78.4 - - - +
214A MET* 1.3 56.9 + - - +
217A GLY* 3.0 28.8 + - - +
218A LYS* 4.0 13.7 - - - -
219A PRO* 4.2 16.5 - - + +
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Residues in contact with MET 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.7 33.0 - - + -
111A ILE* 3.9 10.1 - - + +
117A THR* 3.9 2.3 - - - -
118A LEU* 3.0 37.4 + - + +
123A ILE* 4.0 20.0 - - + +
126A ILE* 4.3 20.2 - - + -
127A LEU* 3.5 37.2 - - + -
149A ALA* 4.8 2.9 - - + -
152A ILE* 5.5 3.1 - - + -
210A THR* 3.1 35.1 + - + +
211A SER* 3.8 10.8 - - - +
212A ILE 3.1 0.2 - - - -
213A GLU* 1.3 77.9 - - - +
215A ALA* 1.3 60.3 + - - +
217A GLY 4.4 0.6 + - - -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.2 21.5 + - - +
118A LEU 4.1 4.9 - - - -
123A ILE* 3.9 15.5 - - + -
211A SER 3.4 12.2 + - - +
212A ILE 3.2 3.9 + - - +
214A MET* 1.3 81.8 - - - +
216A GLU* 1.3 63.4 + - + +
217A GLY 3.6 0.2 - - - -
241A PHE* 4.5 4.3 - - + -
247A TRP* 3.6 37.1 - - + -
251A PHE* 4.2 8.7 - - + -
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.9 9.4 - - - +
212A ILE* 2.9 33.4 + - + +
215A ALA* 1.3 85.8 - - + +
217A GLY* 1.3 58.0 + - - +
218A LYS* 3.2 32.3 + - + +
220A PRO* 5.7 1.6 - - - +
240A THR 4.8 1.6 - - - +
241A PHE* 3.1 18.1 - - + +
242A ARG* 2.9 66.9 + - - +
243A LYS 4.6 0.7 + - - -
247A TRP* 4.7 5.5 + - + +
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Residues in contact with GLY 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.7 15.3 - - - +
117A THR* 4.0 10.2 - - - +
213A GLU* 3.0 21.9 + - - +
214A MET 4.4 0.4 - - - -
215A ALA 3.6 1.6 - - - +
216A GLU* 1.3 78.0 - - - +
218A LYS* 1.3 67.4 + - - +
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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