Contacts of the helix formed by residues 219 - 240 (chain N) in PDB entry 1L0V
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 ASP 219 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N GLN* 3.8 22.5 + - - +
145N PHE* 3.7 2.2 - - + -
211N SER* 3.0 28.0 + - - +
214N CYS* 4.4 1.2 - - - +
217N HIS* 3.5 2.3 - - - +
218N VAL* 1.3 82.9 - - - +
220N PRO* 1.3 76.1 - - - +
222N ALA* 2.8 36.5 + - + +
223N ALA 3.4 2.8 + - - -
92O LYS* 3.5 24.0 + - - +
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Residues in contact with PRO 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154N CYS* 4.7 1.1 - - + -
170N PRO* 4.1 18.8 - - + -
174N THR* 3.4 26.0 - - + +
210N CYS* 3.8 12.3 - - + +
211N SER* 3.2 24.9 - - - +
214N CYS* 4.3 7.0 - - + -
218N VAL* 3.4 10.2 - - + -
219N ASP* 1.3 89.1 - - - +
221N ALA* 1.3 59.7 + - - +
223N ALA* 2.4 37.9 + - + +
224N ILE* 3.0 8.6 + - - +
246N SF4 4.4 12.6 - - - -
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Residues in contact with ALA 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204N CYS* 5.6 0.7 - - - -
206N PHE* 3.8 21.3 - - + -
208N GLY* 4.4 3.4 - - - -
210N CYS* 3.7 18.9 - - - -
211N SER* 3.0 20.2 + - - +
219N ASP* 4.5 1.6 - - - +
220N PRO* 1.3 78.1 - - - +
222N ALA* 1.3 60.8 + - - +
224N ILE* 3.4 7.7 + - - +
225N GLN* 3.1 25.1 + - - +
245N F3S 3.8 17.7 - - - -
92O LYS* 4.6 2.9 - - - +
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Residues in contact with ALA 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145N PHE* 4.5 7.2 - - + -
219N ASP* 2.8 39.5 + - + +
220N PRO 2.7 1.6 + - - -
221N ALA* 1.3 72.9 - - - +
223N ALA* 1.3 59.7 + - - +
225N GLN* 4.7 0.2 - - - -
226N GLN* 2.5 38.6 + - - +
92O LYS* 3.4 32.5 - - + +
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Residues in contact with ALA 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145N PHE* 3.7 17.4 - - + -
173N ILE* 5.1 1.1 - - - -
174N THR* 3.7 32.1 - - + +
177N HIS* 3.5 27.7 - - + -
219N ASP 3.4 1.8 + - - -
220N PRO 2.4 25.5 + - - +
222N ALA* 1.3 70.1 - - - +
224N ILE* 1.3 63.8 + - - +
226N GLN* 2.9 9.8 + - - +
227N GLY* 2.8 18.0 + - - -
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Residues in contact with ILE 224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170N PRO* 3.9 18.6 - - + +
173N ILE* 3.9 30.7 - - + +
201N VAL* 4.1 20.5 - - + +
204N CYS* 3.3 31.9 - - + -
220N PRO 3.0 5.8 + - - +
221N ALA* 3.7 16.8 - - - +
223N ALA* 1.3 75.8 - - + +
225N GLN* 1.3 52.4 + - - +
227N GLY* 2.7 21.9 + - - +
228N LYS* 2.7 21.2 + - + +
245N F3S 3.2 36.1 - - - -
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Residues in contact with GLN 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204N CYS* 5.6 1.1 - - - -
206N PHE* 3.5 27.7 - - + -
221N ALA 3.1 12.5 + - - +
222N ALA* 4.7 0.2 - - - -
223N ALA 3.3 0.4 + - - -
224N ILE* 1.3 77.5 - - - +
226N GLN* 1.3 61.9 + - - +
228N LYS* 3.2 17.4 - - + +
229N VAL* 3.1 25.6 + - - +
801N MQ7 2.6 63.4 - - + +
89O LEU 4.4 4.3 + - - -
92O LYS 3.9 12.3 - - - +
93O ALA* 2.6 37.7 - - - +
14P TRP* 4.6 4.7 - - - -
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Residues in contact with GLN 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145N PHE* 3.5 15.0 - - - -
177N HIS* 3.1 33.4 + - + +
181N GLU* 5.7 0.7 - - - +
222N ALA* 2.5 33.3 + - - +
223N ALA 2.9 5.1 + - - +
225N GLN* 1.3 75.4 - - - +
227N GLY* 1.3 64.7 + - - +
229N VAL* 3.3 10.8 + - - +
230N GLU* 3.0 23.0 + - - +
92O LYS 4.0 5.0 - - - +
93O ALA 3.6 20.2 - - - +
94O ALA 3.4 27.2 + - - +
95O ASN* 3.7 16.0 + - + +
102O LYS* 5.6 1.9 - - - +
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Residues in contact with GLY 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173N ILE* 5.3 4.0 - - - -
177N HIS* 4.9 7.6 - - - -
195N LEU* 5.4 7.7 - - - +
201N VAL* 3.9 15.3 - - - -
223N ALA 2.8 8.6 + - - -
224N ILE* 2.7 15.9 + - - -
226N GLN* 1.3 68.8 - - - +
228N LYS* 1.3 52.8 + - - -
230N GLU* 2.8 9.6 + - - +
231N SER* 2.6 35.3 + - - -
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Residues in contact with LYS 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201N VAL* 3.7 38.6 - - + +
202N TRP* 3.5 16.9 - - + +
204N CYS* 2.6 35.2 + - - -
205N THR* 4.5 0.2 - - - +
206N PHE* 4.6 3.0 - - - +
224N ILE* 2.7 17.7 + - + +
225N GLN* 3.2 22.4 - - + +
227N GLY* 1.3 70.4 - - - +
229N VAL* 1.3 57.7 + - - +
231N SER* 3.3 2.0 + - - -
232N SER* 2.8 35.9 + - - -
801N MQ7 2.7 33.1 + - - +
14P TRP* 3.4 31.2 - - + +
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Residues in contact with VAL 229 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N GLN 3.1 15.0 + - - +
226N GLN* 3.4 11.9 - - - +
227N GLY 3.1 0.6 - - - -
228N LYS* 1.3 77.6 - - - +
230N GLU* 1.3 67.0 + - - +
232N SER* 3.2 7.2 + - - -
233N LYS* 3.0 40.3 + - + +
801N MQ7 5.7 4.5 - - + -
93O ALA* 4.4 22.2 - - + +
14P TRP* 3.9 19.3 - - + -
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Residues in contact with GLU 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N HIS* 6.5 0.7 - - + -
180N ASN* 6.4 2.5 - - + -
181N GLU* 5.5 2.8 - - - +
192N MET* 3.6 25.7 - - + +
226N GLN 3.0 13.1 + - - +
227N GLY* 2.8 12.9 + - - +
229N VAL* 1.3 74.2 - - - +
231N SER* 1.3 68.3 + - - +
233N LYS* 2.9 29.7 + - - +
234N ASP* 2.8 21.7 + - - +
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Residues in contact with SER 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N MET* 4.6 3.7 - - - +
195N LEU* 5.3 1.6 - - - -
196N ASN* 3.0 27.6 + - - +
201N VAL* 4.1 9.6 - - - -
202N TRP* 2.6 34.9 + - - -
227N GLY 2.6 19.8 + - - -
228N LYS 3.4 5.6 - - - -
230N GLU* 1.3 71.5 - - - +
232N SER* 1.3 58.3 + - - +
234N ASP* 2.9 8.4 + - - +
235N PHE* 2.9 27.4 + - - +
11P PRO* 4.1 2.6 - - - +
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Residues in contact with SER 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N TRP* 3.3 18.4 - - - -
228N LYS 2.8 22.1 + - - -
229N VAL* 3.3 8.7 - - - -
231N SER* 1.3 76.7 + - - +
233N LYS* 1.3 62.9 + - - +
235N PHE* 3.1 12.5 + - - +
236N LEU* 3.2 13.0 + - - +
11P PRO* 3.8 19.3 + - - +
14P TRP* 3.5 16.8 - - - -
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Residues in contact with LYS 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229N VAL* 3.0 33.2 + - + +
230N GLU* 2.9 28.5 + - - +
232N SER* 1.3 74.2 - - - +
234N ASP* 1.3 63.8 + - - +
236N LEU* 3.6 3.9 + - - +
237N ILE* 2.9 40.2 + - + +
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Residues in contact with ASP 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N MET* 3.5 25.9 - - + +
196N ASN* 2.4 34.5 + - - +
230N GLU 2.8 11.5 + - - +
231N SER* 3.1 14.1 - - - +
233N LYS* 1.3 78.5 - - - +
235N PHE* 1.3 53.9 + - - +
237N ILE* 3.4 9.9 + - - +
238N ALA* 2.9 33.0 + - - +
7P ARG* 3.9 12.1 + - - -
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Residues in contact with PHE 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TRP* 5.3 3.8 - + - -
710D CE1 4.3 38.6 - - - -
231N SER 2.9 11.4 + - - +
232N SER 3.1 10.3 + - - +
234N ASP* 1.3 77.9 - - - +
236N LEU* 1.3 61.6 + - - +
238N ALA* 3.5 3.1 + - - +
239N THR* 3.0 39.8 + - - -
7P ARG* 3.7 28.9 - - + +
8P SER 2.8 30.1 - - - -
9P ASP* 4.3 4.5 - - - -
11P PRO* 3.8 25.6 - - + -
12P VAL* 4.2 23.3 - - + -
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Residues in contact with LEU 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N SER 3.2 9.4 + - - +
233N LYS* 4.0 7.2 - - - +
234N ASP 3.4 0.2 - - - -
235N PHE* 1.3 78.4 - - - +
237N ILE* 1.3 77.0 + - + +
239N THR* 2.8 27.8 + - - -
240N LEU* 3.1 40.6 + - + +
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Residues in contact with ILE 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233N LYS* 2.9 36.4 + - + +
234N ASP* 3.7 11.9 - - - +
236N LEU* 1.3 95.4 - - + +
238N ALA* 1.3 61.1 + - + +
240N LEU* 3.5 4.2 + - - +
241N LYS* 3.1 28.3 + - + +
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Residues in contact with ALA 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N ASP* 2.9 18.6 + - - +
235N PHE 3.8 5.8 - - - +
236N LEU 3.1 0.2 - - - -
237N ILE* 1.3 79.1 - - + +
239N THR* 1.3 58.0 + - - +
241N LYS* 3.6 9.4 - - + +
242N PRO* 3.0 24.8 - - - +
7P ARG* 3.8 28.9 - - - +
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Residues in contact with THR 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PRO* 4.8 0.3 - - - +
95D ALA* 3.5 39.6 + - + -
98D TRP* 4.0 17.9 + - + +
710D CE1 4.3 13.8 + - - +
235N PHE* 3.0 31.7 + - - -
236N LEU* 2.8 16.0 + - - -
238N ALA* 1.3 78.0 - - - +
240N LEU* 1.3 60.1 + - + +
241N LYS 3.2 2.3 + - - -
242N PRO* 3.9 9.6 - - - +
243N ARG 4.9 0.7 + - - -
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Residues in contact with LEU 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D PRO* 4.4 14.2 - - + +
95D ALA* 4.0 21.8 - - + +
236N LEU* 3.1 38.0 + - + +
237N ILE* 3.5 4.9 + - - +
239N THR* 1.3 92.1 - - + +
241N LYS* 1.3 58.2 + - - +
242N PRO 3.9 0.2 - - - -
243N ARG* 3.1 35.5 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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