Contacts of the helix formed by residues 215 - 228 (chain N) in PDB entry 2GLJ
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 GLN 215 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119N TYR* 4.8 2.0 - - - +
120N GLU* 3.2 41.0 + - - +
213N GLU* 2.8 11.9 + - + +
214N LYS* 1.3 78.3 - - + +
216N LYS* 1.3 57.2 + - - +
218N LYS* 3.4 45.8 + - + +
219N HIS* 2.9 27.4 + - - +
6O LEU* 4.4 9.8 - - + +
358O ARG* 6.1 1.6 - - - +
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Residues in contact with LYS 216 (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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120N GLU* 3.2 1.2 + - - -
206N ILE* 3.4 31.6 + - + +
207N PRO* 3.1 41.0 - - + +
210N ASP* 5.1 3.0 - - - +
212N GLU* 3.3 39.0 + - - +
213N GLU 3.3 6.3 - - - +
214N LYS* 2.6 15.6 + - - +
215N GLN* 1.3 70.2 - - - +
217N VAL* 1.3 69.1 + - - +
219N HIS* 3.1 4.6 + - - +
220N ASN 2.9 20.6 + - - -
11W ASN* 5.9 0.2 + - - -
14W ASP* 5.9 1.8 + - - -
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Residues in contact with VAL 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120N GLU* 2.6 15.5 + - - +
123N ASP* 3.2 27.8 - - + +
124N LEU* 3.8 2.5 - - - +
125N ALA 3.6 11.7 - - - +
202N LEU* 2.9 62.0 - - + +
203N ILE 4.1 0.9 - - - +
204N GLY* 3.6 14.6 - - - +
206N ILE* 3.5 34.3 - - + +
216N LYS* 1.3 72.2 - - - +
218N LYS* 1.3 59.7 + - - +
220N ASN* 3.5 1.9 + - - +
221N ILE 3.3 4.3 + - - -
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Residues in contact with LYS 218 (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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118N LEU* 3.5 47.9 + - + -
119N TYR* 4.3 7.1 - - - +
120N GLU* 2.7 26.0 + - + +
125N ALA* 4.1 9.0 - - + -
215N GLN* 3.4 43.5 + - + +
216N LYS 3.1 0.2 - - - -
217N VAL* 1.3 70.2 - - - +
219N HIS* 1.3 68.4 + - - +
221N ILE* 2.8 19.0 + - - +
222N MET* 3.0 11.5 + - - +
233N GLU* 3.3 31.4 + - - -
6O LEU* 3.9 13.5 - - + +
7O LYS 5.3 0.2 + - - -
358O ARG* 5.9 3.0 - - - +
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Residues in contact with HIS 219 (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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207N PRO* 5.1 1.8 - - + -
208N LEU* 3.6 48.9 + - + +
211N GLY* 6.1 1.8 - - - -
212N GLU 5.3 4.9 - - - -
213N GLU* 2.9 28.8 + - + +
215N GLN 2.9 16.7 + - - +
216N LYS* 3.4 7.6 - - - +
218N LYS* 1.3 79.3 - - - +
220N ASN* 1.3 62.8 + - - +
222N MET* 3.4 1.9 + - - +
223N LYS* 3.1 22.3 + - + +
5O LEU* 6.5 0.4 - - - -
6O LEU* 3.3 30.5 - - + +
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Residues in contact with ASN 220 (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 LEU* 3.7 10.5 - - - +
205N SER* 2.7 37.9 + - - +
207N PRO* 3.4 28.4 - - + +
208N LEU* 4.0 10.0 + - - +
216N LYS 2.9 9.6 + - - +
217N VAL 3.6 2.9 - - - +
219N HIS* 1.3 78.0 - - - +
221N ILE* 1.3 57.9 + - - +
223N LYS* 3.2 14.6 + - - +
224N ILE* 2.9 60.1 + - - +
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Residues in contact with ILE 221 (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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118N LEU* 3.6 33.4 - - + -
201N ILE* 4.0 12.1 - - + -
202N LEU* 3.1 45.8 - - + -
217N VAL 3.3 1.6 + - - -
218N LYS* 2.8 18.1 + - - +
220N ASN* 1.3 72.7 - - - +
222N MET* 1.3 59.7 + - - +
224N ILE* 3.0 18.1 + - + +
225N LEU* 2.6 42.4 + - + +
254W PHE* 3.2 34.8 - - + -
255W ASP* 4.2 1.6 - - + +
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Residues in contact with MET 222 (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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118N LEU* 3.6 25.1 - - + -
218N LYS 3.0 5.2 + - - +
219N HIS 3.7 8.1 - - - +
221N ILE* 1.3 80.9 - - - +
223N LYS* 1.3 52.2 + - - +
225N LEU* 3.2 20.1 + - + -
226N ASN* 2.7 34.6 + - + +
231N ILE* 4.0 19.5 - - + +
232N SER* 3.6 25.4 - - - +
233N GLU* 3.7 26.0 - - + +
236N PHE* 4.2 6.1 - - + -
5O LEU* 4.8 4.9 - - - +
6O LEU* 3.7 29.2 - - + +
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Residues in contact with LYS 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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208N LEU* 3.3 54.1 - - + +
219N HIS* 3.1 7.1 + - + +
220N ASN* 3.3 22.3 + - - +
221N ILE 3.1 0.2 - - - -
222N MET* 1.3 76.9 - - - +
224N ILE* 1.3 71.8 + - + +
226N ASN* 2.9 24.8 + - - +
227N GLU* 3.0 46.3 + - + +
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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
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220N ASN* 2.9 48.0 + - - +
221N ILE* 3.4 17.3 - - + +
223N LYS* 1.3 89.3 - - + +
225N LEU* 1.3 64.9 + - + +
226N ASN 3.3 0.5 + - - -
227N GLU* 3.4 20.2 + - - +
228N LYS* 3.5 26.4 + - + +
254W PHE* 4.1 19.3 - - + +
255W ASP* 3.8 22.7 - - + -
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Residues in contact with LEU 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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118N LEU* 5.8 1.8 - - + -
151N ILE* 6.0 0.2 - - + -
201N ILE* 5.6 5.6 - - + -
221N ILE* 2.6 25.0 + - + +
222N MET* 3.4 15.7 - - + +
224N ILE* 1.3 74.9 - - + +
226N ASN* 1.3 53.3 + - - +
228N LYS* 2.6 24.0 - - + +
229N TYR* 3.6 20.7 - - + -
231N ILE* 3.8 23.6 - - + +
236N PHE* 3.7 31.0 - - + -
254W PHE* 3.6 53.8 - - + -
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Residues in contact with ASN 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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222N MET* 2.7 14.3 + - + +
223N LYS* 2.9 18.3 + - - +
225N LEU* 1.3 75.5 - - - +
227N GLU* 1.3 71.2 + - - +
228N LYS 2.9 8.5 - - - +
229N TYR 3.6 7.4 - - - +
230N ASP* 3.8 17.9 - - - +
231N ILE 3.3 24.1 - - - +
5O LEU 5.5 4.9 + - - +
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Residues in contact with GLU 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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223N LYS* 3.0 49.8 + - + +
224N ILE* 3.4 13.2 + - - +
226N ASN* 1.3 83.1 - - - +
228N LYS* 1.3 63.6 + - + +
229N TYR 3.7 5.4 + - - +
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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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163N VAL* 6.0 3.6 - - - +
170N PRO* 5.7 5.3 - - - +
224N ILE* 3.5 21.6 + - + +
225N LEU* 2.6 23.6 - - + +
226N ASN 2.9 4.0 - - - +
227N GLU* 1.3 76.8 - - + +
229N TYR* 1.3 93.8 + - + +
254W PHE* 4.8 22.9 + - + -
256W ARG* 4.6 15.4 - - - +
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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