Contacts of the helix formed by residues 212 - 224 (chain N) in PDB entry 5GJQ
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 212 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205N TYR* 5.4 0.5 - - - +
210N LYS 4.0 0.4 + - - -
211N PRO* 1.3 73.1 - - - +
213N PHE* 1.3 60.5 + - - +
214N ILE* 3.6 11.1 + - - +
215N ASN* 2.9 53.5 + - + +
216N VAL* 3.5 11.3 - - - +
904N LYS* 4.5 15.8 - - - +
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Residues in contact with PHE 213 (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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211N PRO* 3.5 16.4 + - + -
212N ASP* 1.3 72.6 + - - +
214N ILE* 1.3 53.7 + - - +
215N ASN 3.0 2.0 - - - -
216N VAL* 2.5 14.6 + - + +
217N CYS* 2.3 36.9 + - + +
232N ILE* 5.3 8.5 - - + -
235N LYS* 5.3 8.7 - - - -
244N MET* 5.8 4.0 - - + -
248N ILE* 4.1 31.4 - - + -
251N ASP* 3.7 11.4 - - - +
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Residues in contact with ILE 214 (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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212N ASP* 3.6 11.0 + - - +
213N PHE* 1.3 73.9 - - - +
215N ASN* 1.3 53.9 - - - +
217N CYS* 3.5 7.9 - - + -
218N GLN* 2.7 35.3 + - + +
251N ASP* 3.0 35.3 + - + +
255N SER* 5.9 2.2 - - - +
752N THR* 4.4 28.7 - - + +
904N LYS* 6.1 3.4 - - + -
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Residues in contact with ASN 215 (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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178N ALA* 5.5 11.4 - - + -
181N LEU* 5.0 23.3 - - - +
201N LEU* 6.2 1.3 - - - -
205N TYR* 4.9 12.3 - - - -
212N ASP* 2.9 34.0 + - + +
214N ILE* 1.3 76.9 - - - +
216N VAL* 1.3 58.6 + - - +
218N GLN* 3.1 4.0 + - - +
219N CYS* 2.7 34.5 + - - +
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Residues in contact with VAL 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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202N VAL* 4.7 21.8 - - + -
205N TYR* 4.2 22.7 - - + -
206N MET 5.8 0.2 - - - +
211N PRO* 4.6 6.5 - - + -
212N ASP 3.5 15.9 - - - +
213N PHE* 2.5 17.2 + - + +
215N ASN* 1.3 80.1 - - - +
217N CYS* 1.3 51.7 + - - +
219N CYS* 3.2 9.7 - - - +
220N LEU* 2.3 41.8 + - + +
232N ILE* 6.3 5.2 - - + -
235N LYS* 6.3 0.7 - - - +
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Residues in contact with CYS 217 (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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213N PHE* 2.3 26.3 + - + +
214N ILE* 3.2 19.7 - - + +
216N VAL* 1.3 68.3 - - - +
218N GLN* 1.3 54.1 + - - +
220N LEU* 2.9 6.1 + - - +
221N ILE* 2.3 39.4 + - - +
248N ILE 5.1 0.2 - - - -
251N ASP* 3.3 41.3 - - + -
252N LEU* 4.1 10.5 - - - -
255N SER* 4.1 13.5 - - - -
256N ALA 5.7 0.2 - - - -
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Residues in contact with GLN 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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181N LEU* 5.9 4.7 - - + -
185N MET* 5.8 3.8 - - + -
214N ILE* 2.7 21.8 + - + +
215N ASN* 3.6 4.3 - - - +
217N CYS* 1.3 71.6 - - - +
219N CYS* 1.3 52.3 + - - +
221N ILE* 3.1 8.4 - - - +
222N PHE* 2.3 52.2 + - + -
255N SER* 5.8 1.1 - - - -
752N THR 5.1 2.5 - - - +
753N GLY 3.6 19.5 - - - +
754N HIS* 3.3 26.9 - - + -
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Residues in contact with CYS 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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181N LEU* 4.7 8.7 - - + +
198N LEU* 3.4 51.3 - - + +
201N LEU* 3.7 9.9 - - + -
202N VAL* 4.5 9.9 - - - -
215N ASN* 2.7 19.0 + - - +
216N VAL* 3.2 13.0 - - - +
218N GLN* 1.3 72.3 - - - +
220N LEU* 1.3 52.4 + - - +
222N PHE* 2.9 11.7 + - - +
223N LEU* 2.6 39.3 + - - +
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Residues in contact with LEU 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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216N VAL* 2.3 31.9 + - + +
217N CYS* 3.3 5.2 - - - +
219N CYS* 1.3 68.3 - - - +
221N ILE* 1.3 52.1 + - - +
223N LEU* 2.6 12.1 + - - +
224N ASP* 2.0 40.5 + - - -
225N ASP 3.4 29.4 - - - +
228N ALA* 4.7 10.3 - - + -
229N VAL* 4.1 21.8 - - + +
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Residues in contact with ILE 221 (chain N).
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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217N CYS* 2.3 32.8 + - - +
218N GLN* 3.4 9.0 - - - +
220N LEU* 1.3 69.5 - - - +
222N PHE* 1.3 57.0 + - - +
224N ASP* 3.0 29.4 - - - +
255N SER* 4.2 32.1 - - - +
256N ALA* 4.7 7.2 - - + +
257N SER 5.6 0.7 - - - +
754N HIS* 3.8 27.6 - - + -
755N THR 5.8 0.4 - - - +
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Residues in contact with PHE 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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181N LEU* 6.4 0.2 - - + -
185N MET* 4.6 17.5 - - + -
195N ASN* 5.6 2.1 - - - -
198N LEU* 3.8 17.7 - - + -
218N GLN* 2.3 56.0 + - + +
219N CYS* 3.1 10.1 - - - +
221N ILE* 1.3 72.5 - - - +
223N LEU* 1.3 61.0 + - - +
224N ASP* 4.6 1.9 - - - -
754N HIS* 4.7 5.6 - + - -
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Residues in contact with LEU 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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195N ASN* 3.5 14.1 - - + -
198N LEU* 3.5 39.5 - - + -
199N ARG* 3.1 56.1 + - + +
202N VAL* 6.0 0.7 - - + -
219N CYS* 2.6 24.3 + - - +
220N LEU* 2.6 8.1 + - - +
222N PHE* 1.3 73.6 - - - +
224N ASP* 1.3 63.8 + - - +
225N ASP* 2.9 35.2 - - + +
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Residues in contact with ASP 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 LEU* 2.0 27.1 + - - -
221N ILE* 3.0 29.6 - - - +
222N PHE 4.6 2.0 - - - -
223N LEU* 1.3 70.5 - - - +
225N ASP* 1.3 60.5 + - - +
226N PRO* 3.5 4.2 - - - +
256N ALA* 6.5 0.4 - - - -
257N SER* 5.6 4.0 - - - -
260N PHE* 4.2 34.3 - - + -
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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