Contacts of the helix formed by residues 241 - 254 (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 ASN 241 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236N LEU* 4.6 0.2 - - - +
239N GLU 3.2 5.4 + - - +
240N ASP* 1.3 79.8 - - - +
242N LEU* 1.3 61.7 + - - +
243N LEU* 3.4 12.6 - - - -
244N MET* 3.0 20.4 + - + +
245N ALA* 2.6 37.1 + - - +
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Residues in contact with LEU 242 (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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240N ASP* 5.1 1.2 - - - -
241N ASN* 1.3 75.1 - - - +
243N LEU* 1.3 53.9 + - - +
245N ALA* 3.0 5.1 + - - +
246N TYR* 2.3 42.9 + - + +
324N LYS* 6.5 1.6 - - + -
793N LYS* 4.0 32.5 - - + -
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Residues in contact with LEU 243 (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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241N ASN* 4.1 8.4 - - - -
242N LEU* 1.3 78.2 - - - +
244N MET* 1.3 55.8 + - - +
246N TYR* 3.6 9.0 - - - -
247N GLN* 2.3 42.3 + - + +
793N LYS* 6.0 0.8 - - - +
903N PHE* 4.9 6.1 - - + -
913N ILE* 6.1 2.7 - - + -
915N LYS* 2.5 44.9 - - + -
916N ASP* 4.7 3.6 - - + +
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Residues in contact with MET 244 (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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210N LYS* 6.5 0.9 - - + -
213N PHE* 5.8 3.6 - - + -
236N LEU* 4.5 4.7 - - + -
239N GLU* 4.9 14.6 - - + +
241N ASN* 3.0 28.9 + - + +
243N LEU* 1.3 76.0 - - - +
245N ALA* 1.3 53.8 + - - +
247N GLN* 3.9 3.6 - - - +
248N ILE* 2.6 55.9 + - + +
903N PHE* 5.3 11.3 - - + -
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Residues in contact with ALA 245 (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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236N LEU* 3.4 34.1 - - + +
240N ASP* 5.1 6.3 - - - -
241N ASN 2.6 16.8 + - - +
242N LEU* 3.4 8.5 - - - +
244N MET* 1.3 72.7 - - - +
246N TYR* 1.3 52.0 + - - +
248N ILE* 3.3 1.9 - - - +
249N CYS* 2.4 41.2 + - - +
322N THR* 5.5 4.9 - - - -
325N MET* 4.2 17.0 - - + +
328N ILE* 4.9 0.4 - - - -
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Residues in contact with TYR 246 (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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242N LEU* 2.3 33.9 + - + +
243N LEU* 3.5 10.8 - - - +
245N ALA* 1.3 66.1 - - - +
247N GLN* 1.3 51.0 + - - +
249N CYS* 2.8 5.0 + - - +
250N PHE* 2.4 63.1 + - + -
324N LYS* 6.4 0.7 - - + -
328N ILE* 3.5 16.6 - - + -
913N ILE* 5.3 0.7 - - + -
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Residues in contact with GLN 247 (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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243N LEU* 2.3 34.9 + - + +
244N MET* 3.9 3.6 - - - +
246N TYR* 1.3 67.9 - - - +
248N ILE* 1.3 50.9 + - + +
250N PHE* 2.9 21.2 + - - +
251N ASP* 2.4 55.4 + - - +
902N PRO* 5.8 3.1 - - - +
903N PHE* 6.1 5.2 - - + +
904N LYS* 3.9 30.0 - - + +
907N SER* 5.7 3.3 + - - -
911N ILE* 5.4 8.3 - - - +
912N ILE 4.9 1.6 + - - +
913N ILE* 3.8 29.1 - - + +
915N LYS* 5.7 3.5 - - + +
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Residues in contact with ILE 248 (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* 4.1 28.3 - - + -
232N ILE* 4.2 20.9 - - + -
233N LEU* 5.7 4.3 - - + -
236N LEU* 3.8 42.6 - - + -
244N MET* 2.6 39.1 + - + +
245N ALA 3.3 4.3 - - - +
247N GLN* 1.3 73.4 - - + +
249N CYS* 1.3 52.9 + - - +
251N ASP* 2.9 13.2 + - + +
252N LEU* 2.5 40.4 + - + +
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Residues in contact with CYS 249 (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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245N ALA 2.4 26.7 + - - +
246N TYR 3.3 4.7 - - - +
248N ILE* 1.3 76.1 - - + +
250N PHE* 1.3 51.8 + - - +
252N LEU* 3.3 15.8 - - + +
253N TYR* 2.4 37.1 + - - +
325N MET* 4.5 14.6 - - + +
328N ILE* 3.3 32.0 - - + +
329N LEU* 5.5 1.5 - - + +
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Residues in contact with PHE 250 (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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246N TYR* 2.4 49.0 + - + -
247N GLN* 2.9 24.4 + - - +
249N CYS* 1.3 67.2 - - - +
251N ASP* 1.3 52.4 + - - +
252N LEU 3.0 1.1 + - - -
253N TYR* 3.6 11.1 - + + -
254N GLU* 2.6 37.9 + - - +
328N ILE* 3.5 42.2 - - + -
333N MET* 6.3 2.7 - - + -
791N LEU* 6.2 1.3 - - + -
792N ASN 5.9 3.4 - - - -
911N ILE* 5.3 11.0 - - + +
913N ILE* 3.3 41.7 - - + -
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Residues in contact with ASP 251 (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* 3.7 10.8 - - + +
214N ILE* 3.0 45.9 + - + +
217N CYS* 3.3 22.2 - - + -
247N GLN* 2.4 46.6 + - - +
248N ILE* 3.1 14.3 - - + +
250N PHE* 1.3 66.2 - - - +
252N LEU* 1.3 59.0 + - - +
254N GLU* 3.2 7.3 - - - +
255N SER* 2.9 28.9 + - - -
904N LYS* 5.6 1.4 - - - +
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Residues in contact with LEU 252 (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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217N CYS* 4.3 9.9 - - - -
229N VAL* 5.8 7.4 - - + -
248N ILE* 2.5 24.3 + - + +
249N CYS* 3.3 13.2 - - + +
250N PHE 3.0 0.2 - - - -
251N ASP* 1.3 71.9 - - - +
253N TYR* 1.3 66.9 + - - +
254N GLU 3.0 1.8 - - - -
255N SER 2.9 12.1 + - - -
256N ALA* 3.1 42.8 + - + +
261N LEU* 3.5 28.1 - - + +
264N VAL* 5.1 13.0 - - + -
268N LEU* 6.6 0.2 - - + -
329N LEU* 3.9 14.8 - - + -
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Residues in contact with TYR 253 (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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249N CYS 2.4 32.8 + - - +
250N PHE* 3.6 21.3 - + - -
252N LEU* 1.3 70.8 - - - +
254N GLU* 1.3 64.1 + - + +
255N SER 3.7 0.2 + - - -
256N ALA 5.2 2.6 - - - +
261N LEU* 4.9 12.1 - - - +
328N ILE* 3.7 31.6 - - + +
329N LEU* 5.2 2.7 - - + +
331N GLY* 5.2 8.3 - - - -
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Residues in contact with GLU 254 (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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250N PHE 2.6 27.4 - - - +
251N ASP* 3.2 13.9 - - - +
253N TYR* 1.3 82.9 - - + +
255N SER* 1.3 62.0 + - - +
752N THR* 5.9 6.3 - - + -
756N HIS* 6.0 1.7 - - - +
911N ILE* 4.7 20.9 - - + -
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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