Contacts of the helix formed by residues 243 - 257 (chain F) in PDB entry 2Q5E
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 THR 243 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145F TYR* 3.0 39.7 - - + +
241F ALA 3.7 8.0 + - - +
242F ASP* 1.3 74.8 + - - +
244F GLU* 1.3 65.1 + - - +
245F LEU 3.3 2.5 - - - -
246F LEU* 3.0 21.1 + - + +
247F ASN* 2.9 34.6 + - - -
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Residues in contact with GLU 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ARG* 3.8 16.2 - - - +
232F PRO 4.6 1.7 - - - +
233F VAL* 3.6 19.9 - - + +
234F GLN* 3.5 34.0 + - + +
242F ASP* 3.1 25.0 + - - +
243F THR* 1.3 75.8 - - - +
245F LEU* 1.3 63.2 + - - +
247F ASN* 3.2 18.1 + - - +
248F LEU* 3.0 29.9 + - - +
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Residues in contact with LEU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F THR 4.1 13.7 - - - +
112F LEU* 4.3 13.2 - - + -
143F ARG* 4.0 27.4 - - + +
144F PRO 3.9 15.4 + - - +
145F TYR* 4.3 2.5 - - + -
146F VAL* 3.7 38.8 - - + -
149F PHE* 3.5 28.5 - - + -
216F LEU* 4.9 2.9 - - + -
233F VAL* 4.8 2.9 - - + -
242F ASP* 4.3 1.2 + - - -
243F THR 3.3 1.0 - - - -
244F GLU* 1.3 75.9 - - - +
246F LEU* 1.3 55.5 + - - +
248F LEU* 2.9 38.7 + - + +
249F ILE* 3.1 17.4 + - - +
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Residues in contact with LEU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F TYR* 3.6 46.1 - - + +
148F GLU* 5.7 3.8 - - + -
243F THR* 3.0 34.0 + - + +
245F LEU* 1.3 77.3 - - - +
247F ASN* 1.3 66.7 + - - +
248F LEU 3.1 1.2 + - - -
249F ILE* 3.6 14.8 + - + +
250F PRO* 3.3 17.7 - - - +
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Residues in contact with ASN 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F THR* 2.9 31.6 + - - +
244F GLU* 3.2 21.0 + - - +
246F LEU* 1.3 80.6 - - - +
248F LEU* 1.3 58.0 + - + +
250F PRO* 3.4 12.6 - - - +
251F ILE* 3.3 21.9 - - + +
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Residues in contact with LEU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PHE* 3.7 11.9 - - + -
216F LEU* 4.0 17.7 - - + -
231F VAL* 3.6 30.7 - - + -
232F PRO 4.4 6.5 - - - +
233F VAL* 4.1 13.7 - - + -
244F GLU* 3.0 21.2 + - + +
245F LEU* 2.9 30.0 + - + +
247F ASN* 1.3 76.2 - - + +
249F ILE* 1.3 56.5 + - - +
250F PRO* 3.3 2.6 - - - -
251F ILE* 3.3 17.1 - - + +
252F PHE* 2.7 45.5 + - + -
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Residues in contact with ILE 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F TYR* 5.5 1.6 - - + +
148F GLU* 3.6 14.8 - - + +
149F PHE* 3.6 38.1 - - + +
152F ARG* 3.9 27.4 - - + -
153F MET* 5.7 1.8 - - - -
156F LEU* 5.4 1.0 - - - +
245F LEU 3.1 14.5 + - - +
246F LEU* 3.9 16.8 - - + +
248F LEU* 1.3 76.2 - - - +
250F PRO* 1.4 56.1 - - + +
252F PHE* 3.1 7.3 + - - +
253F GLU* 2.8 46.2 + - - +
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Residues in contact with PRO 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F LEU 3.3 17.3 - - - +
247F ASN* 3.4 9.9 - - - +
248F LEU 3.4 4.7 - - - -
249F ILE* 1.4 87.8 - - + +
251F ILE* 1.3 69.0 + - + +
253F GLU* 2.8 27.8 + - + +
254F GLU* 2.8 20.6 + - - +
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Residues in contact with ILE 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F VAL* 4.6 11.0 - - + -
247F ASN* 3.3 23.6 - - + +
248F LEU* 3.3 28.0 - - + +
250F PRO* 1.3 79.1 - - + +
252F PHE* 1.3 64.2 + - + +
254F GLU* 3.4 2.8 + - - -
255F LEU* 3.4 24.5 + - + +
268F LEU* 3.6 42.2 - - + +
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Residues in contact with PHE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F VAL* 4.2 12.1 - - + -
149F PHE* 4.1 13.0 - + - -
153F MET* 3.6 42.4 - - + -
156F LEU* 4.7 2.0 - - + -
157F PHE* 3.5 22.0 - + + -
214F LEU* 3.9 25.4 - - + -
216F LEU* 4.2 13.5 - - + -
231F VAL* 4.0 36.1 - - + -
248F LEU* 2.7 43.7 + - + +
249F ILE* 3.5 5.2 - - - +
251F ILE* 1.3 72.8 - - + +
253F GLU* 1.3 55.7 + - - +
255F LEU* 3.3 7.1 + - + +
256F SER* 2.8 35.4 + - - -
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Residues in contact with GLU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F ARG* 2.5 47.1 + - - +
156F LEU* 4.1 10.0 - - + +
249F ILE* 2.8 25.1 + - - +
250F PRO* 2.8 26.8 + - + +
252F PHE* 1.3 67.8 - - - +
254F GLU* 1.3 64.3 + - + +
256F SER* 3.1 21.3 + - - +
257F GLY 4.4 1.0 + - - -
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Residues in contact with GLU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F PRO* 2.8 19.2 + - - +
251F ILE* 3.8 2.4 + - - +
252F PHE 3.4 0.4 - - - -
253F GLU* 1.3 74.3 - - - +
255F LEU* 1.4 60.1 + - - +
257F GLY* 4.3 3.5 + - - -
258F ALA* 4.8 3.8 + - - +
264F SER* 5.4 3.3 + - - -
267F GLN 5.7 0.7 - - - -
268F LEU* 3.8 36.7 - - + +
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Residues in contact with LEU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ILE* 3.4 7.1 - - + +
157F PHE* 4.8 1.1 - - + -
214F LEU* 4.3 25.4 - - + -
231F VAL* 4.5 8.1 - - + -
251F ILE* 3.4 27.5 + - + +
252F PHE* 3.3 12.0 + - + +
253F GLU 3.2 0.4 - - - -
254F GLU* 1.4 72.3 - - - +
256F SER* 1.3 56.6 + - - +
257F GLY 2.6 17.2 + - - -
258F ALA* 2.7 21.5 + - + +
261F VAL* 4.4 11.9 - - + +
264F SER* 3.9 37.9 - - - +
265F LEU* 4.0 29.4 - - + +
268F LEU* 4.5 5.8 - - + -
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Residues in contact with SER 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ARG* 5.8 0.9 - - - -
102F ILE* 3.6 16.5 + - - +
156F LEU* 3.8 43.1 + - - +
157F PHE* 3.7 16.9 - - - -
252F PHE 2.8 20.7 + - - -
253F GLU* 3.1 13.3 + - - +
255F LEU* 1.3 72.0 - - - +
257F GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F GLU 4.4 1.0 + - - -
254F GLU 4.3 4.7 + - - -
255F LEU 2.6 5.7 + - - -
256F SER* 1.3 79.1 + - - +
258F ALA* 1.3 64.0 + - - +
259F GLU* 3.7 7.8 + - - +
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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