Contacts of the helix formed by residues 245 - 257 (chain F) in PDB entry 3EXE
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 245 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196F GLY 3.2 23.7 - - - +
197F LYS* 3.6 17.5 + - - +
198F ALA* 2.8 35.3 + - + +
238F MET* 5.2 2.1 + - - +
240F THR* 4.7 2.6 + - - -
243F PRO 3.5 1.0 + - - -
244F MET* 1.3 69.6 - - - +
246F MET* 1.3 60.5 + - - +
247F GLU* 3.5 10.2 + - - +
248F THR* 2.5 40.9 + - - -
249F ILE* 3.6 18.5 + - - +
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Residues in contact with MET 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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244F MET* 3.1 26.6 + - + +
245F ASP* 1.3 72.0 - - - +
247F GLU* 1.3 57.0 + - - +
249F ILE* 3.2 27.1 + - + -
250F GLU* 2.7 57.9 + - + +
275F ILE* 4.0 11.2 - - + +
278F ARG* 3.8 46.0 - - + +
279F ILE* 3.4 39.7 - - + +
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Residues in contact with GLU 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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245F ASP* 3.3 8.4 + - - +
246F MET* 1.3 79.2 - - - +
248F THR* 1.3 57.9 + - - +
250F GLU* 3.8 11.1 + - - +
251F ALA* 3.0 30.1 + - + +
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Residues in contact with THR 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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197F LYS* 5.4 1.4 - - - +
198F ALA* 4.2 19.9 + - + +
200F ILE* 4.2 30.2 - - + +
236F ILE* 4.3 9.2 - - + -
245F ASP* 2.5 36.0 + - - -
247F GLU* 1.3 73.3 - - - +
249F ILE* 1.3 66.6 + - - +
251F ALA* 3.4 6.0 + - - +
252F SER* 3.1 22.0 + - - -
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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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198F ALA* 5.6 0.7 - - + -
208F THR* 4.7 0.4 - - + -
210F VAL* 3.8 44.4 - - + -
236F ILE* 3.9 15.5 - - + -
238F MET* 5.0 6.1 - - + -
244F MET* 5.1 3.8 - - + -
245F ASP 3.6 14.3 + - - +
246F MET* 3.2 36.9 + - + +
248F THR* 1.3 76.1 - - - +
250F GLU* 1.3 64.6 + - - +
252F SER* 3.0 4.2 + - - -
253F VAL* 3.0 27.2 + - + +
259F LEU* 4.3 15.0 - - + -
275F ILE* 4.3 15.5 - - + -
279F ILE* 4.4 4.0 - - + -
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Residues in contact with GLU 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 MET* 2.7 52.4 + - + +
247F GLU* 3.8 8.9 + - - +
249F ILE* 1.3 71.3 - - - +
251F ALA* 1.3 62.8 + - - +
253F VAL 3.3 0.5 + - - -
254F MET* 3.0 37.7 + - + +
278F ARG 3.9 14.6 - - - +
279F ILE* 4.0 4.6 - - + -
282F GLY* 4.1 2.3 - - - -
283F PRO* 3.7 31.9 - - + +
284F ALA* 3.8 21.1 - - + +
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Residues in contact with ALA 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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247F GLU* 3.0 22.3 + - + +
248F THR* 3.9 6.3 - - - +
249F ILE 3.3 0.2 - - - -
250F GLU* 1.3 73.7 - - - +
252F SER* 1.3 61.9 + - - +
254F MET* 3.6 13.2 + - - +
255F LYS* 3.4 20.3 + - - +
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Residues in contact with SER 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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200F ILE* 5.5 3.6 - - - -
208F THR* 2.7 27.5 + - - +
234F GLU* 2.7 32.1 + - - +
236F ILE* 3.8 14.4 - - - -
248F THR 3.1 13.0 + - - -
249F ILE 3.0 8.7 + - - -
251F ALA* 1.3 78.5 - - - +
253F VAL* 1.3 57.3 + - - +
255F LYS* 3.2 6.2 + - - +
256F THR* 2.9 29.3 + - - +
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Residues in contact with VAL 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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208F THR* 4.0 11.7 - - + -
249F ILE* 3.0 18.4 + - + +
250F GLU 4.0 3.1 - - - +
252F SER* 1.3 74.5 - - - +
254F MET* 1.3 57.9 + - - +
256F THR* 3.6 5.8 - - - -
257F ASN* 2.7 30.1 + - - -
258F HIS 4.1 4.9 - - - +
259F LEU* 3.8 29.8 - - + -
279F ILE* 4.0 19.5 - - + -
284F ALA* 4.3 15.7 - - + +
287F PHE* 4.1 1.2 - - - +
288F LEU* 3.5 33.9 - - + +
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Residues in contact with MET 254 (chain F).
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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250F GLU* 3.0 24.1 + - + +
251F ALA* 3.8 12.1 - - - +
252F SER 3.3 0.2 - - - -
253F VAL* 1.3 75.5 - - - +
255F LYS* 1.3 59.5 + - - +
257F ASN* 3.5 12.1 - - - +
283F PRO* 3.8 44.2 - - + +
284F ALA* 3.9 8.3 - - + +
287F PHE* 3.6 50.3 - - + -
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Residues in contact with LYS 255 (chain F).
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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203F GLN* 3.8 16.2 + - - +
204F GLY 3.0 18.7 + - - +
205F THR* 4.2 18.3 - - + +
234F GLU* 2.6 41.6 + - - -
251F ALA 3.4 9.0 + - - +
252F SER* 3.2 6.1 + - - +
253F VAL 3.2 0.4 - - - -
254F MET* 1.3 79.5 - - - +
256F THR* 1.3 64.2 + - + +
257F ASN* 3.5 10.9 + - - -
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Residues in contact with THR 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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204F GLY 3.9 21.3 - - - +
205F THR* 3.6 15.0 - - - +
206F HIS* 3.2 6.4 - - - +
207F ILE* 3.7 24.9 - - - +
208F THR* 2.6 25.8 + - - +
234F GLU* 4.5 2.0 - - + -
252F SER* 2.9 21.3 + - - +
253F VAL* 3.6 1.6 - - - -
255F LYS* 1.3 82.6 - - + +
257F ASN* 1.3 67.3 + - - +
258F HIS* 2.9 31.7 + - - -
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Residues in contact with ASN 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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205F THR 5.7 0.2 + - - -
253F VAL 2.7 18.4 + - - -
254F MET 3.5 15.1 - - - +
255F LYS 3.5 9.8 + - - -
256F THR* 1.3 78.7 + - - +
258F HIS* 1.3 68.9 + - - +
287F PHE* 2.9 30.5 - - - +
288F LEU* 3.5 7.2 - - - -
289F ASP* 2.7 52.8 + - - +
290F ALA 3.9 1.4 + - - -
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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