Contacts of the helix formed by residues 245 - 257 (chain B) in PDB entry 3EXG
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B GLY 3.3 18.1 - - - +
197B LYS* 3.1 24.2 - - - +
198B ALA* 2.8 37.0 + - + +
238B MET* 5.4 2.9 + - - +
240B THR* 4.9 2.0 + - - -
243B PRO 3.7 0.4 + - - -
244B MET* 1.3 72.6 - - - +
246B MET* 1.3 60.2 + - - +
247B GLU* 3.5 13.5 + - - +
248B THR* 2.7 40.3 + - - -
249B ILE* 3.7 16.7 + - - +
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B MET* 3.2 21.0 + - + +
245B ASP* 1.3 73.0 - - - +
247B GLU* 1.3 69.2 + - - +
249B ILE* 3.2 23.3 + - + +
250B GLU* 2.9 39.0 + - + +
275B ILE* 3.4 35.9 - - + +
278B ARG* 3.6 50.0 - - + +
279B ILE* 3.7 23.6 - - + +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LYS* 3.1 27.3 + - - -
245B ASP* 3.4 7.0 - - - +
246B MET* 1.3 77.0 - - - +
248B THR* 1.3 51.6 + - - +
250B GLU* 2.8 29.7 + - - +
251B ALA* 2.8 19.3 + - - +
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LYS* 4.4 6.8 + - - +
198B ALA* 4.5 17.4 + - + +
200B ILE* 4.2 26.7 - - + -
236B ILE* 4.2 13.2 - - + -
245B ASP* 2.7 36.6 + - - -
247B GLU* 1.3 76.9 - - - +
249B ILE* 1.3 66.2 + - - +
251B ALA* 3.4 8.5 + - + +
252B SER* 3.1 21.1 + - - -
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ALA* 5.8 0.4 - - + -
208B THR* 4.8 2.7 - - + -
210B VAL* 3.8 45.8 - - + -
236B ILE* 4.3 19.1 - - + -
238B MET* 4.7 8.5 - - + -
244B MET* 5.5 2.7 - - + -
245B ASP 3.7 15.9 + - - +
246B MET* 3.2 35.0 + - + +
248B THR* 1.3 81.4 - - - +
250B GLU* 1.3 61.4 + - - +
252B SER* 3.6 1.6 + - - -
253B VAL* 3.0 34.0 + - + +
259B LEU* 4.5 6.1 - - + -
275B ILE* 4.3 15.3 - - + -
279B ILE* 4.8 1.3 - - + -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B MET* 2.9 33.0 + - + +
247B GLU* 2.8 19.2 + - - +
249B ILE* 1.3 70.1 - - - +
251B ALA* 1.3 70.3 + - - +
253B VAL* 2.9 11.4 + - - +
254B MET* 3.0 25.6 + - + +
278B ARG 4.3 3.5 - - - +
279B ILE* 4.2 16.4 - - + +
282B GLY* 3.4 13.0 + - - -
283B PRO* 3.3 38.6 - - + +
284B ALA* 3.7 19.5 + - + +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLU 2.8 13.8 + - - +
248B THR* 3.5 12.8 - - + +
250B GLU* 1.3 73.2 - - - +
252B SER* 1.3 62.7 + - - +
254B MET* 3.2 26.8 + - + +
255B LYS* 3.3 11.3 + - - +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ILE* 5.7 2.9 - - - -
208B THR* 2.6 32.2 + - - +
234B GLU* 3.0 28.2 + - - +
236B ILE* 4.0 14.8 - - - -
248B THR* 3.1 14.0 + - - -
249B ILE 3.9 3.8 - - - -
251B ALA* 1.3 79.6 - - - +
253B VAL* 1.3 57.5 + - - +
255B LYS* 3.1 5.5 + - - +
256B THR* 2.9 29.8 + - - +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B THR* 3.9 10.5 - - - +
249B ILE* 3.0 22.5 + - + +
250B GLU 2.9 5.2 + - - +
252B SER* 1.3 73.1 - - - +
254B MET* 1.3 62.3 + - - +
256B THR* 4.1 1.8 - - - -
257B ASN* 2.7 30.8 + - - -
258B HIS 4.0 16.8 - - - +
259B LEU* 4.1 17.3 - - + -
279B ILE* 4.1 12.8 - - + -
284B ALA* 4.2 19.7 - - + +
287B PHE* 4.0 2.7 - - + +
288B LEU* 3.1 32.5 - - + -
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Residues in contact with MET 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 3.0 15.7 + - + +
251B ALA* 3.3 33.4 - - - +
253B VAL* 1.3 78.9 - - - +
255B LYS* 1.3 60.2 + - - +
257B ASN* 4.2 5.0 + - - -
283B PRO* 5.2 11.4 - - + -
284B ALA* 3.9 19.3 - - + -
287B PHE* 3.5 54.2 - - + -
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Residues in contact with LYS 255 (chain B).
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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203B GLN* 4.6 8.7 + - - +
204B GLY 3.6 18.1 + - - +
205B THR* 4.0 24.3 - - + +
234B GLU* 3.0 36.6 + - - +
251B ALA 3.3 9.0 + - - +
252B SER* 3.1 8.1 + - - +
253B VAL 3.1 0.6 - - - -
254B MET* 1.3 80.7 - - - +
256B THR* 1.3 63.5 + - + +
257B ASN* 3.7 8.3 - - - +
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLY 4.2 10.5 - - - +
205B THR 3.5 20.9 - - - +
206B HIS* 3.2 20.8 - - - +
207B ILE* 3.8 11.2 - - - +
208B THR* 2.9 23.6 + - - +
234B GLU* 4.4 1.8 - - + +
252B SER* 2.9 18.6 + - - +
253B VAL 4.1 0.5 + - - -
255B LYS* 1.3 80.1 - - + +
257B ASN* 1.3 69.0 + - - +
258B HIS* 3.0 32.0 + - - -
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Residues in contact with ASN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B VAL 2.7 19.8 + - - -
254B MET 4.2 6.9 + - - -
255B LYS 3.7 8.8 - - - +
256B THR* 1.3 74.3 + - - +
258B HIS* 1.3 69.6 + - + +
287B PHE* 2.7 42.2 + - - +
288B LEU* 3.7 6.6 - - - +
289B ASP* 3.0 45.8 + - - +
290B ALA 3.9 1.0 + - - -
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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