Contacts of the helix formed by residues 273 - 284 (chain B) in PDB entry 5NEU
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 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A LEU* 3.7 19.7 - - + -
311A GLU* 2.9 26.4 + - - +
337A PHE* 3.9 2.2 - - + -
339A ARG* 3.4 30.3 - - - +
239B GLY* 4.5 13.0 - - - +
250B PRO* 5.9 0.7 - - + -
271B TYR 4.6 2.2 - - - +
272B PRO* 1.3 78.8 - - - +
274B ILE* 1.3 67.1 + - - +
276B GLN* 3.4 28.2 + - - +
277B LEU* 3.2 20.4 + - - +
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Residues in contact with ILE 274 (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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271A GLN* 5.4 1.8 - - - +
272A MET 5.7 0.9 - - - +
273A ALA* 4.5 24.7 - - + +
299A LEU* 5.5 10.2 - - + +
301A MET* 3.7 24.0 - - + -
311A GLU* 5.5 0.4 - - - -
205B PHE* 4.4 16.2 - - + -
238B PHE* 4.8 13.0 - - + -
273B THR* 1.3 74.6 - - - +
275B GLY* 1.3 60.8 + - - +
277B LEU* 3.1 19.8 + - + +
278B ILE* 2.9 40.5 + - + +
303B TYR* 5.6 8.5 - - + -
306B LEU* 5.0 15.0 - - + -
307B ILE* 4.5 13.0 - - + -
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Residues in contact with GLY 275 (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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301A MET* 3.7 24.1 - - - +
311A GLU* 3.7 17.1 + - - -
337A PHE* 3.5 13.1 - - - -
273B THR* 3.3 3.8 + - - -
274B ILE* 1.3 79.6 - - - +
276B GLN* 1.3 55.8 + - - +
278B ILE* 3.9 1.4 - - - +
279B ASP* 2.9 31.2 + - - +
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Residues in contact with GLN 276 (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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337A PHE* 3.7 19.8 - - + -
209B MET* 3.4 14.5 - - + +
250B PRO* 5.7 3.0 - - - +
251B ASN* 3.5 24.5 + - - +
252B ASP 5.0 1.8 - - - -
253B GLY* 4.5 16.3 + - - +
272B PRO* 3.3 20.7 - - - +
273B THR* 3.4 30.4 + - - +
274B ILE 3.2 0.6 - - - -
275B GLY* 1.3 73.2 - - - +
277B LEU* 1.3 60.5 + - - +
279B ASP* 4.3 3.6 - - - -
280B LYS* 2.9 38.1 + - + +
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Residues in contact with LEU 277 (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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205B PHE* 3.7 50.9 - - + +
208B ILE* 4.4 20.6 - - + -
209B MET* 3.7 20.0 - - + -
272B PRO* 4.4 9.4 - - + +
273B THR 3.2 15.1 + - - +
274B ILE* 3.1 20.3 + - + +
276B GLN* 1.3 75.2 - - - +
278B ILE* 1.3 59.9 + - - +
281B LEU* 2.9 42.4 + - + +
288B LEU* 6.5 0.2 - - + -
307B ILE* 4.0 20.9 - - + -
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Residues in contact with ILE 278 (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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301A MET* 3.7 33.0 - - + -
308A LYS* 3.7 28.0 + - + +
309A LEU* 4.6 12.3 - - + +
274B ILE* 2.9 19.0 + - + +
275B GLY 4.2 2.5 - - - +
277B LEU* 1.3 76.4 - - - +
279B ASP* 1.3 61.9 + - - +
282B VAL* 3.2 25.5 + - - +
306B LEU* 3.4 24.7 - - + +
307B ILE* 3.8 22.2 - - + -
308B PRO* 3.7 19.5 - - + -
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Residues in contact with ASP 279 (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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308A LYS* 5.1 13.8 - - + +
337A PHE* 4.7 12.1 - - + -
275B GLY 2.9 21.3 + - - +
276B GLN* 4.0 5.6 - - - +
278B ILE* 1.3 78.8 - - - +
280B LYS* 1.3 66.0 + - - +
282B VAL* 4.7 0.2 - - - +
283B GLN* 2.7 64.4 + - - +
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Residues in contact with LYS 280 (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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209B MET* 3.6 26.0 - - + -
212B ALA* 4.7 10.1 - - + +
213B VAL* 4.3 13.6 - - + +
253B GLY* 4.1 24.9 + - - -
254B LEU* 5.7 2.6 - - - +
276B GLN* 2.9 24.3 + - + +
277B LEU* 5.1 0.2 - - - -
279B ASP* 1.3 87.8 + - - +
281B LEU* 1.3 63.7 + - + +
282B VAL 3.2 0.4 - - - -
283B GLN* 4.0 15.0 + - - +
284B ASN* 2.7 50.9 + - - +
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Residues in contact with LEU 281 (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 ILE* 3.7 32.3 - - + -
209B MET* 6.3 0.4 - - + -
212B ALA* 4.1 10.8 - - + -
228B LEU* 4.8 0.9 - - + -
277B LEU* 2.9 32.6 + - + +
278B ILE* 5.0 0.7 - - - -
280B LYS* 1.3 77.8 - - + +
282B VAL* 1.3 61.9 + - + +
285B ASN* 3.3 1.7 + - - -
286B VAL* 2.7 67.4 + - + +
287B LEU* 5.9 0.3 - - - +
288B LEU* 4.3 23.8 - - + -
307B ILE* 4.3 21.5 - - + -
308B PRO 6.1 0.2 - - - +
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Residues in contact with VAL 282 (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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308A LYS* 3.4 24.2 - - - +
278B ILE* 3.2 22.2 + - + +
281B LEU* 1.3 82.1 - - + +
283B GLN* 1.3 66.0 + - - +
284B ASN 3.3 0.2 - - - -
285B ASN* 3.3 12.3 + - - +
307B ILE* 5.7 0.9 - - + -
308B PRO* 3.9 32.3 - - + +
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Residues in contact with GLN 283 (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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308A LYS* 6.0 0.4 - - - +
279B ASP* 2.7 48.6 + - - +
280B LYS* 4.0 15.6 + - - +
282B VAL* 1.3 80.3 - - - +
284B ASN* 1.3 67.3 + - - +
285B ASN* 3.6 1.2 + - - +
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Residues in contact with ASN 284 (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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212B ALA 3.3 25.6 + - - +
213B VAL* 3.6 12.3 - - - +
215B LYS* 3.6 32.7 + - - +
226B HIS* 3.7 8.0 + - - -
280B LYS* 2.7 52.7 + - - +
283B GLN* 1.3 81.0 - - - +
285B ASN* 1.3 71.1 + - - +
286B VAL* 3.8 6.9 - - + +
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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