Contacts of the helix formed by residues 282 - 290 (chain B) in PDB entry 1B3U
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 LEU 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B MET* 5.2 3.8 - - + -
247B LEU* 4.8 19.7 - - + -
266B PHE* 3.5 29.3 - - + +
269B LEU* 4.2 7.0 - - + -
270B GLN* 3.6 38.1 - - + +
273B VAL* 3.7 17.3 - - + -
277B ILE* 3.7 2.2 + - + +
278B THR* 3.0 24.0 + - - +
281B ASP* 1.3 79.5 - - + +
283B VAL* 1.3 58.9 + - - +
285B ALA* 4.0 5.6 - - + -
286B PHE* 2.8 37.1 + - - +
308B PHE* 4.2 5.4 - - + -
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Residues in contact with VAL 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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278B THR 2.9 21.6 + - - +
279B LYS* 3.2 24.2 - - + +
282B LEU* 1.3 78.5 - - - +
284B PRO* 1.3 70.1 - - + +
286B PHE* 3.3 9.0 + - - +
287B GLN* 3.3 24.5 + - + +
308B PHE* 4.1 19.2 - - + -
312B LEU* 5.0 8.3 - - + -
316B CYS* 5.9 1.3 - - - -
320B VAL* 4.7 19.1 - - + -
324B GLN* 4.1 22.7 - - + +
325B ILE* 6.3 3.6 - - + -
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Residues in contact with PRO 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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279B LYS 4.4 0.9 - - - +
280B THR 3.5 22.4 - - - +
281B ASP* 3.1 18.6 - - - +
283B VAL* 1.3 97.2 - - + +
285B ALA* 1.3 58.9 + - - +
287B GLN* 3.3 18.6 + - - +
288B ASN* 2.8 32.1 + - - +
324B GLN* 6.2 0.4 - - - +
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Residues in contact with ALA 285 (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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251B ALA* 5.0 16.3 - - + +
266B PHE* 4.2 10.8 - - + -
281B ASP 3.1 20.1 + - - +
282B LEU* 3.6 11.4 - - + +
283B VAL 3.2 0.2 - - - -
284B PRO* 1.3 76.5 - - - +
286B PHE* 1.3 64.3 + - - +
288B ASN* 3.2 13.8 + - - +
289B LEU* 3.1 24.6 + - + +
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Residues in contact with PHE 286 (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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263B ALA* 5.9 0.9 - - - -
266B PHE* 3.5 38.1 - + + -
282B LEU 2.8 21.2 + - - +
283B VAL 3.6 5.2 - - - +
285B ALA* 1.3 74.0 - - - +
287B GLN* 1.3 63.1 + - + +
289B LEU* 3.1 9.9 + - + +
290B MET* 3.0 58.6 + - + +
301B ALA* 3.4 39.3 - - + -
304B LYS* 4.1 15.0 - - + -
305B VAL* 4.0 20.4 - - + -
308B PHE* 3.9 26.5 - + + -
325B ILE* 5.3 7.0 - - + -
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Residues in contact with GLN 287 (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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283B VAL* 3.5 19.6 + - + +
284B PRO* 3.3 17.5 + - - +
285B ALA 3.2 0.6 - - - -
286B PHE* 1.3 76.4 - - + +
288B ASN* 1.3 65.5 + - - +
290B MET* 3.1 26.0 + - + +
291B LYS* 3.1 25.1 + - - +
324B GLN* 3.3 57.7 - - + +
325B ILE* 5.8 2.5 - - + -
328B CYS* 3.9 16.9 - - - -
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Residues in contact with ASN 288 (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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284B PRO* 2.8 27.3 + - - +
285B ALA* 3.2 10.7 + - - +
287B GLN* 1.3 77.1 - - - +
289B LEU* 1.3 60.7 + - + +
291B LYS* 3.1 11.1 + - - +
292B ASP* 3.0 24.8 + - - +
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Residues in contact with LEU 289 (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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251B ALA* 4.6 13.9 - - + +
259B ARG* 4.0 23.1 - - + +
262B VAL* 4.2 12.6 - - + -
263B ALA* 4.2 11.4 - - + -
266B PHE* 3.6 36.8 - - + -
285B ALA* 3.1 16.8 + - + +
286B PHE* 3.1 11.2 + - + +
288B ASN* 1.3 73.0 - - + +
290B MET* 1.3 61.1 + - - +
291B LYS 2.9 5.2 - - - -
292B ASP* 3.0 22.9 + - - +
297B VAL* 3.7 28.7 - - + +
298B ARG* 3.8 6.8 - - - +
301B ALA* 4.1 13.5 - - + -
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Residues in contact with MET 290 (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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286B PHE* 3.0 46.8 + - + +
287B GLN* 3.1 24.6 + - + +
289B LEU* 1.3 74.8 - - - +
291B LYS* 1.3 62.6 + - + +
292B ASP 3.5 0.4 - - - -
298B ARG* 3.3 20.6 - - - +
301B ALA* 3.9 20.0 - - + -
305B VAL* 4.6 2.9 - - - -
325B ILE* 4.7 13.2 - - + -
328B CYS* 3.8 31.6 - - + +
329B ILE* 4.3 12.8 - - - -
332B LEU* 3.9 37.1 - - + +
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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