Contacts of the helix formed by residues 281 - 291 (chain B) in PDB entry 3WOO
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B ALA* 1.3 78.3 - - - +
282B ALA* 1.3 59.8 + - - +
283B ALA* 4.1 5.6 - - + +
284B GLU* 2.9 48.4 + - + +
285B PHE* 3.2 9.0 + - - +
351B LYS* 4.4 0.2 - - - -
355B GLU* 3.5 6.7 - - - +
376B HIS* 4.1 23.1 - - + +
379B LEU* 3.7 34.3 - - + -
380B LEU* 3.8 29.4 - - + +
383B LEU* 5.6 0.9 - - + -
553B ARG* 4.4 4.5 - - - +
556B TYR* 3.4 34.5 - - + -
557B LEU* 5.5 0.9 - - + -
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Residues in contact with ALA 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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280B ALA 3.5 1.8 + - - -
281B LEU* 1.3 71.7 - - - +
283B ALA* 1.3 56.4 + - - +
285B PHE* 3.2 5.2 + - - +
286B ASP* 3.0 38.1 + - - +
351B LYS* 3.9 20.6 - - + +
352B LEU* 3.9 30.3 - - + +
355B GLU* 2.9 26.9 + - + +
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Residues in contact with ALA 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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281B LEU* 3.2 3.4 - - + +
282B ALA* 1.3 76.0 - - - +
284B GLU* 1.3 64.9 + - - +
286B ASP* 3.6 12.6 - - - +
287B ASN* 3.0 31.0 + - - +
355B GLU* 5.0 2.0 + - - +
380B LEU* 3.8 22.9 - - + -
383B LEU* 3.3 21.1 - - + -
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Residues in contact with GLU 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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280B ALA* 3.6 12.5 - - + +
281B LEU* 2.9 44.7 + - + +
283B ALA* 1.3 75.7 - - - +
285B PHE* 1.3 65.0 + - - +
287B ASN* 3.5 4.8 + - - +
288B THR* 3.0 27.7 + - - -
379B LEU* 5.1 2.4 - - - +
383B LEU* 3.9 27.4 - - + +
553B ARG* 2.8 42.7 + - - -
684B TRP* 4.2 6.5 - - + -
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Residues in contact with PHE 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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281B LEU 3.2 3.4 + - - -
282B ALA 3.4 7.9 - - - +
284B GLU* 1.3 79.5 - - - +
286B ASP* 1.4 70.5 + - - +
288B THR* 3.0 3.5 + - - -
289B ALA* 2.9 38.4 + - + -
342B PHE* 3.5 49.6 - + + -
347B ALA* 3.5 22.9 - - + -
348B ALA* 3.5 31.4 - - + -
351B LYS* 3.8 26.0 - - + -
684B TRP* 3.8 38.3 - + + -
685B VAL* 5.6 0.2 - - + -
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Residues in contact with ASP 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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282B ALA* 3.0 26.5 + - - +
283B ALA* 3.3 13.3 + - - +
285B PHE* 1.4 90.4 - - - +
287B ASN* 1.3 62.5 + - - +
289B ALA* 4.5 2.0 - - - +
290B GLN* 2.8 54.6 + - - +
348B ALA* 4.5 11.8 - - - +
351B LYS* 5.5 0.2 - - - +
352B LEU* 6.0 2.3 - - - +
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Residues in contact with ASN 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 ALA* 3.0 22.3 + - - +
284B GLU* 3.6 5.4 - - - +
286B ASP* 1.3 80.8 - - - +
288B THR* 1.3 58.5 + - - +
290B GLN* 5.1 0.4 - - - -
291B TRP* 2.9 30.7 + - - +
292B THR* 3.1 12.1 + - - +
383B LEU* 4.0 24.8 - - + +
384B GLU* 5.2 1.2 + - - -
387B LYS* 3.6 29.8 - - - +
390B ARG* 2.5 31.6 + - - +
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Residues in contact with THR 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 GLU 3.0 12.8 + - - -
285B PHE* 3.0 8.5 + - - -
287B ASN* 1.3 78.8 - - - +
289B ALA* 1.3 60.9 + - - +
292B THR* 3.2 17.8 + - + +
293B TYR* 2.9 73.1 + - + +
342B PHE* 5.5 0.4 - - + -
684B TRP* 3.4 28.9 - - + -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 2.9 30.4 + - + +
286B ASP* 4.2 2.5 - - - +
288B THR* 1.3 78.1 - - - +
290B GLN* 1.3 60.7 + - + +
294B PRO* 3.2 20.6 - - - +
339B LEU* 3.6 17.8 - - + +
342B PHE* 3.8 28.9 - - + -
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Residues in contact with GLN 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 ASP* 2.8 42.3 + - - +
287B ASN* 5.1 0.4 - - - -
289B ALA* 1.3 78.8 - - + +
291B TRP* 1.3 61.2 + - + +
294B PRO* 3.3 13.9 - - - +
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Residues in contact with TRP 291 (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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287B ASN* 2.9 13.0 + - - +
290B GLN* 1.3 81.0 - - + +
292B THR* 1.3 89.9 + - + +
293B TYR 3.5 1.6 - - - -
294B PRO* 3.5 2.0 - - - +
295B THR* 2.5 58.5 + - + +
390B ARG* 3.3 90.2 - - + +
391B ASP* 3.8 22.5 + - - -
394B LEU* 3.7 29.8 - - + -
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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