Contacts of the helix formed by residues 283 - 294 (chain B) in PDB entry 5U03
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 MET 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B PRO* 6.1 0.7 - - + -
281B MET* 4.0 9.3 - - + +
282B LEU* 1.3 98.3 - - + +
284B LYS* 1.3 67.0 + - - +
286B LYS* 3.9 20.0 - - + -
287B GLU* 2.8 39.2 + - + +
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Residues in contact with LYS 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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25B THR* 3.9 18.8 + - - -
76B ARG 5.9 0.4 + - - -
77B PHE* 4.3 7.5 + - - +
281B MET* 3.6 32.9 - - + +
282B LEU 2.9 2.4 + - - -
283B MET* 1.3 82.0 - - - +
285B TRP* 1.3 84.1 + - + +
287B GLU* 4.2 1.0 - - - +
288B MET* 3.2 39.5 + - + +
534B ILE* 5.4 13.2 - - - +
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Residues in contact with TRP 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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25B THR* 3.8 35.6 + - + +
26B ILE* 6.0 0.6 - - + +
77B PHE* 3.5 34.1 - + + -
251B TYR* 3.7 43.0 - - + -
254B PRO* 4.2 17.6 - - + +
255B LEU* 3.9 24.3 - - + +
280B LYS* 5.0 2.5 - - - -
281B MET* 3.7 20.2 - - + +
282B LEU 3.1 3.6 + - - +
284B LYS* 1.3 101.9 - - + +
286B LYS* 1.3 56.2 + - - +
288B MET* 3.6 27.0 - - + +
289B ALA* 2.8 35.2 + - - +
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.5 8.9 - - + +
282B LEU* 3.0 39.1 + - + +
283B MET* 3.9 21.1 - - + -
285B TRP* 1.3 75.8 - - - +
287B GLU* 1.3 59.6 + - - +
289B ALA* 3.1 8.6 + - + +
290B ASP* 2.8 69.2 + - - +
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Residues in contact with GLU 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 MET* 2.8 34.3 + - + +
284B LYS 4.2 1.3 - - - +
286B LYS* 1.3 73.6 - - - +
288B MET* 1.3 64.1 + - + +
290B ASP* 2.9 12.6 + - + +
291B ARG* 2.8 62.1 + - + +
294B ARG* 6.1 1.8 - - - +
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Residues in contact with MET 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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251B TYR* 5.7 0.4 - - + -
284B LYS* 3.2 38.5 + - + +
285B TRP* 3.6 42.0 - - + +
286B LYS 3.2 0.8 - - - -
287B GLU* 1.3 78.4 - - + +
289B ALA* 1.3 52.5 + - - +
291B ARG* 2.9 12.0 + - - +
292B TYR* 2.7 58.4 + - + -
326B LEU* 4.4 19.7 - - + -
533B PRO* 4.8 15.5 - - - -
534B ILE* 6.3 2.2 - - - -
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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
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251B TYR* 3.5 29.1 - - + -
252B ARG* 5.4 2.0 - - - +
255B LEU* 3.8 15.9 - - + -
285B TRP 2.8 19.1 + - - +
286B LYS* 3.1 8.9 + - + +
288B MET* 1.3 76.8 - - - +
290B ASP* 1.3 61.5 + - - +
292B TYR* 3.2 2.5 + - - +
293B ASP* 2.9 37.5 + - - +
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Residues in contact with ASP 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 LYS* 2.8 53.2 + - - +
287B GLU* 2.9 11.2 + - + +
289B ALA* 1.3 77.0 - - - +
291B ARG* 1.3 51.4 + - - +
293B ASP* 3.3 8.0 + - - +
294B ARG* 2.7 67.0 + - - +
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Residues in contact with ARG 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 GLU* 2.8 49.3 + - + +
288B MET* 3.4 11.9 - - - +
290B ASP* 1.3 74.3 - - + +
292B TYR* 1.3 65.7 + - - +
294B ARG* 2.8 34.9 + - - +
295B LEU* 3.1 10.5 - - - +
326B LEU* 3.7 26.9 - - + -
329B ASN* 3.8 30.1 + - - +
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Residues in contact with TYR 292 (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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249B SER* 5.6 1.8 - - - -
251B TYR* 3.3 60.8 - + + +
252B ARG* 5.6 0.2 - - - -
288B MET* 2.7 47.8 + - + +
289B ALA 3.2 0.9 + - - +
291B ARG* 1.3 78.4 - - - +
293B ASP* 1.3 60.9 + - - +
295B LEU* 3.2 29.3 - - + +
319B LYS* 6.0 0.9 + - - +
322B GLU* 5.4 15.0 + - + +
323B HIS* 5.7 4.0 - - - -
326B LEU* 3.5 36.9 - - + +
533B PRO* 5.3 5.9 - - - +
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Residues in contact with ASP 293 (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 TYR* 3.4 1.8 + - - -
252B ARG* 2.7 37.9 + - - -
289B ALA* 2.9 22.6 + - - +
290B ASP* 3.6 7.8 - - - +
292B TYR* 1.3 79.1 - - - +
294B ARG* 1.3 63.0 + - + +
295B LEU* 3.5 3.5 + - - +
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Residues in contact with ARG 294 (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 GLU* 6.1 1.6 - - - +
290B ASP* 2.7 47.1 + - - +
291B ARG* 2.8 22.0 + - - +
293B ASP* 1.3 79.1 - - + +
295B LEU* 1.3 62.1 + - - +
329B ASN* 5.2 6.4 - - - +
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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