Contacts of the helix formed by residues 283 - 294 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A PRO* 6.1 0.4 - - + -
281A MET* 4.0 8.8 - - + +
282A LEU* 1.3 97.9 - - + +
284A LYS* 1.3 67.1 + - - +
286A LYS* 3.9 20.2 - - + -
287A GLU* 2.8 39.2 + - + +
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.9 19.2 + - - -
76A ARG 5.9 0.4 + - - -
77A PHE* 4.3 7.5 + - - +
281A MET* 3.6 33.5 - - + +
282A LEU 2.9 2.8 + - - -
283A MET* 1.3 82.1 - - - +
285A TRP* 1.3 83.6 + - + +
287A GLU* 4.2 0.7 - - - +
288A MET* 3.2 40.1 + - + +
534A ILE* 5.4 13.3 - - + +
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Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.8 35.6 + - + +
26A ILE* 6.4 0.2 - - + -
77A PHE* 3.5 34.3 - + - -
251A TYR* 3.7 42.9 - - + -
254A PRO* 4.2 17.0 - - + +
255A LEU* 3.9 23.8 - - + +
280A LYS* 5.0 2.7 - - - -
281A MET* 3.7 18.6 - - + +
282A LEU 3.1 3.3 + - - +
284A LYS* 1.3 102.5 - - + +
286A LYS* 1.3 56.4 + - - +
288A MET* 3.6 26.6 - - + +
289A ALA* 2.8 34.9 + - - +
292A TYR* 6.1 0.2 - + - -
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Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 4.5 8.9 - - + +
282A LEU* 3.0 38.7 + - + +
283A MET* 3.9 21.1 - - + -
285A TRP* 1.3 75.6 - - - +
287A GLU* 1.3 61.7 + - - +
289A ALA* 3.1 8.4 + - + +
290A ASP* 2.8 68.0 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A MET* 2.8 34.9 + - + +
284A LYS 4.2 1.1 - - - +
286A LYS* 1.3 72.7 - - - +
288A MET* 1.3 65.6 + - + +
290A ASP* 2.9 14.0 + - + +
291A ARG* 2.8 61.0 + - + +
294A ARG* 6.1 1.3 - - - +
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 5.7 0.2 - - + -
284A LYS* 3.2 39.4 + - + +
285A TRP* 3.6 42.0 - - + +
286A LYS 3.2 0.4 - - - -
287A GLU* 1.3 78.8 - - + +
289A ALA* 1.3 51.6 + - - +
291A ARG* 2.9 12.6 + - - +
292A TYR* 2.7 58.2 + - + -
326A LEU* 4.4 21.1 - - + -
533A PRO* 4.8 15.5 - - - -
534A ILE* 6.3 2.0 - - - -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.5 28.9 + - + +
252A ARG* 5.4 1.8 - - - +
255A LEU* 3.8 15.9 - - + -
285A TRP 2.8 19.1 + - - +
286A LYS* 3.4 8.3 - - + +
288A MET* 1.3 75.4 - - - +
290A ASP* 1.3 61.4 + - - +
292A TYR* 3.2 2.5 + - - +
293A ASP* 2.9 36.9 + - - +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LYS* 2.8 53.2 + - - +
287A GLU* 2.9 11.3 + - + +
289A ALA* 1.3 78.0 - - - +
291A ARG* 1.3 52.9 + - - +
293A ASP* 3.3 8.5 + - - +
294A ARG* 2.7 64.7 + - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU* 2.8 49.5 + - + +
288A MET* 3.4 11.4 - - - +
290A ASP* 1.3 77.0 - - + +
292A TYR* 1.3 64.4 + - - +
294A ARG* 2.8 34.1 - - - +
295A LEU* 3.1 9.7 - - - +
326A LEU* 3.7 27.1 - - + -
329A ASN* 3.8 29.7 + - - +
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Residues in contact with TYR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A SER* 5.6 1.6 - - - -
251A TYR* 3.3 60.4 - + + +
252A ARG* 5.6 0.2 - - - -
288A MET* 2.7 47.8 + - + +
289A ALA 3.6 0.7 - - - +
291A ARG* 1.3 77.0 - - - +
293A ASP* 1.3 62.1 + - - +
295A LEU* 3.2 29.9 - - + +
319A LYS* 5.9 1.4 + - - +
322A GLU* 5.4 15.6 + - + +
323A HIS* 5.7 4.0 - - - -
326A LEU* 3.5 37.2 - - + +
533A PRO* 5.3 5.7 - - - +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.4 2.5 + - - -
252A ARG* 2.7 37.7 + - - -
289A ALA* 2.9 21.2 + - - +
290A ASP* 3.6 8.7 - - - +
292A TYR* 1.3 79.2 - - - +
294A ARG* 1.3 62.1 + - + +
295A LEU* 3.5 4.2 + - - +
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU* 6.1 1.6 - - - +
290A ASP* 2.7 46.9 + - - +
291A ARG* 2.8 21.4 + - - +
293A ASP* 1.3 79.1 - - + +
295A LEU* 1.3 61.0 + - - +
329A ASN* 5.2 6.8 - - - +
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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