Contacts of the helix formed by residues 278 - 285 (chain A) in PDB entry 1BOO
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ARG* 4.8 0.7 - - - +
250A PHE* 3.6 31.7 + - + +
252A ALA* 3.6 36.6 - - + +
255A PRO* 4.2 2.7 - - + -
274A GLY 4.5 0.2 + - - -
276A SER* 3.4 2.4 + - - -
277A ASN* 1.3 74.7 - - - +
279A THR* 1.3 66.2 + - - +
281A LEU* 3.1 12.2 + - + +
282A VAL* 2.8 18.8 + - - +
306A ARG* 3.4 25.7 + - - +
401A SAH 3.2 17.8 + - - -
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Residues in contact with THR 279 (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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51A MET* 4.0 16.8 + - + +
250A PHE* 3.8 15.4 - - - -
255A PRO* 4.4 15.0 - - + -
259A ILE* 4.5 2.2 - - + -
269A VAL* 3.8 29.6 - - + +
270A VAL 4.9 0.4 - - - +
271A ASP* 2.4 43.0 + - + +
277A ASN* 3.1 1.7 - - - -
278A THR* 1.3 75.9 - - - +
280A GLY* 1.3 67.1 + - - +
282A VAL* 2.7 16.6 + - - +
283A ALA* 2.8 11.6 + - - +
290A TRP* 6.1 0.2 - - + -
401A SAH 6.1 0.2 - - - -
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Residues in contact with GLY 280 (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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277A ASN* 3.3 17.3 + - - -
279A THR* 1.3 79.2 - - - +
281A LEU* 1.3 62.0 + - - +
283A ALA* 4.2 0.4 - - - -
284A GLU* 2.9 28.4 + - - +
290A TRP* 3.3 37.9 + - - -
292A SER* 4.3 1.0 + - - -
307A PHE* 4.0 4.0 - - - -
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Residues in contact with LEU 281 (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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252A ALA* 5.4 2.2 - - + -
277A ASN 3.1 14.2 + - - +
278A THR* 3.1 15.9 - - + +
279A THR 2.8 4.2 + - - -
280A GLY* 1.3 72.7 - - - +
282A VAL* 1.3 65.0 + - + +
284A GLU* 3.0 19.0 + - + +
285A ARG* 3.2 35.2 + - + +
306A ARG* 3.6 54.3 - - + +
307A PHE* 3.6 22.0 - - + -
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Residues in contact with VAL 282 (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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252A ALA* 3.6 34.3 - - + +
255A PRO* 3.9 8.5 - - + -
256A GLU* 3.6 35.9 - - + +
259A ILE* 3.7 12.6 - - + -
278A THR 2.8 17.3 + - - +
279A THR 2.7 10.8 + - - +
281A LEU* 1.3 72.6 - - + +
283A ALA* 1.3 63.0 + - - +
284A GLU 2.9 1.6 + - - -
285A ARG* 3.1 16.6 + - - +
286A GLU* 3.0 38.9 + - + +
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Residues in contact with ALA 283 (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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259A ILE* 3.7 19.6 - - + +
269A VAL* 4.1 14.6 - - + -
279A THR 2.8 18.4 + - - +
280A GLY* 3.8 5.2 - - - +
282A VAL* 1.3 72.3 - - - +
284A GLU* 1.3 57.6 + - - +
286A GLU 4.0 1.1 - - - +
287A SER 3.4 1.6 + - - -
288A ARG* 2.8 44.1 + - + +
290A TRP* 3.8 24.0 - - + -
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Residues in contact with GLU 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* 2.6 31.3 + - - -
26A SER* 4.3 7.4 + - - -
27A ASN* 2.7 47.4 + - - +
280A GLY 2.9 9.7 + - - +
281A LEU* 3.1 11.7 - - + +
282A VAL 2.9 1.2 + - - -
283A ALA* 1.3 73.2 - - - +
285A ARG* 1.3 58.3 + - - +
286A GLU 3.0 3.8 - - - -
287A SER* 3.0 18.2 + - - -
290A TRP* 2.9 23.1 + - + +
307A PHE* 3.7 17.4 - - + -
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Residues in contact with ARG 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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252A ALA* 3.8 24.4 - - - +
256A GLU* 3.2 25.7 + - - -
281A LEU* 3.6 35.3 - - + +
282A VAL* 3.1 18.8 + - - +
284A GLU* 1.3 78.1 - - + +
286A GLU* 1.3 65.1 + - + +
287A SER* 3.4 2.9 + - - -
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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