Contacts of the helix formed by residues 289 - 297 (chain B) in PDB entry 2NT0
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 PRO 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LEU* 1.3 86.2 - - + +
290B HIS* 1.3 66.3 + - - +
291B TRP 3.3 2.5 - - - -
292B ALA* 3.1 5.6 + - + +
293B LYS* 2.9 32.7 + - + +
322B ALA 3.5 17.7 - - - +
323B THR* 4.6 0.7 - - - -
326B GLU* 3.9 18.8 - - + -
327B THR* 3.5 19.3 - - + +
330B LEU* 3.9 20.6 - - + -
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Residues in contact with HIS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 4.0 18.3 - - + +
254B GLU* 4.6 5.5 + - - -
287B LEU 3.5 6.0 + - - +
288B LEU 3.4 2.6 - - - -
289B PRO* 1.3 78.5 - - - +
291B TRP* 1.3 73.3 + + - +
293B LYS* 3.1 15.4 + - - +
294B VAL* 3.1 48.2 + - + +
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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
----------------------------------------------------------
236B PRO* 3.3 29.8 - - + -
237B SER* 4.6 12.1 - - - -
240B LEU* 5.3 1.3 - - + -
251B PHE* 3.2 28.3 - - + -
252B THR 3.9 1.6 - - - -
253B PRO* 3.6 45.1 - - + +
256B GLN* 3.5 36.1 - - + -
280B MET* 3.8 8.5 - - + -
281B LEU* 3.7 28.0 - - + -
287B LEU* 2.8 55.7 + - + +
288B LEU* 4.7 1.6 - - + -
290B HIS* 1.3 82.2 - + - +
292B ALA* 1.3 61.8 + - - +
294B VAL* 3.4 1.6 + - - +
295B VAL* 3.2 30.2 + - + +
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Residues in contact with ALA 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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280B MET* 3.8 12.2 - - + +
288B LEU* 3.8 9.0 - - + +
289B PRO 3.1 9.6 + - - +
291B TRP* 1.3 73.2 - - - +
293B LYS* 1.3 61.2 + - - +
296B LEU* 2.8 38.3 + - + +
308B ILE* 3.9 10.5 - - + -
327B THR* 3.7 30.1 - - + -
331B PHE* 3.7 14.6 - - + -
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Residues in contact with LYS 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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289B PRO* 2.9 29.7 + - + +
290B HIS* 3.1 14.8 + - - +
292B ALA* 1.3 76.4 - - - +
294B VAL* 1.3 57.7 + - + +
297B THR* 2.7 41.7 + - + +
330B LEU* 3.7 36.4 - - + +
331B PHE* 3.8 11.7 - - + -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 3.6 40.8 - - + +
254B GLU* 3.6 19.5 - - + +
257B ARG* 3.4 29.3 + - - +
290B HIS* 3.1 42.0 + - + +
291B TRP 3.8 1.3 - - - +
292B ALA 3.3 0.2 - - - -
293B LYS* 1.3 78.8 - - + +
295B VAL* 1.3 63.9 + - - +
297B THR* 3.8 8.2 + - - -
298B ASP* 4.2 2.3 + - - +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO 3.9 19.7 - - - +
256B GLN* 4.4 9.9 - - + +
257B ARG* 3.9 13.9 - - + +
260B ILE* 4.3 9.6 - - + -
280B MET* 3.6 32.5 - - + -
291B TRP* 3.2 16.6 + - + +
294B VAL* 1.3 77.9 - - + +
296B LEU* 1.3 63.0 + - + +
298B ASP* 3.4 20.4 + - - +
301B ALA* 3.5 22.9 - - + +
302B ALA 4.2 0.3 + - - -
305B VAL* 4.2 16.6 - - + -
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Residues in contact with LEU 296 (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 MET* 4.0 11.4 - - - -
292B ALA* 2.8 25.5 + - + +
295B VAL* 1.3 70.4 - - + +
297B THR* 1.3 60.9 + - - +
298B ASP 3.2 5.9 + - - -
299B PRO* 4.8 0.7 - - - +
302B ALA* 3.5 30.9 - - + +
305B VAL* 3.7 33.9 - - + +
308B ILE* 3.8 29.4 - - + -
331B PHE* 3.6 37.1 - - + -
334B THR* 4.0 15.7 - - + +
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Residues in contact with THR 297 (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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293B LYS* 2.7 29.0 + - + +
294B VAL* 3.8 5.7 + - - -
296B LEU* 1.3 77.8 - - - +
298B ASP* 1.3 56.7 + - - +
299B PRO* 3.3 12.5 - - - +
331B PHE* 3.9 20.9 - - + -
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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