Contacts of the helix formed by residues 337 - 347 (chain B) in PDB entry 1NOZ
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 PHE 337 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 4.4 13.0 - - + -
270B TYR* 3.5 26.7 - + + +
273B LEU* 3.6 30.3 - - + -
274B TYR* 3.5 30.5 - + - -
277B PHE* 3.5 44.4 - - + -
278B ALA* 3.7 6.7 - - + -
332B ASP* 3.2 3.6 + - - -
335B ARG* 3.5 41.3 - - + -
336B GLY* 1.3 75.0 - - - +
338B ILE* 1.3 68.4 + - - +
340B LEU* 3.1 7.7 + - + +
341B VAL* 2.9 27.6 + - + +
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Residues in contact with ILE 338 (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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103B ARG* 3.3 37.5 - - - +
108B VAL* 4.2 26.0 - - + -
209B ILE* 4.4 23.3 - - + -
211B THR* 4.5 11.7 - - + -
268B LEU* 5.4 0.9 - - + -
270B TYR* 4.0 17.5 - - + -
273B LEU* 4.3 13.5 - - + -
332B ASP* 3.1 23.8 + - - +
336B GLY 3.4 0.8 - - - -
337B PHE* 1.3 77.6 - - - +
339B ASP* 1.3 62.0 + - - +
341B VAL* 3.4 7.4 + - + +
342B LEU* 3.3 21.7 + - + +
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Residues in contact with ASP 339 (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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370A LEU* 4.7 12.3 - - + -
101B TYR* 4.2 3.2 + - - -
103B ARG* 3.2 29.4 + - - +
336B GLY* 3.2 21.9 + - - +
337B PHE 3.1 0.2 - - - -
338B ILE* 1.3 77.9 - - - +
340B LEU* 1.3 63.8 + - - +
342B LEU* 3.0 7.7 + - - +
343B SER* 2.9 26.2 + - - -
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Residues in contact with LEU 340 (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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56A ALA* 3.5 23.3 - - + -
57A PRO* 4.1 5.4 - - + -
366A ILE* 3.8 11.7 - - + +
369A SER* 3.7 13.0 - - - +
370A LEU* 3.3 30.4 - - + +
277B PHE* 3.6 44.4 - - + -
336B GLY 3.2 7.5 + - - +
337B PHE* 3.1 10.3 + - + +
339B ASP* 1.3 78.2 - - - +
341B VAL* 1.3 54.8 + - + +
343B SER* 4.1 4.7 - - - -
344B MET* 2.8 53.4 + - + +
355B VAL* 5.5 0.2 - - + -
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Residues in contact with VAL 341 (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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209B ILE* 4.2 11.0 - - + -
268B LEU* 3.4 35.4 - - + -
273B LEU* 4.3 14.4 - - + -
277B PHE* 5.7 3.4 - - + -
337B PHE* 2.9 22.3 + - + +
338B ILE* 3.5 12.6 - - + +
339B ASP 3.1 0.2 - - - -
340B LEU* 1.3 76.6 - - + +
342B LEU* 1.3 60.0 + - - +
345B SER* 2.7 33.1 + - - -
352B PHE* 4.1 21.3 - - + +
355B VAL* 4.0 21.1 - - + +
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Residues in contact with LEU 342 (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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101B TYR* 3.4 24.9 - - + -
103B ARG* 3.8 32.3 - - - +
106B VAL* 4.0 29.6 - - + -
209B ILE* 3.7 19.1 - - + -
338B ILE* 3.3 11.4 + - + +
339B ASP* 3.0 5.1 + - - +
341B VAL* 1.3 71.6 - - - +
343B SER* 1.3 65.3 + - - +
345B SER 3.9 0.2 - - - -
346B TYR* 2.7 42.1 + - + +
352B PHE* 3.4 34.3 - - + -
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Residues in contact with SER 343 (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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369A SER* 3.7 28.4 + - - -
370A LEU* 3.0 28.5 - - - +
101B TYR* 2.6 25.8 + - - -
339B ASP* 2.9 9.9 + - - +
340B LEU 3.4 7.6 - - - -
342B LEU* 1.3 73.7 - - - +
344B MET* 1.3 65.5 + - - +
346B TYR* 2.9 4.3 + - - +
347B TYR* 2.8 25.1 + - - +
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Residues in contact with MET 344 (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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362A TRP* 3.9 11.7 - - + +
365A ILE* 4.2 14.5 - - + +
366A ILE* 3.3 37.2 - - + -
369A SER* 3.6 24.4 - - - +
277B PHE* 4.4 2.9 - - - -
340B LEU* 2.8 32.8 + - + +
343B SER* 1.3 71.8 - - - +
345B SER* 1.3 57.8 + - - +
347B TYR* 3.7 2.0 - - - +
348B ALA* 2.9 34.3 + - - +
350B MET* 3.8 3.5 - - + +
355B VAL* 3.4 50.9 - - + +
361B THR* 4.3 3.6 - - - +
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Residues in contact with SER 345 (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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5B TYR* 2.4 22.6 + - - -
341B VAL 2.7 22.5 + - - -
342B LEU 4.1 1.3 - - - -
344B MET* 1.3 77.3 - - - +
346B TYR* 1.3 53.5 + - - +
349B LYS 3.0 2.8 + - - -
350B MET* 2.8 40.5 + - - +
351B PRO 3.9 1.0 + - - -
352B PHE* 3.2 38.2 + - - -
355B VAL* 3.3 10.2 - - - +
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Residues in contact with TYR 346 (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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4B PHE* 3.7 14.6 - + + -
5B TYR* 2.6 68.9 + + - -
6B ILE* 4.3 3.1 - - - +
99B ILE* 3.5 40.6 + - + +
101B TYR* 3.4 46.9 - + + -
106B VAL* 4.6 1.1 - - + +
342B LEU* 2.7 37.9 + - + +
343B SER 2.9 3.7 + - - +
345B SER* 1.3 75.8 - - - +
347B TYR* 1.3 64.0 + - - +
349B LYS* 3.4 10.4 + - - +
352B PHE* 3.1 21.7 - + - -
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Residues in contact with TYR 347 (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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92A SER* 5.6 0.2 + - - -
347A TYR* 3.7 29.0 + + - -
348A ALA 2.7 25.8 + - - -
349A LYS* 3.6 15.3 - - + +
365A ILE* 3.7 35.0 - - + -
368A ASN* 3.2 37.3 - - + +
369A SER* 3.8 12.6 - - - +
343B SER 2.8 18.8 + - - +
344B MET* 3.7 4.5 - - - +
346B TYR* 1.3 79.6 - - - +
348B ALA* 1.3 60.2 + - - +
349B LYS* 4.7 1.6 - - - +
365B ILE* 5.3 0.2 - - + -
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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