Contacts of the helix formed by residues 337 - 348 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TYR* 3.0 36.3 + + + +
273A LEU* 3.7 28.3 - - + -
274A TYR* 3.8 15.0 - + - -
277A PHE* 3.6 34.5 - + + -
278A ALA* 3.5 32.8 - - + -
332A ASP* 3.3 0.2 + - - -
335A ARG* 3.4 38.4 - - + -
336A GLY* 1.3 74.8 - - - +
338A ILE* 1.3 65.9 + - - +
340A LEU* 3.1 7.7 + - + +
341A VAL* 3.0 25.1 + - - +
56B ALA* 3.8 16.8 - - + -
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Residues in contact with ILE 338 (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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103A ARG* 3.4 30.3 - - - +
108A VAL* 3.8 20.6 - - + -
209A ILE* 4.2 28.9 - - + -
211A THR* 4.3 17.3 - - + +
268A LEU* 5.5 1.3 - - + +
270A TYR* 3.8 9.4 - - + -
273A LEU* 4.0 18.6 - - + -
329A GLN* 6.2 0.4 - - - +
332A ASP* 3.3 30.0 + - - +
337A PHE* 1.3 76.2 - - - +
339A ASP* 1.3 62.5 + - - +
341A VAL* 3.4 8.6 + - + +
342A LEU* 3.3 22.9 + - + +
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Residues in contact with ASP 339 (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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101A TYR* 4.9 1.6 + - - -
103A ARG* 2.8 42.9 + - - +
336A GLY* 3.2 18.3 + - - +
337A PHE 3.1 0.2 - - - -
338A ILE* 1.3 79.5 - - - +
340A LEU* 1.3 56.2 + - - +
342A LEU* 3.2 10.3 + - - +
343A SER* 2.9 28.7 + - - -
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Residues in contact with LEU 340 (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 PHE* 3.9 36.3 - - + -
336A GLY 3.2 9.3 + - - +
337A PHE* 3.1 11.9 + - + +
339A ASP* 1.3 75.4 - - - +
341A VAL* 1.3 58.5 + - + +
343A SER* 2.6 27.2 + - - +
344A MET* 2.7 38.7 + - + +
56B ALA* 3.9 28.7 - - + +
57B PRO* 3.8 20.4 - - + -
366B ILE* 4.2 7.0 - - + +
369B SER* 3.7 14.4 - - - +
370B LEU* 4.5 4.0 - - + -
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 4.8 5.4 - - + -
268A LEU* 3.8 18.4 - - + -
273A LEU* 4.0 22.9 - - + -
277A PHE* 5.2 2.9 - - + -
337A PHE 3.0 19.7 + - - +
338A ILE* 3.5 10.8 - - + +
340A LEU* 1.3 76.3 - - - +
342A LEU* 1.3 52.6 + - - +
345A SER* 2.7 40.7 + - - -
352A PHE* 3.7 42.2 - - + +
355A VAL* 3.4 22.9 - - + +
356A MET* 5.3 1.3 - - - -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.8 21.7 - - + -
103A ARG* 3.6 44.0 - - + -
106A VAL* 4.5 12.8 - - + -
209A ILE* 4.1 16.6 - - + -
338A ILE* 3.3 13.0 + - + +
339A ASP* 3.2 11.1 + - - +
341A VAL* 1.3 77.1 - - - +
343A SER* 1.3 68.9 + - - +
345A SER* 4.5 2.9 - - - -
346A TYR* 3.0 40.3 + - + +
352A PHE* 3.8 27.4 - - + -
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Residues in contact with SER 343 (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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101A TYR* 3.2 20.4 + - - -
339A ASP 2.9 13.9 + - - -
340A LEU* 2.6 27.7 + - - +
342A LEU* 1.3 78.2 - - - +
344A MET* 1.3 64.2 + - - -
346A TYR* 3.7 0.7 - - - +
347A TYR* 2.9 24.0 + - - +
369B SER* 3.1 39.5 + - - -
370B LEU* 4.4 6.4 - - - +
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Residues in contact with MET 344 (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 PHE* 4.4 1.8 - - + -
340A LEU* 2.7 33.7 + - + +
343A SER* 1.3 72.8 + - - +
345A SER* 1.3 63.1 + - - +
347A TYR* 3.9 0.7 - - - +
348A ALA* 3.1 27.0 + - - +
350A MET* 4.5 0.8 - - - +
355A VAL* 3.4 40.2 - - + +
361A THR* 4.3 2.9 - - + +
362B TRP* 3.4 38.8 - - + +
365B ILE* 4.1 11.0 - - + +
366B ILE* 3.3 39.3 - - + +
369B SER* 3.2 21.0 - - - +
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Residues in contact with SER 345 (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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5A TYR* 3.9 1.8 - - - -
341A VAL 2.7 28.6 + - - -
342A LEU 4.2 0.9 - - - -
343A SER 3.0 0.2 + - - -
344A MET* 1.3 74.4 - - - +
346A TYR* 1.3 52.6 + - - +
347A TYR 3.1 0.2 + - - -
349A LYS 2.7 32.1 + - - -
350A MET* 3.1 28.0 + - - +
351A PRO 3.9 1.0 + - - -
352A PHE* 3.0 47.3 + - - -
355A VAL* 3.4 7.0 - - - +
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Residues in contact with TYR 346 (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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4A PHE* 3.4 19.8 - + - -
5A TYR* 2.6 66.3 + + - -
6A ILE* 4.0 2.3 - - - +
99A ILE* 3.6 36.5 + - + +
101A TYR* 3.1 46.4 - + + -
106A VAL* 4.7 1.3 - - + +
342A LEU* 3.0 34.5 + - + +
343A SER 3.0 3.5 + - - +
345A SER* 1.3 75.2 - - - +
347A TYR* 1.3 59.5 + - - +
349A LYS* 3.4 18.5 + - - +
352A PHE* 3.2 21.3 - + - -
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Residues in contact with TYR 347 (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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98A GLU* 5.0 11.4 - - - -
343A SER 2.9 16.0 + - - +
344A MET 3.9 2.5 - - - +
346A TYR* 1.3 74.7 - - - +
348A ALA* 1.3 65.6 + - - +
349A LYS* 3.0 9.2 + - - +
347B TYR* 3.6 29.1 + + - -
348B ALA 3.7 5.9 + - - -
349B LYS* 3.4 30.8 - - - +
365B ILE* 3.5 41.5 - - + -
368B ASN* 3.3 48.6 + - + +
369B SER* 4.3 11.9 - - - +
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Residues in contact with ALA 348 (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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344A MET 3.1 10.4 + - - +
347A TYR* 1.3 81.5 - - - +
349A LYS* 1.3 54.5 + - - +
350A MET* 3.3 34.1 - - + -
361A THR* 4.9 0.7 - - + -
364A ALA* 5.2 0.2 - - + -
365A ILE* 3.7 24.9 - - + -
368A ASN* 2.7 24.4 + - - +
347B TYR* 2.7 21.2 + - - -
365B ILE* 4.4 8.5 - - + -
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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