Contacts of the helix formed by residues 358 - 368 (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 PRO 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A PRO* 3.7 8.2 - - + +
359A ILE* 3.9 34.3 - - + +
362A TRP* 3.5 41.7 - - + -
276B LYS* 5.9 1.3 - - - +
356B MET 3.5 10.5 - - - +
357B SER* 1.3 80.6 - - - +
359B ILE* 1.3 69.6 + - + +
361B THR* 3.2 1.0 + - - -
362B TRP* 2.8 28.1 + - - +
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Residues in contact with ILE 359 (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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358A PRO* 3.6 28.3 - - + -
52B GLY 4.3 13.5 - - - +
357B SER* 3.8 8.5 - - - +
358B PRO* 1.3 77.5 - - + +
360B LYS* 1.3 58.0 + - + +
362B TRP* 3.5 8.0 - - + +
363B ASP* 2.7 43.0 + - + +
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Residues in contact with LYS 360 (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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84B ASN* 5.6 9.4 - - - +
88B LEU* 5.3 1.4 - - - +
350B MET* 4.4 3.5 - - - +
353B SER* 4.1 19.2 + - - +
354B GLY* 3.8 21.8 - - - +
357B SER* 3.1 33.9 + - - +
359B ILE* 1.3 81.6 - - + +
361B THR* 1.3 63.7 + - - +
363B ASP* 3.9 7.8 - - - +
364B ALA* 3.2 21.8 + - - +
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Residues in contact with THR 361 (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* 2.9 37.8 - - + -
365A ILE* 3.7 42.2 - - + -
344B MET* 4.7 0.7 - - + -
348B ALA* 4.7 1.1 - - + -
350B MET* 3.8 22.9 - - + +
354B GLY 3.0 15.8 + - - -
355B VAL* 4.1 0.7 - - - -
357B SER 2.9 3.6 + - - -
358B PRO 3.7 0.7 - - - -
360B LYS* 1.3 72.8 - - - +
362B TRP* 1.3 57.7 + - - +
364B ALA* 2.8 23.0 + - - +
365B ILE* 2.8 21.6 + - + +
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Residues in contact with TRP 362 (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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276A LYS* 4.6 6.7 - - + -
277A PHE* 3.7 24.2 - + - -
344A MET* 3.4 12.1 - - + +
355A VAL 2.9 24.5 + - - -
357A SER 3.5 9.9 - - - -
358A PRO* 3.4 32.5 + - + +
361A THR* 3.0 37.0 + - - -
52B GLY* 3.6 36.8 - - - -
53B LYS 4.0 3.4 - - - -
54B ASN* 3.7 28.7 - - + -
358B PRO 2.8 21.2 + - - +
359B ILE* 3.5 10.8 - - + +
361B THR* 1.3 72.6 - - - +
363B ASP* 1.3 65.8 + - + +
365B ILE* 3.1 4.5 + - - +
366B ILE* 2.9 39.7 + - + +
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Residues in contact with ASP 363 (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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39B ARG* 3.0 26.2 + - - +
42B LYS* 3.0 13.5 + - - -
54B ASN* 2.9 27.8 + - - +
88B LEU* 3.8 15.6 - - - +
359B ILE* 2.7 30.0 + - + +
360B LYS* 3.9 7.6 - - - +
362B TRP* 1.3 77.4 - - + +
364B ALA* 1.3 60.4 + - - +
366B ILE* 4.3 7.6 - - - -
367B PHE* 3.3 13.3 + - - +
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Residues in contact with ALA 364 (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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88B LEU* 3.9 32.3 - - + -
348B ALA* 4.3 8.5 - - + +
350B MET* 4.0 18.8 - - + -
360B LYS 3.2 14.1 + - - +
361B THR 2.8 13.2 + - - +
363B ASP* 1.3 70.9 - - - +
365B ILE* 1.3 63.7 + - - +
367B PHE* 3.3 1.2 + - - +
368B ASN* 2.9 35.3 + - - +
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Residues in contact with ILE 365 (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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344A MET* 4.1 31.9 - - + +
347A TYR* 3.5 34.0 - - + -
348A ALA* 4.4 3.8 - - + -
361A THR* 4.1 18.2 - - + -
365A ILE* 3.7 33.4 - - + -
347B TYR 5.1 0.2 - - - +
348B ALA* 3.8 19.5 - - + -
361B THR* 2.8 16.7 + - + +
362B TRP 3.4 7.2 - - - +
364B ALA* 1.3 74.2 - - - +
366B ILE* 1.3 66.0 + - - +
368B ASN 3.7 0.4 - - - +
369B SER* 2.8 28.8 + - - -
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Residues in contact with ILE 366 (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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277A PHE* 3.8 19.7 - - + -
340A LEU* 4.2 6.7 - - + +
344A MET* 3.3 30.1 - - + -
39B ARG* 3.4 12.1 - - - +
54B ASN* 3.1 42.4 - - + +
55B CYS 3.5 8.7 - - - +
57B PRO* 3.6 16.9 - - + +
362B TRP* 2.9 33.6 + - + +
363B ASP* 3.7 7.2 - - - +
365B ILE* 1.3 72.4 - - - +
367B PHE* 1.3 65.7 + - - +
369B SER* 2.5 22.0 + - - -
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Residues in contact with PHE 367 (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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37B MET* 4.6 24.4 - - + +
38B PHE 4.1 3.6 - - - -
39B ARG* 3.0 53.8 - - + -
42B LYS* 4.3 2.7 - - - -
57B PRO* 4.1 8.4 - - + +
85B ASP* 2.8 61.9 - - - -
88B LEU* 4.3 17.0 - - + -
89B ALA* 4.8 8.5 - - + -
92B SER* 6.0 0.4 - - - -
363B ASP* 3.3 11.6 + - - +
364B ALA* 3.4 10.3 - - - +
366B ILE* 1.3 86.9 - - - +
368B ASN* 1.3 64.3 + - - +
369B SER 3.1 3.8 + - - -
370B LEU* 3.2 19.4 + - - +
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Residues in contact with ASN 368 (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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347A TYR* 3.3 38.5 + - + +
88B LEU* 4.1 17.6 + - - +
92B SER* 3.6 18.5 - - - -
348B ALA 3.7 11.6 + - - +
349B LYS* 3.2 39.8 + - - +
364B ALA 2.9 18.7 + - - +
367B PHE* 1.3 78.1 - - - +
369B SER* 1.3 63.7 + - - +
370B LEU* 3.1 10.4 + - - +
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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