Contacts of the helix formed by residues 358 - 369 (chain A) in PDB entry 1NOY
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LYS* 6.0 0.4 - - - -
356A MET 3.9 4.7 - - - +
357A SER* 1.3 84.9 - - - +
359A ILE* 1.3 61.5 + - + +
361A THR* 3.2 2.3 + - - -
362A TRP* 2.8 32.2 + - - +
52B GLY 3.4 29.6 - - - +
358B PRO* 3.9 14.6 - - + +
359B ILE* 3.5 26.9 - - + +
362B TRP* 3.6 33.2 - - + -
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Residues in contact with ILE 359 (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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49A ASP* 3.9 40.8 - - + +
357A SER* 4.1 7.4 - - - +
358A PRO* 1.3 81.5 - - + +
360A LYS* 1.3 63.0 + - + +
362A TRP* 3.6 4.7 - - + +
363A ASP* 2.9 33.6 + - + +
358B PRO* 3.8 25.8 - - + -
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Residues in contact with LYS 360 (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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84A ASN* 4.1 24.5 - - - +
350A MET* 3.6 12.3 - - + +
353A SER* 5.2 8.7 - - - +
354A GLY* 3.9 28.5 - - - +
357A SER* 2.8 30.1 + - - +
359A ILE* 1.3 79.4 - - + +
361A THR* 1.3 61.5 + - - +
363A ASP* 3.6 8.4 - - - +
364A ALA* 3.3 15.9 + - - +
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Residues in contact with THR 361 (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* 4.5 3.1 - - + +
348A ALA* 4.9 0.4 - - + -
350A MET* 4.2 18.2 - - - -
354A GLY 3.6 10.2 + - - -
355A VAL* 4.1 5.9 - - - -
357A SER 2.9 21.4 + - - -
358A PRO 3.6 3.1 - - - -
360A LYS* 1.3 75.4 - - - +
362A TRP* 1.3 66.4 + - - +
364A ALA* 3.2 4.0 + - - +
365A ILE* 3.0 29.2 + - + +
362B TRP* 3.2 29.4 + - + +
365B ILE* 4.0 33.2 - - + -
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Residues in contact with TRP 362 (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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49A ASP* 3.5 30.7 - - - -
52A GLY 4.0 3.6 - - - -
54A ASN* 4.0 16.6 - - + -
358A PRO 2.8 20.7 + - - +
359A ILE* 3.6 7.2 - - + +
361A THR* 1.3 71.5 - - - +
363A ASP* 1.3 62.7 + - - +
365A ILE* 2.9 20.1 + - - +
366A ILE* 3.0 26.2 + - + +
276B LYS* 4.0 28.0 - - + -
277B PHE* 3.7 31.2 - + - -
344B MET* 3.6 12.0 - - + +
355B VAL 2.7 25.2 + - - -
356B MET 4.6 2.0 - - - -
358B PRO* 3.6 35.5 - - + +
361B THR* 3.3 34.0 - - - +
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Residues in contact with ASP 363 (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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39A ARG* 2.5 45.9 + - - +
42A LYS* 2.9 19.2 + - - -
54A ASN* 2.9 28.3 + - - +
84A ASN* 5.0 8.5 + - - -
85A ASP* 4.4 3.5 - - - +
88A LEU* 4.5 4.7 - - - +
359A ILE* 2.9 21.6 + - + +
360A LYS* 3.6 10.0 - - - +
362A TRP* 1.3 79.3 - - + +
364A ALA* 1.3 61.8 + - - +
366A ILE* 3.5 5.6 + - - -
367A PHE 3.4 5.7 + - - -
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Residues in contact with ALA 364 (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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88A LEU* 4.0 26.7 - - + -
348A ALA 5.0 1.6 - - - +
350A MET* 4.1 30.3 - - + -
360A LYS 3.3 13.0 + - - +
361A THR 3.2 6.2 + - - +
363A ASP* 1.3 75.8 + - - +
365A ILE* 1.3 61.0 + - + +
367A PHE* 3.8 0.4 - - - +
368A ASN* 2.9 38.6 + - - +
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Residues in contact with ILE 365 (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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348A ALA* 4.1 17.3 - - + +
361A THR* 3.0 17.2 + - + +
362A TRP 2.9 7.7 + - - +
364A ALA* 1.3 75.8 - - - +
366A ILE* 1.3 58.1 + - - +
368A ASN* 4.5 1.3 - - - +
369A SER* 2.8 38.5 + - - +
344B MET* 4.2 33.7 - - + +
347B TYR* 3.9 27.1 - - + -
348B ALA* 4.4 7.0 - - + -
361B THR* 3.8 21.3 - - + -
365B ILE* 3.7 24.9 - - + -
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Residues in contact with ILE 366 (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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39A ARG* 3.4 11.4 - - - +
54A ASN* 3.6 30.7 - - + +
55A CYS 3.4 24.9 - - - +
57A PRO* 3.7 5.9 - - + +
362A TRP* 3.0 29.3 + - + +
363A ASP* 4.3 0.2 - - - -
365A ILE* 1.3 78.0 - - - +
367A PHE* 1.3 63.3 + - - +
369A SER* 3.2 4.3 + - - -
370A LEU* 3.2 27.0 - - - +
277B PHE* 3.9 19.1 - - + -
340B LEU* 3.8 19.5 - - + -
344B MET* 3.5 27.6 - - + +
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Residues in contact with PHE 367 (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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37A MET* 3.9 34.2 - - + +
38A PHE* 4.0 18.6 - - - -
39A ARG* 3.5 37.7 - - + +
57A PRO* 3.8 21.7 - - + +
85A ASP* 3.4 47.6 - - + -
88A LEU* 3.9 13.7 - - + -
89A ALA* 3.8 18.6 - - + -
92A SER* 4.9 1.3 - - - -
363A ASP 3.4 3.4 + - - +
364A ALA 3.8 5.8 - - - +
365A ILE 3.3 0.4 - - - -
366A ILE* 1.3 82.6 - - - +
368A ASN* 1.3 72.5 + - - +
370A LEU* 3.8 4.3 + - - +
372A GLY* 4.3 9.2 - - - -
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Residues in contact with ASN 368 (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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88A LEU* 3.8 9.2 - - - +
92A SER* 3.6 24.7 - - - -
348A ALA 3.0 24.0 + - - +
349A LYS* 3.2 18.0 + - - +
364A ALA* 2.9 26.9 + - - +
365A ILE 4.4 0.9 - - - +
367A PHE* 1.3 89.4 - - - +
369A SER* 1.3 63.8 + - - +
370A LEU 3.3 1.2 + - - -
371A LYS* 3.7 2.3 + - - -
372A GLY* 3.5 16.2 + - - +
347B TYR* 3.7 29.3 - - + +
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Residues in contact with SER 369 (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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365A ILE 2.8 24.3 + - - -
366A ILE 3.2 1.2 + - - -
368A ASN* 1.3 68.9 - - - +
370A LEU* 1.3 74.7 + - - +
371A LYS* 2.8 15.2 + - - +
343B SER* 3.4 38.7 + - - +
344B MET* 3.4 19.9 + - - +
347B TYR* 4.0 17.6 - - - +
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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