Contacts of the helix formed by residues 372 - 382 (chain B) in PDB entry 1Y8Q
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 SER 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B ASP 3.0 19.9 + - - -
310B GLN* 3.6 16.1 + - - -
311B GLN 3.5 19.1 - - - -
312B VAL* 3.8 8.3 - - - +
318B TYR* 4.3 2.5 - - - -
371B LYS* 1.3 78.2 - - - +
373B ARG* 1.3 61.5 + - - +
374B PHE* 3.7 3.5 + - - +
375B ASP* 3.2 32.1 + - - -
376B ILE* 3.0 21.5 + - - +
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Residues in contact with ARG 373 (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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309B ASP* 2.9 42.7 + - - +
311B GLN 4.6 1.2 + - - -
318B TYR* 4.6 5.2 + - + +
321B LEU* 5.3 4.3 - - - -
349B PRO* 3.3 28.1 + - - +
352B MET* 3.5 25.0 - - + +
353B ASP* 2.6 31.0 + - - +
356B THR* 3.5 33.6 + - + +
371B LYS 3.8 0.2 + - - -
372B SER* 1.3 74.1 - - - +
374B PHE* 1.3 57.9 + - - +
376B ILE* 3.9 1.0 - - - +
377B LYS* 2.9 42.5 + - - +
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Residues in contact with PHE 374 (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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20A ASP* 4.4 9.9 - - - -
23A ILE* 4.3 10.5 - - + -
24A ARG* 3.0 84.6 + - + +
307B LEU* 4.2 19.3 - - + -
309B ASP* 3.1 36.9 + - + +
310B GLN* 3.8 31.0 - - + -
372B SER* 3.1 4.5 - - - +
373B ARG* 1.3 79.1 - - - +
375B ASP* 1.3 74.1 + - - +
377B LYS* 4.5 0.7 - - - -
378B SER* 3.5 6.9 + - - -
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Residues in contact with ASP 375 (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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371B LYS* 3.1 32.9 + - + +
372B SER* 3.2 23.2 + - - +
374B PHE* 1.3 89.3 - - - +
376B ILE* 1.3 66.6 + - - +
377B LYS 3.1 0.2 - - - -
378B SER* 3.2 16.4 + - - -
379B MET* 3.2 25.0 + - + +
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Residues in contact with ILE 376 (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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186B ILE* 4.2 28.9 - - + -
352B MET* 4.0 18.2 - - + -
355B VAL* 4.2 11.7 - - + +
356B THR* 3.5 28.7 - - + +
359B ALA* 4.3 7.0 - - + -
360B ASN* 3.3 35.7 - - - +
363B MET* 4.4 2.0 - - + -
371B LYS* 3.6 16.2 - - + +
372B SER 3.0 16.0 + - - +
373B ARG 3.9 3.4 - - - +
375B ASP* 1.3 75.2 - - - +
377B LYS* 1.3 53.5 + - - +
379B MET* 4.4 0.4 - - + -
380B ALA* 2.7 33.9 + - + +
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Residues in contact with LYS 377 (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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20A ASP* 4.0 13.9 - - - +
21A ARG* 4.4 4.9 - - - +
24A ARG* 3.1 20.6 - - - +
309B ASP* 5.3 2.5 - - - +
346B LYS* 2.9 31.5 + - + +
347B ASP* 4.0 14.3 + - - +
352B MET* 3.7 30.4 - - + +
373B ARG* 2.9 31.1 + - - +
374B PHE* 3.6 6.1 - - - +
376B ILE* 1.3 78.2 - - - +
378B SER* 1.3 56.9 + - - +
380B ALA* 4.4 0.2 - - - +
381B GLY* 3.0 24.1 + - - -
383B ILE* 3.5 24.5 - - + +
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.6 36.0 + - - +
374B PHE* 3.5 3.2 + - - -
375B ASP* 3.2 12.3 + - - -
377B LYS* 1.3 79.1 - - - +
379B MET* 1.3 59.3 + - - +
382B ASN* 2.9 24.9 + - - -
383B ILE* 3.1 24.1 + - - +
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Residues in contact with MET 379 (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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182B PRO* 5.2 1.6 - - - -
183B ILE* 4.2 30.5 - - + +
186B ILE* 3.7 29.8 - - + -
371B LYS* 3.5 39.5 - - + +
375B ASP* 3.2 28.3 + - + +
376B ILE* 3.9 1.6 - - - +
378B SER* 1.3 76.1 - - - +
380B ALA* 1.3 66.4 + - - +
382B ASN* 3.2 22.1 + - - +
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Residues in contact with ALA 380 (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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186B ILE* 3.6 24.5 - - + +
190B LYS* 2.8 37.9 + - + +
344B TRP* 3.7 17.8 - - + -
352B MET* 4.1 5.4 - - + -
355B VAL* 4.0 13.0 - - + -
376B ILE 2.7 22.8 + - - +
377B LYS 4.4 0.4 - - - +
379B MET* 1.3 74.6 - - - +
381B GLY* 1.3 58.7 + - - +
382B ASN* 3.6 2.4 - - - +
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Residues in contact with GLY 381 (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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344B TRP* 4.1 4.4 - - - -
346B LYS* 3.9 35.6 + - - +
377B LYS 3.0 16.2 + - - -
380B ALA* 1.3 75.8 - - - +
382B ASN* 1.3 75.1 + - - +
383B ILE* 3.1 6.1 + - - -
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Residues in contact with ASN 382 (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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167B GLN* 5.8 7.7 - - - +
190B LYS* 4.4 6.6 + - - -
378B SER 2.9 11.9 + - - -
379B MET* 3.2 11.1 + - - +
380B ALA 3.6 10.0 - - - +
381B GLY* 1.3 82.1 - - - +
383B ILE* 1.3 63.6 + - - +
384B ILE* 3.6 14.5 + - + +
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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