Contacts of the helix formed by residues 363 - 374 (chain A) in PDB entry 5Y41
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 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A VAL* 1.3 77.8 - - - +
364A LEU* 1.3 64.6 + - - +
365A ILE* 3.6 12.7 - - - +
366A SER* 3.2 26.4 + - - -
367A ALA* 3.0 19.8 + - - +
499B ASP* 5.6 0.2 + - - -
542B ASN* 5.4 12.0 + - - -
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Residues in contact with LEU 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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362A VAL 4.0 0.4 + - - -
363A SER* 1.3 73.0 - - - +
365A ILE* 1.3 57.2 + - - +
367A ALA* 3.1 6.0 + - - +
368A LEU* 2.8 44.7 + - + +
425A PRO* 3.8 33.7 - - + -
527A LEU* 5.0 5.2 - - + -
530A LYS* 3.8 37.2 - - + +
531A ILE* 4.1 12.3 - - + +
534A CYS* 3.5 27.4 - - - -
603A PEG 4.8 6.5 - - - +
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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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363A SER* 3.6 12.1 - - - +
364A LEU* 1.3 77.2 - - - +
366A SER* 1.3 55.6 + - - +
368A LEU* 3.2 7.4 + - + +
369A VAL* 2.8 35.4 + - + +
501A SER* 3.9 24.0 - - - +
505A CYS* 3.8 26.9 - - - -
534A CYS* 3.9 20.3 - - + +
538A HIS* 3.7 37.9 - - + -
602A PGE 4.2 11.2 - - - +
541B PHE* 6.0 2.7 - - + -
542B ASN* 5.9 4.7 - - - +
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 3.6 15.7 - - - -
363A SER* 3.2 26.7 + - - -
365A ILE* 1.3 77.4 - - - +
367A ALA* 1.3 58.3 + - - +
369A VAL* 3.3 1.5 + - - -
370A ARG* 2.9 64.6 + - - +
499B ASP* 3.9 16.1 + - - +
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Residues in contact with ALA 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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362A VAL* 3.9 13.2 - - + +
363A SER 3.0 14.1 + - - +
364A LEU* 3.1 5.8 + - - +
366A SER* 1.3 75.5 - - - +
368A LEU* 1.3 57.9 + - - +
370A ARG* 3.4 7.0 + - - +
371A ALA* 3.0 28.8 + - - +
423A LYS 4.2 5.3 - - - +
425A PRO* 3.4 33.0 - - + -
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Residues in contact with LEU 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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364A LEU* 2.8 40.8 + - + +
365A ILE* 3.2 8.0 + - - +
367A ALA* 1.3 70.2 - - - +
369A VAL* 1.3 64.7 + - - +
371A ALA* 3.4 5.7 + - + +
372A HIS* 3.1 17.7 + - - +
420A TRP* 4.9 1.4 + - - -
424A ILE* 4.0 26.0 - - + -
425A PRO* 4.2 9.2 - - + -
504A SER* 3.4 24.2 - - - +
505A CYS* 4.1 17.3 - - - +
508A ALA* 3.9 22.0 - - + -
531A ILE* 3.9 29.2 - - + -
534A CYS* 4.8 1.3 - - - -
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Residues in contact with VAL 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 21.1 + - + +
366A SER* 3.8 4.7 - - - +
367A ALA 3.3 0.2 - - - -
368A LEU* 1.3 72.7 - - - +
370A ARG* 1.3 71.8 + - - +
372A HIS* 3.1 3.3 + - - +
373A VAL* 2.8 48.9 + - + +
500A ILE* 4.1 10.3 - - + +
501A SER* 3.6 41.1 - - - +
504A SER* 3.4 12.3 - - - +
369B VAL* 5.6 4.5 - - + -
373B VAL* 5.7 0.9 - - + -
500B ILE* 4.6 12.6 - - + -
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Residues in contact with ARG 370 (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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362A VAL* 5.4 6.2 - - + +
366A SER* 2.9 59.3 + - - +
367A ALA* 3.8 6.5 - - - +
368A LEU 3.3 0.2 - - - -
369A VAL* 1.3 86.1 - - - +
371A ALA* 1.3 59.0 + - - +
373A VAL* 4.5 4.3 - - - +
374A ASP* 2.8 47.2 + - - +
423A LYS* 5.4 1.1 - - - -
453B TYR* 5.0 0.8 + - - -
499B ASP* 3.4 17.8 - - - +
500B ILE* 3.1 61.4 - - - +
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Residues in contact with ALA 371 (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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367A ALA 3.0 17.2 + - - +
368A LEU* 3.6 9.4 - - + +
370A ARG* 1.3 76.9 - - - +
372A HIS* 1.3 54.8 + - - +
374A ASP 4.0 0.9 - - - -
375A SER* 2.7 33.1 + - - -
420A TRP* 3.4 22.8 - - + +
423A LYS* 3.7 40.3 - - + +
424A ILE* 4.5 4.0 - - + +
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Residues in contact with HIS 372 (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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368A LEU 3.1 8.4 + - - +
369A VAL 3.1 2.9 + - - +
371A ALA* 1.3 77.0 - - - +
373A VAL* 1.3 70.3 + - + +
375A SER* 3.1 11.1 + - - -
376A ASN* 2.6 55.2 + - + +
420A TRP* 3.8 8.7 + - - +
450A ARG* 4.5 6.9 + - + -
453A TYR* 4.2 16.7 - + - -
500A ILE* 4.2 23.9 - - + +
503A PHE* 3.4 39.0 - + - -
504A SER* 3.3 26.0 - - - +
507A ALA* 5.4 1.4 - - - +
373B VAL* 6.2 0.7 - - + -
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 2.8 38.1 + - + +
370A ARG* 4.1 4.3 - - - +
372A HIS* 1.3 82.1 - - + +
374A ASP* 1.3 65.1 + - - +
375A SER 3.3 3.8 + - - -
376A ASN* 3.4 13.4 + - - +
500A ILE* 4.4 2.2 - - + -
373B VAL* 4.0 38.1 - - + +
377B PRO 5.3 3.1 - - - +
378B ALA* 3.2 33.4 - - + +
500B ILE* 5.5 7.4 - - + -
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Residues in contact with ASP 374 (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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370A ARG* 2.8 33.9 + - - +
371A ALA 4.0 0.7 - - - -
373A VAL* 1.3 78.6 - - - +
375A SER* 1.3 58.5 + - - +
376A ASN 3.6 0.9 - - - -
423A LYS* 3.7 26.8 + - + +
378B ALA* 4.1 7.7 - - - +
379B MET* 3.3 46.6 + - + +
380B THR* 3.2 18.8 - - - +
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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