Contacts of the helix formed by residues 363 - 374 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A ASN* 2.6 49.4 + - - +
361B PRO 3.7 2.0 + - - -
362B VAL* 1.3 78.1 - - - +
364B LEU* 1.3 65.2 + - - +
365B ILE* 3.6 5.4 - - - +
366B SER* 3.2 16.2 + - - -
367B ALA* 3.0 20.2 + - - +
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Residues in contact with LEU 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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362B VAL 4.0 0.4 + - - -
363B SER* 1.3 72.1 - - - +
365B ILE* 1.3 59.5 + - - +
367B ALA* 3.1 6.4 + - - +
368B LEU* 2.9 45.3 + - + +
424B ILE* 5.4 0.2 - - + -
425B PRO* 3.7 39.5 - - + +
527B LEU* 4.8 9.0 - - + -
530B LYS* 3.8 36.1 - - + -
531B ILE* 4.0 9.0 - - + +
534B CYS* 3.5 25.8 - - - -
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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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541A PHE* 4.5 8.5 - - + -
542A ASN* 3.7 6.7 - - - +
602A PGE 3.7 21.5 - - - +
363B SER* 3.6 12.3 - - - +
364B LEU* 1.3 77.9 - - - +
366B SER* 1.3 54.8 + - - +
368B LEU* 3.2 9.5 + - + +
369B VAL* 2.8 35.6 + - + +
501B SER* 3.9 18.6 - - - +
505B CYS* 3.8 26.2 - - - -
534B CYS* 3.9 19.7 - - - +
538B HIS* 3.7 38.4 - - + -
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Residues in contact with SER 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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499A ASP* 2.6 36.4 + - - +
500A ILE* 5.8 0.2 - - - +
542A ASN* 3.5 3.3 + - - -
602A PGE 3.0 20.3 + - - -
362B VAL* 3.1 26.9 - - - +
363B SER* 3.2 18.5 + - - -
365B ILE* 1.3 76.4 - - - +
367B ALA* 1.3 55.3 + - - +
369B VAL* 3.3 2.6 + - - +
370B ARG* 3.0 29.3 + - - +
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Residues in contact with ALA 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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362B VAL* 3.5 11.5 - - + +
363B SER 3.0 12.0 + - - +
364B LEU* 3.1 7.8 + - - +
366B SER* 1.3 77.5 - - - +
368B LEU* 1.3 57.9 + - - +
370B ARG* 3.4 6.9 + - - +
371B ALA* 3.0 29.0 + - - +
423B LYS 4.2 7.4 - - - +
425B PRO* 3.5 28.3 - - + -
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Residues in contact with LEU 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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364B LEU* 2.9 35.0 + - + +
365B ILE* 3.2 10.5 + - + +
367B ALA* 1.3 73.1 - - - +
369B VAL* 1.3 65.7 + - - +
371B ALA* 3.4 6.1 + - + +
372B HIS* 3.1 17.3 + - - +
420B TRP* 4.8 3.9 + - - +
424B ILE* 3.9 30.3 - - + -
425B PRO* 4.3 8.1 - - + -
504B SER* 3.4 24.1 - - - +
505B CYS* 4.1 18.6 - - - -
508B ALA* 3.9 19.7 - - + -
531B ILE* 3.9 27.8 - - + -
534B CYS* 4.8 1.1 - - - -
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Residues in contact with VAL 369 (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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369A VAL* 5.6 4.0 - - + -
500A ILE* 4.6 10.8 - - + -
501A SER* 5.5 0.9 - - - +
602A PGE 3.9 23.6 - - - +
365B ILE 2.8 19.4 + - - +
366B SER 3.3 4.2 + - - +
368B LEU* 1.3 73.7 - - - +
370B ARG* 1.3 61.4 + - - +
372B HIS* 3.1 3.3 + - - +
373B VAL* 2.8 36.9 + - + +
500B ILE* 4.1 16.2 - - + -
501B SER* 3.6 41.3 - - - +
504B SER* 3.4 11.7 - - - +
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Residues in contact with ARG 370 (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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453A TYR* 3.0 47.1 + - - -
498A ILE 4.6 1.8 + - - -
499A ASP* 5.7 0.8 - - - +
500A ILE* 3.7 29.0 - - + +
362B VAL* 6.3 0.4 - - + -
366B SER 3.0 16.6 + - - +
367B ALA* 3.8 6.7 - - - +
369B VAL* 1.3 76.9 - - - +
371B ALA* 1.3 56.8 + - - +
373B VAL* 5.4 1.0 - - - +
374B ASP* 2.8 79.7 + - - +
423B LYS* 4.6 7.0 - - + +
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Residues in contact with ALA 371 (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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367B ALA 3.0 17.5 + - - +
368B LEU* 3.6 8.7 - - - +
369B VAL 3.3 0.2 - - - -
370B ARG* 1.3 75.6 - - - +
372B HIS* 1.3 55.2 + - - +
374B ASP* 3.7 1.6 + - - +
375B SER* 2.8 34.1 + - - -
420B TRP* 3.4 24.8 - - + +
423B LYS* 3.7 39.6 - - + +
424B ILE* 4.8 2.9 - - + +
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Residues in contact with HIS 372 (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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368B LEU 3.1 7.8 + - - +
369B VAL 3.4 3.1 - - - +
371B ALA* 1.3 77.2 - - - +
373B VAL* 1.3 69.4 + - + +
375B SER* 3.1 10.7 + - - -
376B ASN* 2.7 55.5 + - + +
420B TRP* 3.8 9.1 + - - +
450B ARG* 4.6 6.6 + - + -
453B TYR* 4.2 17.1 - + - -
500B ILE* 3.9 25.1 - - + +
503B PHE* 3.4 38.2 - + - -
504B SER* 3.3 26.4 - - - +
507B ALA* 5.4 1.8 - - - +
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Residues in contact with VAL 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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369A VAL* 5.7 0.9 - - + -
372A HIS* 6.2 0.7 - - + -
373A VAL* 4.0 37.5 - - + -
378A ALA* 5.6 1.0 - - - +
379A MET 5.3 2.4 + - - -
500A ILE* 3.9 24.0 - - + -
369B VAL* 2.8 36.4 + - + +
370B ARG* 4.0 1.1 - - - +
372B HIS* 1.3 76.2 - - + +
374B ASP* 1.3 66.6 + - - +
375B SER 3.3 4.0 + - - -
376B ASN* 3.4 19.9 - - - +
500B ILE* 4.4 15.3 - - + -
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Residues in contact with ASP 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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379A MET* 3.4 49.2 + - + +
380A THR* 3.7 6.4 - - - +
370B ARG* 2.8 61.8 + - - +
371B ALA 4.0 1.3 - - - +
373B VAL* 1.3 78.4 - - - +
375B SER* 1.3 58.0 + - - +
376B ASN 3.6 0.9 - - - -
423B LYS* 3.1 28.2 + - - +
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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