Contacts of the helix formed by residues 363 - 374 (chain C) in PDB entry 5YD6
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A ASP* 5.6 1.8 + - - -
541A PHE* 6.4 2.7 - - - -
361C PRO 3.8 2.4 + - - -
362C VAL* 1.3 79.1 - - - +
364C LEU* 1.3 61.7 + - - +
365C ILE* 3.4 22.7 - - - +
366C SER* 3.4 17.3 + - - -
367C ALA* 2.9 26.5 + - - +
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C VAL 3.9 1.0 + - - -
363C SER* 1.3 71.3 + - - +
365C ILE* 1.3 59.2 + - - +
367C ALA* 3.3 5.4 + - - +
368C LEU* 3.1 37.2 + - + +
424C ILE* 5.5 0.7 - - + -
425C PRO* 3.8 36.8 - - + +
527C LEU* 5.4 5.4 - - + -
530C LYS* 3.9 51.8 - - + +
531C ILE* 4.5 8.3 - - + +
534C CYS* 4.0 13.9 - - + -
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Residues in contact with ILE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A HIS* 6.1 2.5 - - - +
363C SER* 3.4 13.2 - - - +
364C LEU* 1.3 77.8 - - - +
366C SER* 1.3 62.5 + - - +
368C LEU* 3.1 7.7 + - + +
369C VAL* 2.9 29.5 + - + +
501C SER* 3.7 28.0 - - - +
502C ALA* 5.4 0.2 - - - -
505C CYS* 3.7 20.9 - - - -
534C CYS* 3.5 41.8 - - + +
538C HIS* 3.6 26.9 - - + -
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Residues in contact with SER 366 (chain C).
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* 3.2 38.7 + - - +
500A ILE* 5.5 2.4 + - - +
501A SER* 5.8 0.2 - - - -
538A HIS* 4.4 9.0 + - - -
362C VAL* 4.1 10.0 - - - +
363C SER* 3.4 25.4 + - - -
364C LEU 3.3 0.4 - - - -
365C ILE* 1.3 82.8 - - - +
367C ALA* 1.3 56.2 + - - +
369C VAL* 3.6 8.3 + - - +
370C ARG* 3.1 27.2 + - - +
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C VAL* 4.5 11.6 - - + +
363C SER 2.9 14.3 + - - +
364C LEU* 3.5 9.6 - - - +
365C ILE 3.2 0.2 - - - -
366C SER* 1.3 78.1 - - - +
368C LEU* 1.3 58.7 + - - +
370C ARG* 3.3 8.5 + - - +
371C ALA* 2.9 28.5 + - - +
423C LYS 4.2 6.4 - - - +
425C PRO* 3.6 27.4 - - + -
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Residues in contact with LEU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C LEU* 3.1 25.8 + - + +
365C ILE* 3.1 9.4 + - - +
367C ALA* 1.3 74.6 - - - +
369C VAL* 1.3 63.5 + - - +
371C ALA* 3.5 4.6 + - + +
372C HIS* 3.1 18.2 + - - +
420C TRP* 4.8 3.9 + - - +
424C ILE* 3.8 40.6 - - + -
425C PRO* 4.4 6.7 - - + -
504C SER* 3.3 23.2 + - - +
505C CYS* 4.1 18.4 - - - -
508C ALA* 3.9 15.5 - - + -
531C ILE* 3.8 33.4 - - + -
534C CYS* 5.1 1.3 - - - -
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Residues in contact with VAL 369 (chain C).
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* 5.1 3.6 - - + -
500A ILE* 4.1 26.9 - - + -
501A SER* 5.7 4.9 - - - +
365C ILE* 2.9 21.5 + - + +
366C SER* 3.8 8.5 - - - +
368C LEU* 1.3 75.5 - - - +
370C ARG* 1.3 57.3 + - - +
372C HIS* 3.2 3.5 + - - +
373C VAL* 2.8 31.8 + - + +
500C ILE* 3.9 17.9 - - + -
501C SER* 3.7 39.5 - - - +
504C SER* 3.4 10.3 - - - +
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Residues in contact with ARG 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A HIS* 6.3 0.6 - - - -
379A MET* 5.6 3.4 - - - +
453A TYR* 3.2 46.7 + - - -
498A ILE 4.7 1.0 + - - -
499A ASP* 5.5 0.6 - - - +
500A ILE* 3.9 29.3 - - + +
362C VAL* 6.2 1.6 - - + -
366C SER 3.1 19.5 + - - +
367C ALA* 3.6 8.1 - - - +
368C LEU 3.3 0.4 - - - -
369C VAL* 1.3 76.3 - - - +
371C ALA* 1.3 57.4 + - - +
373C VAL* 4.0 1.0 - - - +
374C ASP* 2.9 73.6 + - - +
423C LYS* 5.4 7.2 - - + -
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Residues in contact with ALA 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C ALA 2.9 15.9 + - - +
368C LEU* 3.7 8.7 - - - +
369C VAL 3.3 0.2 - - - -
370C ARG* 1.3 76.9 - - - +
372C HIS* 1.3 52.7 + - - +
374C ASP* 4.1 1.2 - - - +
375C SER* 2.7 33.8 + - - -
420C TRP* 3.5 36.3 - - + +
423C LYS* 3.9 27.8 - - + +
424C ILE* 4.8 3.1 - - + +
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Residues in contact with HIS 372 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A VAL* 6.5 0.4 - - + -
368C LEU 3.1 8.5 + - - +
369C VAL 3.6 1.6 - - - +
371C ALA* 1.3 74.3 - - - +
373C VAL* 1.3 70.9 + - + +
375C SER* 3.2 11.0 + - - -
376C ASN* 2.6 55.7 + - + +
420C TRP* 3.7 9.3 - - - +
450C ARG* 4.5 7.3 - - + +
453C TYR* 4.2 20.6 - + - -
500C ILE* 3.9 23.1 - - + +
503C PHE* 3.6 34.0 - + - -
504C SER* 3.5 24.5 - - - +
507C ALA* 5.7 2.0 - - + -
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Residues in contact with VAL 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A HIS* 5.9 3.8 - - + +
373A VAL* 3.8 46.2 - - + +
378A ALA* 5.8 1.0 - - - -
379A MET* 5.6 2.3 + - + -
500A ILE* 3.9 22.0 - - + -
369C VAL* 2.8 31.3 + - + +
370C ARG* 4.1 1.8 - - - +
372C HIS* 1.3 83.5 - - + +
374C ASP* 1.3 69.1 + - - +
375C SER 3.2 1.2 + - - -
376C ASN* 3.4 17.9 + - - +
500C ILE* 4.5 4.5 - - + -
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Residues in contact with ASP 374 (chain C).
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* 3.8 42.2 - - + +
380A THR* 3.5 16.5 + - - +
370C ARG* 2.9 58.7 + - - +
371C ALA 4.4 0.4 - - - +
373C VAL* 1.3 81.6 - - - +
375C SER* 1.3 58.9 + - - +
376C ASN 3.6 1.8 - - - -
423C LYS* 4.0 27.8 + - - +
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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