Contacts of the helix formed by residues 499 - 512 (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 ASP 499 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A SER* 5.8 0.9 - - - -
366A SER* 3.4 27.6 + - - +
370A ARG* 4.9 8.7 - - - +
453C TYR* 3.3 3.6 + - - -
497C ASN 3.4 6.9 + - - +
498C ILE* 1.3 76.1 - - - +
500C ILE* 1.3 58.9 + - - +
501C SER* 4.0 3.1 - - - +
502C ALA* 2.9 32.9 + - - +
503C PHE 3.0 24.9 + - - -
538C HIS* 2.9 28.4 + - - -
542C ASN* 3.2 15.2 + - - -
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Residues in contact with ILE 500 (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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366A SER* 4.9 3.1 - - - +
369A VAL* 3.8 27.4 - - + -
370A ARG* 4.6 31.8 - - + +
373A VAL* 4.8 9.9 - - + -
369C VAL* 3.9 25.1 - - + -
372C HIS* 3.9 25.4 - - + +
373C VAL* 4.5 5.8 - - + -
453C TYR* 3.7 18.8 - - + +
499C ASP* 1.3 75.5 - - - +
501C SER* 1.3 53.7 + - - +
503C PHE* 3.9 2.4 - - - +
504C SER* 2.7 40.0 + - - +
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Residues in contact with SER 501 (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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501A SER* 4.8 8.7 + - - -
365C ILE* 3.7 19.6 - - - +
369C VAL* 3.7 19.9 - - - +
499C ASP* 3.3 3.7 - - - -
500C ILE* 1.3 80.4 - - - +
502C ALA* 1.3 62.3 + - - +
504C SER* 3.5 3.3 + - - -
505C CYS* 3.4 24.3 + - - -
538C HIS* 3.4 30.8 + - - -
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Residues in contact with ALA 502 (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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365C ILE* 5.4 0.2 - - - -
498C ILE* 3.6 18.2 - - + -
499C ASP* 2.9 21.8 + - - +
501C SER* 1.3 69.5 - - - +
503C PHE* 1.3 67.4 + - - +
505C CYS* 3.0 8.2 + - - +
506C ILE* 3.0 23.5 + - - +
535C LEU* 4.1 21.9 - - + +
538C HIS* 4.1 10.0 + - - +
539C VAL* 5.1 3.1 - - + -
551C TYR* 6.0 0.4 - - - +
555C LEU* 4.7 9.6 - - + -
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Residues in contact with PHE 503 (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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372C HIS* 3.6 35.4 - + - -
449C LEU* 3.6 45.5 - - + -
450C ARG* 4.2 13.7 - - + -
453C TYR* 3.5 60.1 - + + -
493C LEU* 4.3 4.9 - - + -
498C ILE* 3.4 12.3 - - + +
499C ASP 3.0 18.5 + - - +
500C ILE 3.9 2.7 - - - +
501C SER 3.4 0.2 - - - -
502C ALA* 1.3 74.8 - - - +
504C SER* 1.3 58.7 + - - +
506C ILE* 3.0 10.4 + - + +
507C ALA* 2.8 36.5 + - + +
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Residues in contact with SER 504 (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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368C LEU* 3.3 41.4 + - - +
369C VAL* 3.4 13.1 - - - -
372C HIS* 3.5 16.4 - - - +
420C TRP* 4.9 3.5 + - - +
500C ILE* 2.7 23.1 + - - +
501C SER 3.7 6.5 - - - -
502C ALA 3.2 0.2 - - - -
503C PHE* 1.3 81.1 - - - +
505C CYS* 1.3 56.4 + - - +
507C ALA* 3.9 4.9 - - - +
508C ALA* 3.2 25.8 + - - +
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Residues in contact with CYS 505 (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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365C ILE* 3.7 24.2 - - - -
368C LEU* 4.1 13.7 - - - -
501C SER 3.4 15.7 - - - -
502C ALA* 3.0 9.7 + - - +
504C SER* 1.3 74.6 - - - +
506C ILE* 1.3 54.9 + - - +
508C ALA* 3.2 2.6 + - - +
509C LEU* 2.8 40.1 + - - +
531C ILE* 3.7 14.3 - - + +
534C CYS* 4.6 2.2 - - - -
535C LEU* 3.8 35.4 - - + -
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Residues in contact with ILE 506 (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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449C LEU* 4.4 17.7 - - + -
493C LEU* 5.7 3.1 - - + -
498C ILE* 5.1 2.0 - - + -
502C ALA 3.0 14.9 + - - +
503C PHE* 3.0 12.9 + - + +
505C CYS* 1.3 72.8 - - - +
507C ALA* 1.3 57.7 + - - +
509C LEU* 3.1 7.4 + - + +
510C ALA* 2.9 25.6 + - - +
535C LEU* 3.8 24.9 - - + -
555C LEU* 3.8 49.8 - - + +
556C LEU* 4.6 6.5 - - + -
558C LYS* 5.3 5.8 - - + -
559C LEU* 3.6 25.7 - - + +
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Residues in contact with ALA 507 (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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372C HIS* 5.7 2.5 - - + -
420C TRP* 3.3 25.4 - - + +
446C LEU* 3.4 24.1 - - + +
449C LEU* 3.7 18.1 - - + +
450C ARG* 5.2 3.1 - - + -
503C PHE* 2.8 32.9 + - + +
504C SER* 3.9 6.5 - - - +
506C ILE* 1.3 73.2 - - - +
508C ALA* 1.3 61.8 + - - +
510C ALA* 3.4 10.2 + - - +
511C MET 3.5 1.0 + - - -
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Residues in contact with ALA 508 (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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368C LEU* 3.9 23.3 - - + -
420C TRP* 3.6 13.9 - - + -
424C ILE* 4.5 5.6 - - + -
504C SER 3.2 11.9 + - - +
505C CYS 3.2 9.3 + - - +
507C ALA* 1.3 79.3 - - - +
509C LEU* 1.3 50.9 + - - +
511C MET* 3.0 5.5 + - - +
512C VAL* 2.7 39.1 + - + +
531C ILE* 4.1 18.8 - - + -
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Residues in contact with LEU 509 (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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505C CYS 2.8 25.5 + - - +
506C ILE* 3.1 7.2 + - - +
508C ALA* 1.3 67.3 - - - +
510C ALA* 1.3 65.7 + - - +
511C MET 3.1 1.7 + - - -
512C VAL 3.4 17.1 + - - +
513C THR* 3.9 8.0 - - - -
528C GLN* 3.6 40.5 + - + +
531C ILE* 3.8 16.2 - - + -
532C VAL* 3.7 18.8 - - + -
535C LEU* 3.7 28.7 - - + -
556C LEU* 3.9 17.0 - - + -
559C LEU* 3.8 16.9 - - + +
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Residues in contact with ALA 510 (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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442C ALA* 3.5 14.7 - - - +
445C GLU* 4.8 11.0 - - + +
446C LEU* 3.8 15.5 - - + -
449C LEU* 4.4 1.6 - - + -
506C ILE 2.9 12.6 + - - +
507C ALA 3.4 12.1 - - - +
508C ALA 3.3 0.2 - - - -
509C LEU* 1.3 75.4 - - - +
511C MET* 1.3 59.0 + - - +
513C THR* 3.8 4.2 - - - +
515C ARG* 3.7 12.1 + - - -
559C LEU* 3.7 19.4 - - + +
562C LEU* 4.1 16.6 - - + -
563C ARG* 5.1 1.2 + - - -
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Residues in contact with MET 511 (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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417C ILE* 5.9 0.4 - - - -
420C TRP* 3.9 11.4 - - + -
421C ALA* 3.6 28.0 - - + -
424C ILE* 3.7 18.8 - - + -
427C PHE* 3.3 37.0 - - + -
438C LEU* 3.4 36.7 - - + +
439C PHE* 3.9 19.7 - - - -
442C ALA* 3.8 7.5 - - + +
446C LEU* 3.9 13.0 - - + -
507C ALA 3.5 0.8 + - - -
508C ALA 3.0 6.8 + - - +
510C ALA* 1.3 80.3 - - - +
512C VAL* 1.3 65.2 + - + +
513C THR* 3.0 13.8 + - - +
515C ARG* 5.0 0.3 + - - -
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Residues in contact with VAL 512 (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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424C ILE* 4.8 7.6 - - + -
427C PHE* 4.9 6.1 - - + -
430C LEU* 5.8 0.9 - - + -
438C LEU* 4.8 4.5 - - + -
508C ALA* 2.7 22.8 + - - +
509C LEU* 3.4 10.0 - - - +
511C MET* 1.3 84.9 - - + +
513C THR* 1.3 58.1 + - - +
524C VAL* 3.5 32.8 - - + +
527C LEU* 4.1 22.2 - - + -
528C GLN* 3.2 39.0 + - - +
531C ILE* 4.0 17.3 - - + -
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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