Contacts of the helix formed by residues 499 - 512 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B SER* 5.4 0.9 + - - -
366B SER* 3.4 16.6 + - - +
370B ARG* 3.3 17.3 - - - +
453D TYR* 3.4 0.9 - - - -
497D ASN 3.7 4.2 + - - +
498D ILE* 1.3 75.9 - - - +
500D ILE* 1.3 55.3 + - - +
501D SER* 4.2 3.0 + - - -
502D ALA* 3.3 12.8 + - - +
503D PHE* 2.8 31.5 + - - +
538D HIS* 2.9 37.4 + - - -
542D ASN* 3.8 16.6 + - - +
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Residues in contact with ILE 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL* 4.2 14.6 - - + -
370B ARG* 3.1 52.0 - - - +
373B VAL* 4.8 15.5 - - + -
369D VAL* 3.9 26.9 - - + -
372D HIS* 4.2 17.3 - - + +
373D VAL* 4.6 6.5 - - + -
453D TYR* 3.7 19.1 - - + +
499D ASP* 1.3 73.4 - - - +
501D SER* 1.3 54.7 + - - +
503D PHE* 3.9 3.0 - - - +
504D SER* 2.6 43.1 + - - +
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Residues in contact with SER 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B SER* 5.0 6.8 + - - -
365D ILE* 3.7 16.4 - - - +
369D VAL* 3.5 22.0 - - - +
499D ASP* 3.3 3.6 + - - -
500D ILE* 1.3 76.2 - - - +
502D ALA* 1.3 61.7 + - - +
504D SER* 3.5 3.8 + - - -
505D CYS* 3.3 27.5 + - - -
538D HIS* 3.4 34.9 + - - -
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Residues in contact with ALA 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D ILE* 3.6 17.5 - - + -
499D ASP* 3.2 18.6 + - - +
501D SER* 1.3 75.4 - - - +
503D PHE* 1.3 65.5 + - - +
505D CYS* 3.3 4.8 + - - +
506D ILE* 3.1 25.5 + - - +
535D LEU* 3.9 23.4 - - + +
538D HIS* 4.1 8.8 + - - +
539D VAL* 4.8 5.4 - - + -
551D TYR* 5.8 2.2 - - + +
555D LEU* 4.5 7.9 - - + -
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Residues in contact with PHE 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D HIS* 3.4 40.2 - + - -
449D LEU* 3.4 50.7 - - + -
450D ARG* 4.0 10.3 - - + -
453D TYR* 3.5 64.4 - + + -
493D LEU* 4.4 4.0 - - + -
498D ILE* 3.4 13.3 - - + +
499D ASP 2.8 15.4 + - - +
500D ILE 4.0 2.5 - - - +
502D ALA* 1.3 71.6 - - - +
504D SER* 1.3 62.6 + - - +
506D ILE* 3.2 9.0 + - + +
507D ALA* 3.0 29.3 + - + +
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Residues in contact with SER 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LEU* 3.5 33.1 - - - +
369D VAL* 3.4 19.0 - - - -
372D HIS* 3.5 17.4 - - - +
420D TRP* 4.9 3.7 + - - +
500D ILE* 2.6 25.0 + - - +
501D SER 3.6 6.1 - - - -
502D ALA 3.2 0.2 - - - -
503D PHE* 1.3 78.9 - - - +
505D CYS* 1.3 57.0 + - - +
507D ALA* 3.9 5.1 + - - +
508D ALA* 3.2 25.8 + - - +
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Residues in contact with CYS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D ILE* 3.6 27.8 - - - -
368D LEU* 3.9 17.5 - - - -
501D SER 3.3 15.7 + - - -
502D ALA 3.3 7.6 + - - +
503D PHE 3.2 0.4 - - - -
504D SER* 1.3 75.2 - - - +
506D ILE* 1.3 55.0 + - - +
508D ALA 3.1 2.1 + - - -
509D LEU* 2.8 39.8 + - - +
531D ILE* 3.5 12.2 - - + +
534D CYS* 4.5 2.0 - - - -
535D LEU* 3.8 36.1 - - + -
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Residues in contact with ILE 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LEU* 4.0 24.7 - - + -
493D LEU* 5.8 2.7 - - + -
498D ILE* 5.6 2.7 - - + -
502D ALA 3.1 14.3 + - - +
503D PHE* 3.2 12.3 + - + +
505D CYS* 1.3 76.5 - - - +
507D ALA* 1.3 57.8 + - - +
509D LEU* 3.2 8.8 + - + +
510D ALA* 3.0 24.1 + - - +
535D LEU* 3.9 23.6 - - + -
555D LEU* 3.5 42.6 - - + +
556D LEU* 3.9 14.8 - - + -
558D LYS* 5.3 6.1 - - + -
559D LEU* 3.7 19.3 - - + +
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Residues in contact with ALA 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D HIS* 5.6 1.6 - - + -
420D TRP* 3.4 30.6 - - + +
446D LEU* 3.6 7.7 - - + +
449D LEU* 3.7 21.2 - - + +
450D ARG* 5.3 4.3 - - + -
503D PHE* 3.0 30.2 + - + +
504D SER* 3.9 4.9 - - - +
506D ILE* 1.3 76.6 - - - +
508D ALA* 1.3 62.7 + - - +
510D ALA* 3.1 17.2 + - - +
511D MET 3.5 1.6 + - - -
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Residues in contact with ALA 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LEU* 3.9 26.2 - - + -
420D TRP* 3.6 12.5 - - + -
424D ILE* 4.2 11.4 - - + -
504D SER 3.2 12.6 + - - +
505D CYS 3.1 8.3 + - - +
507D ALA* 1.3 78.1 - - - +
509D LEU* 1.3 52.0 + - - +
511D MET* 3.2 2.8 + - - +
512D VAL* 2.8 40.2 + - - +
531D ILE* 3.9 15.5 - - + -
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Residues in contact with LEU 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D CYS 2.8 23.7 + - - +
506D ILE* 3.2 11.4 + - + +
508D ALA* 1.3 68.2 - - - +
510D ALA* 1.3 64.3 + - - +
511D MET 3.2 2.1 + - - -
512D VAL 3.6 14.1 - - - +
513D THR* 3.8 10.4 - - - -
528D GLN* 3.5 39.9 + - + +
531D ILE* 3.7 17.0 - - + -
532D VAL* 3.5 17.9 - - + -
535D LEU* 4.0 15.7 - - + -
556D LEU* 3.8 29.2 - - + -
559D LEU* 4.0 18.0 - - + +
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Residues in contact with ALA 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D ALA* 3.4 14.9 - - - +
445D GLU* 4.4 13.9 - - + +
446D LEU* 4.5 12.6 - - + -
449D LEU* 4.5 0.2 - - + -
506D ILE 3.0 12.6 + - - +
507D ALA* 3.1 14.8 + - - +
509D LEU* 1.3 75.3 - - - +
511D MET* 1.3 58.3 + - - +
513D THR* 3.8 4.2 - - - +
515D ARG* 3.6 11.6 + - - -
559D LEU* 4.0 17.2 - - + +
562D LEU* 4.1 18.2 - - + -
563D ARG* 5.0 0.7 + - - +
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Residues in contact with MET 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D TRP* 3.6 12.1 - - + -
421D ALA* 3.6 21.3 - - + -
424D ILE* 3.6 30.5 - - + -
427D PHE* 3.5 26.2 - - + -
438D LEU* 3.4 39.3 - - + +
439D PHE* 3.8 22.7 - - - -
442D ALA* 3.8 9.8 - - + +
446D LEU* 4.0 12.3 - - + -
507D ALA 3.5 1.0 + - - -
508D ALA 3.2 4.9 + - - +
509D LEU 3.2 0.2 - - - -
510D ALA* 1.3 81.8 - - - +
512D VAL* 1.3 62.8 + - + +
513D THR* 3.0 12.5 + - - +
515D ARG* 5.0 0.7 + - - -
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Residues in contact with VAL 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D ILE* 4.5 8.1 - - + -
427D PHE* 5.0 7.0 - - + -
430D LEU* 5.9 0.7 - - + -
438D LEU* 4.7 5.2 - - + -
508D ALA 2.8 23.4 + - - +
509D LEU* 3.6 9.0 - - - +
511D MET* 1.3 83.9 - - + +
513D THR* 1.3 60.3 + - - +
524D VAL* 3.5 34.8 - - + +
527D LEU* 3.8 25.6 - - + -
528D GLN* 3.4 33.3 - - - +
531D ILE* 4.1 16.4 - - + -
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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