Contacts of the helix formed by residues 521 - 533 (chain D) in PDB entry 1Y9D
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 GLN 521 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515D ARG 4.9 3.0 + - - -
516D VAL* 3.2 22.9 - - + +
517D ASN* 2.8 19.4 + - - +
518D LYS* 2.8 63.9 + - + +
520D GLU* 1.3 81.3 - - + +
522D LEU* 1.3 65.9 + - - +
523D PRO 3.5 0.8 - - - -
524D ASP* 3.6 6.0 + - - +
525D VAL* 3.4 24.0 + - + +
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Residues in contact with LEU 522 (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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371D LEU* 3.5 26.0 - - + -
375D GLN* 3.4 44.6 - - + +
376D VAL* 4.4 7.0 - - + -
378D ARG* 4.3 9.2 - - - +
379D ALA* 4.0 10.3 - - + -
516D VAL* 4.2 18.4 - - + -
518D LYS 4.4 1.1 - - - +
519D ILE* 3.2 15.9 - - - +
521D GLN* 1.3 78.8 - - - +
523D PRO* 1.4 72.2 - - + +
524D ASP 3.3 0.2 + - - -
525D VAL* 3.3 2.7 + - - -
526D PHE* 3.0 51.3 + - + +
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Residues in contact with PRO 523 (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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367D GLN* 6.2 2.0 - - - +
378D ARG* 4.5 13.2 - - - +
379D ALA* 5.8 1.6 - - + -
519D ILE 3.9 4.9 - - - +
520D GLU* 3.6 15.9 - - - +
521D GLN 3.6 0.2 - - - -
522D LEU* 1.4 94.5 - - + +
524D ASP* 1.3 69.8 + - - +
526D PHE* 4.0 3.3 - - + +
527D GLU* 3.2 28.4 + - - +
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Residues in contact with ASP 524 (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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520D GLU 5.1 5.4 - - - +
521D GLN 3.6 6.0 + - - +
522D LEU 3.3 1.0 - - - -
523D PRO* 1.3 84.8 - - - +
525D VAL* 1.3 64.8 + - + +
527D GLU* 3.3 9.1 + - - +
528D GLN* 3.1 32.1 + - - +
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Residues in contact with VAL 525 (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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514D PHE* 3.5 41.0 - - + -
516D VAL* 3.6 26.2 - - + -
521D GLN* 3.4 18.1 + - + +
522D LEU* 3.3 3.7 + - - +
524D ASP* 1.3 77.3 - - + +
526D PHE* 1.3 62.0 + - + +
528D GLN* 3.2 13.7 + - - +
529D ALA* 2.9 25.5 + - - +
540D ILE* 3.8 20.4 - - + -
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Residues in contact with PHE 526 (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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376D VAL* 3.9 23.3 - - + -
379D ALA* 3.6 26.7 - - + +
380D VAL* 3.9 22.9 - - + -
383D ILE* 3.7 35.8 - - + +
468D ILE* 5.6 1.1 - - + -
470D VAL* 4.4 8.1 - - + -
522D LEU* 3.0 53.7 + - + +
523D PRO* 4.2 3.4 - - + +
525D VAL* 1.3 80.1 - - + +
527D GLU* 1.3 59.1 + - - +
529D ALA* 3.2 4.3 + - - +
530D LYS* 2.8 31.5 + - - +
540D ILE* 3.6 36.6 - - + -
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Residues in contact with GLU 527 (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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382D LYS* 5.5 2.4 - - - +
383D ILE* 3.9 17.5 - - - +
523D PRO 3.2 17.3 + - - +
524D ASP* 3.3 11.6 + - - +
526D PHE* 1.3 75.9 - - - +
528D GLN* 1.3 63.8 + - + +
530D LYS* 3.5 15.8 - - - +
531D ALA* 3.1 22.9 + - - +
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Residues in contact with GLN 528 (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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512D GLN* 5.5 1.6 - - - +
514D PHE* 3.3 38.3 - - + -
524D ASP* 3.1 18.3 + - - +
525D VAL* 3.2 14.6 + - - +
527D GLU* 1.3 79.2 - - + +
529D ALA* 1.3 50.5 + - - +
531D ALA* 3.2 6.2 + - - +
532D ILE* 2.8 44.1 + - + +
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Residues in contact with ALA 529 (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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383D ILE* 4.7 2.5 - - + -
468D ILE* 4.5 8.5 - - + -
514D PHE* 4.7 0.8 - - + -
525D VAL 2.9 13.8 + - - +
526D PHE* 3.5 8.1 - - - +
528D GLN* 1.3 72.2 - - - +
530D LYS* 1.3 66.9 + - - +
532D ILE* 3.2 0.9 + - - +
533D ALA* 2.9 28.2 + - - +
538D VAL* 3.7 30.7 - - + +
540D ILE* 3.8 26.0 - - + -
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Residues in contact with LYS 530 (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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382D LYS 5.4 1.6 - - - +
383D ILE* 3.2 54.2 + - + +
384D ALA 5.2 0.6 - - - -
385D GLU* 4.0 24.5 + - - +
440D GLN* 4.2 5.4 + - - +
468D ILE* 4.7 5.8 - - - +
526D PHE 2.8 21.0 + - - +
527D GLU* 3.5 17.5 - - - +
529D ALA* 1.3 73.0 - - - +
531D ALA* 1.3 57.4 + - - +
533D ALA* 3.6 7.6 + - - +
534D GLN* 2.7 34.6 + - - +
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Residues in contact with ALA 531 (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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527D GLU 3.1 11.2 + - - +
528D GLN* 3.7 7.9 - - - +
530D LYS* 1.3 77.3 - - - +
532D ILE* 1.3 65.3 + - - +
533D ALA 3.1 1.6 - - - -
534D GLN* 3.0 28.5 + - + +
535D HIS* 4.7 3.5 + - - -
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Residues in contact with ILE 532 (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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512D GLN* 3.5 42.0 - - + +
514D PHE* 3.6 29.2 - - + -
528D GLN* 2.8 29.6 + - + +
529D ALA 3.7 3.1 - - - +
531D ALA* 1.3 72.5 - - + +
533D ALA* 1.3 57.4 + - - +
535D HIS* 2.9 22.1 + - - +
536D GLU* 2.9 32.6 + - + +
537D PRO 4.0 6.1 - - - +
538D VAL* 3.8 18.2 - - + -
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Residues in contact with ALA 533 (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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433D LYS* 4.9 3.5 + - - -
440D GLN* 6.1 1.1 - - + -
466D PRO* 3.2 26.3 - - - +
468D ILE* 3.6 28.7 - - + -
529D ALA 2.9 17.7 + - - +
530D LYS 4.0 6.1 - - - +
531D ALA 3.1 0.4 - - - -
532D ILE* 1.3 72.3 - - - +
534D GLN* 1.3 66.2 + - - +
535D HIS 3.1 0.9 - - - -
536D GLU 3.3 12.3 - - - +
538D VAL* 4.2 3.8 - - + -
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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