Contacts of the helix formed by residues 509 - 520 (chain B) in PDB entry 3P0U
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 TYR 509 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389B LYS 4.6 0.4 - - - -
390B LEU* 3.4 53.0 - - + +
392B MET* 3.5 36.3 - - + +
419B TRP* 5.5 1.1 - - - -
449B GLY* 4.6 1.9 - - - -
452B GLN* 3.8 22.5 + - + +
508B GLY* 1.3 74.9 - - - -
510B GLU* 1.3 55.4 + - - +
511B TYR* 2.9 35.9 - + + +
512B ALA* 3.0 44.6 + - + +
513B TYR* 3.8 5.5 + - - -
515B LYS* 3.4 28.8 + - + -
547B TYR* 4.6 2.6 + - - -
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Residues in contact with GLU 510 (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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506B ILE* 3.3 16.5 - - + +
507B ASP* 2.7 57.5 + - - +
508B GLY 3.2 3.0 + - - -
509B TYR* 1.3 72.2 - - - +
511B TYR* 1.3 55.3 + - - +
513B TYR* 3.0 11.8 + - - +
514B LEU* 2.7 44.6 + - + +
544B LEU* 4.2 12.8 - - + -
547B TYR* 3.6 21.5 - - + -
548B VAL* 3.5 19.4 - - - +
558B ARG* 3.4 18.0 + - - -
562B ILE* 4.3 8.6 - - + +
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Residues in contact with TYR 511 (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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448B LEU* 3.5 41.7 - - + +
449B GLY* 5.6 0.2 - - - -
451B ALA* 2.9 36.1 + - + +
452B GLN* 5.8 2.0 - - + -
501B MET* 3.6 23.8 - - + +
502B ALA* 4.9 1.0 + - - -
506B ILE* 3.4 46.1 - - + +
509B TYR* 3.5 42.8 - + + -
510B GLU* 1.3 76.9 - - - +
512B ALA* 1.3 51.9 + - - +
514B LEU* 3.1 10.3 + - + +
515B LYS* 2.6 43.8 + - - +
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Residues in contact with ALA 512 (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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389B LYS* 2.9 30.7 - - + +
390B LEU* 4.9 2.2 - - + -
419B TRP* 3.2 29.9 - - + -
509B TYR* 3.0 25.7 + - + +
511B TYR* 1.3 77.7 - - - +
513B TYR* 1.3 64.0 + - + +
515B LYS* 3.0 4.0 + - - -
516B ALA* 3.0 22.5 + - - +
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Residues in contact with TYR 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B HIS* 4.2 29.9 + + + +
389B LYS* 6.6 0.4 - - + -
390B LEU* 6.2 7.0 - - + -
509B TYR 3.8 7.4 + - - -
510B GLU* 3.0 10.7 + - - +
512B ALA* 1.3 81.7 - - + +
514B LEU* 1.3 64.4 + - - +
516B ALA* 3.0 17.0 + - + +
517B ILE* 3.1 19.6 + - - +
540B ALA* 4.7 16.6 - - + +
543B GLU* 2.7 41.7 + - + +
544B LEU* 4.1 36.1 - - + -
547B TYR* 4.9 16.8 - + + -
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Residues in contact with LEU 514 (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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448B LEU* 3.8 16.6 - - + -
501B MET* 5.4 5.8 - - - -
506B ILE* 4.9 11.9 - - + -
510B GLU* 2.7 34.4 + - + +
511B TYR* 3.6 13.2 - - + +
513B TYR* 1.3 72.7 - - - +
515B LYS* 1.3 59.4 + - - +
517B ILE* 3.4 7.0 + - + +
518B VAL* 3.0 29.8 + - - +
544B LEU* 4.1 22.4 - - + +
562B ILE* 4.1 25.6 - - + +
563B LEU* 4.2 4.9 - - + -
565B ARG* 6.4 0.4 - - + -
566B LEU* 4.0 31.1 - - + +
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Residues in contact with LYS 515 (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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392B MET* 3.6 18.6 - - - -
416B SER* 5.2 4.0 - - - -
419B TRP* 3.6 33.0 - - + -
445B LEU* 3.6 24.7 - - + +
448B LEU* 3.6 18.2 - - + -
449B GLY* 3.9 26.0 - - - +
509B TYR* 3.4 38.4 + - - -
511B TYR* 2.6 35.5 + - - +
512B ALA* 3.0 10.1 + - - +
514B LEU* 1.3 73.9 - - - +
516B ALA* 1.3 56.3 + - - +
518B VAL 3.8 0.2 - - - -
519B LEU* 2.8 29.6 + - - +
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Residues in contact with ALA 516 (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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385B HIS* 6.3 1.8 - - + +
419B TRP* 4.3 5.8 - - + -
423B ILE* 6.5 0.4 - - + -
512B ALA 3.0 10.9 + - - +
513B TYR* 3.0 15.4 + - + +
515B LYS* 1.3 75.7 - - - +
517B ILE* 1.3 66.6 + - - +
518B VAL 3.0 1.8 - - - -
519B LEU* 4.2 2.7 - - - -
520B PHE* 2.9 49.3 + - + +
540B ALA* 3.7 21.1 - - + -
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Residues in contact with ILE 517 (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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564A VAL* 3.4 26.9 - - + -
567A PRO* 6.5 0.4 - - + -
513B TYR 3.1 13.6 + - - +
514B LEU* 3.4 18.4 + - + +
516B ALA* 1.3 77.7 - - - +
518B VAL* 1.3 62.3 + - + +
520B PHE 3.9 2.9 - - - -
521B SER* 4.0 3.3 + - - -
537B GLN* 2.7 49.2 - - - +
540B ALA* 3.3 41.7 - - + +
541B GLN* 3.6 11.9 - - + +
544B LEU* 4.9 7.9 - - + -
563B LEU* 5.2 2.7 - - + -
566B LEU* 5.1 14.6 - - + -
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Residues in contact with VAL 518 (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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441B CYS* 4.3 11.7 - - + +
444B GLU* 3.4 42.4 - - + +
445B LEU* 3.6 17.9 - - + +
448B LEU* 3.7 14.8 - - + -
514B LEU 3.0 17.9 + - - +
515B LYS 3.6 4.9 - - - +
517B ILE* 1.3 78.9 - - - +
519B LEU* 1.3 68.0 + - - +
521B SER* 3.5 15.8 - - - -
524B HIS* 4.5 0.7 + - - -
566B LEU* 3.9 11.2 - - + -
569B LEU* 3.8 16.4 - - + -
570B ARG* 5.9 0.2 - - - +
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Residues in contact with LEU 519 (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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419B TRP* 4.6 7.9 - - + -
420B ALA* 3.4 30.3 - - + +
423B ILE* 4.5 2.9 - - + -
426B PHE* 3.6 33.2 - - + -
437B LEU* 3.1 28.2 - - + +
438B VAL* 4.4 9.4 - - - +
441B CYS* 3.8 26.0 - - - -
445B LEU* 4.0 15.0 - - + -
515B LYS 2.8 19.1 + - - +
516B ALA* 3.1 5.4 + - - +
518B VAL* 1.3 77.6 - - - +
520B PHE* 1.3 76.1 + - + +
521B SER* 3.1 5.4 + - - -
524B HIS* 5.0 0.9 - - - -
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Residues in contact with PHE 520 (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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385B HIS* 5.6 4.0 - - - -
423B ILE* 4.3 15.3 - - + -
425B ALA* 4.3 9.0 - - + -
426B PHE* 4.2 29.6 - + - -
429B LEU* 5.3 2.5 - - + -
437B LEU* 4.1 14.6 - - + -
516B ALA* 2.9 43.3 + - + +
517B ILE 3.9 4.3 - - - -
519B LEU* 1.3 95.1 - - + +
521B SER* 1.3 58.4 + - - +
522B PRO* 3.5 1.4 - - - +
533B ILE* 3.4 32.0 - - + +
536B PHE* 3.8 37.7 - + + -
537B GLN* 3.0 29.6 - - + +
540B ALA* 6.0 0.2 - - + -
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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