Contacts of the helix formed by residues 413 - 429 (chain B) in PDB entry 3U0Z
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 PRO 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411B LYS 3.6 5.1 - - - +
412B LEU* 1.3 89.6 - - + +
414B ALA* 1.4 64.0 + - - +
415B ASP* 3.5 13.5 - - - +
416B MET* 3.0 43.6 + - + +
417B ARG* 3.1 11.9 + - - +
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Residues in contact with ALA 414 (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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412B LEU 4.0 0.2 + - - -
413B PRO* 1.4 70.7 - - - +
415B ASP* 1.3 60.1 + - - +
417B ARG* 3.6 11.4 + - - +
418B GLN* 2.9 29.5 + - - +
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Residues in contact with ASP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PRO* 4.1 10.0 - - - +
414B ALA* 1.3 77.4 + - - +
416B MET* 1.3 62.3 + - - +
418B GLN* 3.5 9.9 - - + +
419B LYS* 3.0 25.8 + - - +
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.1 22.9 - - + -
413B PRO* 3.0 34.4 + - + +
415B ASP* 1.3 81.8 - - - +
417B ARG* 1.3 59.5 + - - +
418B GLN 3.2 0.2 - - - -
419B LYS* 3.5 7.8 + - + +
420B ILE* 3.0 43.8 + - + +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B TYR* 4.6 0.7 + - - -
404B GLU 4.9 1.0 + - - -
407B MET* 3.4 53.2 + - + +
408B SER* 3.7 30.6 + - - +
411B LYS* 3.5 9.9 - - - +
412B LEU* 2.7 44.7 + - + +
413B PRO 3.1 11.8 + - - +
414B ALA* 3.7 11.2 - - - +
416B MET* 1.3 69.3 - - - +
418B GLN* 1.3 61.3 + - - +
420B ILE* 3.8 1.3 - - - +
421B HIS* 2.9 31.1 + - - +
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Residues in contact with GLN 418 (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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414B ALA 2.9 16.8 + - - +
415B ASP* 3.5 14.1 - - - +
417B ARG* 1.3 73.4 - - - +
419B LYS* 1.3 57.4 + - - +
421B HIS* 2.8 43.3 + - - +
422B ASP* 2.8 30.6 + - - +
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Residues in contact with LYS 419 (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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415B ASP 3.0 15.5 + - - +
416B MET* 3.6 11.2 - - + +
418B GLN* 1.3 78.0 - - - +
420B ILE* 1.3 62.8 + - + +
422B ASP* 3.6 3.5 - - - +
423B TYR* 3.2 8.3 + - - +
486B GLN* 2.9 51.7 + - - +
487B PRO 5.4 5.4 + - - -
489B ASP* 2.9 30.4 + - - -
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Residues in contact with ILE 420 (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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400B TYR* 4.9 1.3 - - + -
403B VAL* 4.2 24.7 - - + -
406B TYR* 6.5 0.2 - - + -
407B MET* 4.1 19.5 - - + -
412B LEU* 4.3 16.2 - - + -
416B MET* 3.0 29.6 + - + +
417B ARG 3.8 3.1 - - - +
419B LYS* 1.3 73.9 - - + +
421B HIS* 1.3 68.8 + - - +
423B TYR* 3.2 10.1 + - + +
424B TYR* 3.1 26.1 + - + +
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Residues in contact with HIS 421 (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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396B TYR* 5.9 0.4 - - - -
400B TYR* 2.9 50.2 + + - +
417B ARG 2.9 16.0 + - - +
418B GLN* 2.8 29.7 + - - +
420B ILE* 1.3 69.4 - - - +
422B ASP* 1.3 72.1 + - - +
423B TYR 3.0 0.7 + - - -
424B TYR* 3.1 12.4 + - - +
425B GLU* 2.8 47.1 + - + +
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLN* 2.8 34.3 + - - +
419B LYS* 3.6 11.2 - - - +
421B HIS* 1.3 77.4 - - - +
423B TYR* 1.3 64.5 + - - +
425B GLU* 3.1 10.5 + - - +
426B HIS* 3.1 31.9 + - - -
486B GLN* 3.6 9.2 - - - +
547B TYR* 2.7 20.3 + - - +
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Residues in contact with TYR 423 (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 LYS 3.2 8.5 + - - +
420B ILE* 3.8 9.9 - - + +
421B HIS 3.1 1.2 - - - -
422B ASP* 1.3 78.5 - - - +
424B TYR* 1.3 68.7 + + - +
426B HIS* 3.1 5.6 + - - +
427B ARG* 2.6 79.5 + - + +
428B TYR* 4.8 5.5 + + - -
484B VAL* 3.5 37.3 + - + -
486B GLN* 3.6 31.0 - - + +
547B TYR* 5.2 0.2 - - - -
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Residues in contact with TYR 424 (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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396B TYR* 3.6 34.7 + + - +
399B LYS* 3.7 15.9 - - - +
400B TYR* 3.9 38.4 - + + -
403B VAL* 4.1 20.8 - - + +
420B ILE* 3.1 15.9 + - + +
421B HIS* 3.3 10.8 - - - +
423B TYR* 1.3 89.0 - + - +
425B GLU* 1.3 64.6 + - + +
427B ARG* 4.3 1.6 - - - -
428B TYR* 2.9 55.5 + + - +
429B GLN 3.7 1.6 + - - -
432B ILE* 3.5 20.4 - - + +
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B TYR* 3.6 20.4 + - - +
421B HIS* 2.8 43.5 + - + +
422B ASP* 3.1 14.6 + - - +
424B TYR* 1.3 77.2 - - + +
426B HIS* 1.3 63.8 + - + +
429B GLN* 2.4 40.0 + - - +
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Residues in contact with HIS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ASP* 3.1 27.9 + - - +
423B TYR* 3.8 4.3 - - - +
425B GLU* 1.3 81.6 + - + +
427B ARG* 1.3 64.7 + - - +
429B GLN* 3.8 22.0 + - - +
482B PHE* 5.6 0.2 - - - -
484B VAL* 4.3 15.4 - - + +
547B TYR* 3.4 58.4 + + + +
549B ARG* 5.2 7.4 + - - -
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B TYR* 2.6 61.4 + - + +
424B TYR 3.8 1.8 - - - +
426B HIS* 1.3 77.4 - - - +
428B TYR* 1.3 96.7 + - + +
482B PHE* 3.4 47.1 + - - +
483B GLU* 4.8 0.8 - - - +
484B VAL* 4.0 26.9 - - + +
549B ARG* 5.8 0.9 + - - -
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Residues in contact with TYR 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B TYR* 3.8 12.1 - - + -
423B TYR* 4.8 6.0 + + - -
424B TYR* 2.9 59.4 + + - +
427B ARG* 1.3 116.7 + - + +
429B GLN* 1.3 72.2 + - - +
431B LYS* 3.2 28.8 + - - +
432B ILE* 3.5 27.1 - - + -
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Residues in contact with GLN 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR 3.7 0.2 + - - -
425B GLU* 2.4 35.0 + - - +
426B HIS* 3.8 22.2 + - - +
427B ARG 5.2 0.2 - - - -
428B TYR* 1.3 74.7 - - - +
430B GLY* 1.3 57.5 + - - +
431B LYS* 3.3 7.0 + - - +
549B ARG* 4.6 17.2 + - - +
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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