Contacts of the helix formed by residues 408 - 426 (chain B) in PDB entry 5ULM
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 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B MET* 4.1 17.4 - - - +
401B PHE* 3.2 11.7 - - - -
404B SER* 2.9 25.1 + - - +
406B PHE 3.6 0.4 - - - -
407B THR* 1.3 73.1 + - - +
409B THR* 1.3 57.1 + - - +
410B GLU* 3.5 12.3 + - - +
411B SER* 2.6 39.4 + - - -
412B ARG 3.1 20.6 + - - -
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B PHE* 4.6 2.2 - - + -
406B PHE 4.5 8.1 - - - +
407B THR* 2.8 20.4 + - - +
408B ASP* 1.3 69.8 - - - +
410B GLU* 1.3 63.0 + - - +
411B SER 3.4 0.2 - - - -
412B ARG* 3.3 39.2 - - - +
413B ASP* 3.0 32.8 + - - -
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP* 3.3 9.3 + - - +
409B THR* 1.3 77.4 + - - +
411B SER* 1.3 61.3 + - - +
413B ASP* 3.2 7.4 + - - +
414B HIS* 2.9 52.3 + - + +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TYR* 3.3 40.3 - - - +
400B MET* 3.4 26.4 - - - +
401B PHE 4.2 0.9 - - - -
408B ASP* 2.6 35.5 + - - -
410B GLU* 1.3 77.2 - - - +
412B ARG* 1.3 57.2 + - - +
414B HIS* 3.4 2.4 + - - -
415B GLY* 2.8 26.0 + - - -
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TYR 5.6 0.4 - - - -
401B PHE* 3.6 51.2 - - + +
408B ASP 3.1 5.9 + - - -
409B THR* 3.3 40.4 - - - +
411B SER* 1.3 76.8 - - - +
413B ASP* 1.3 89.6 + - - +
415B GLY* 3.3 2.1 + - - -
416B ALA* 2.9 27.3 + - + +
438B LEU* 3.9 23.7 - - + +
441B ALA* 3.6 15.5 + - - -
442B ALA* 3.6 33.9 + - - +
524B PHE* 6.2 0.2 - - - -
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Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR 3.0 14.7 + - - +
410B GLU* 3.2 6.2 + - - +
412B ARG* 1.3 110.4 + - - +
414B HIS* 1.3 62.6 + - + +
416B ALA* 3.4 7.8 + - - +
417B SER* 3.0 31.0 + - - -
442B ALA* 4.2 6.9 - - - +
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Residues in contact with HIS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TYR* 3.8 39.0 - + + -
410B GLU* 2.9 45.3 + - + +
411B SER* 3.8 1.4 + - - +
413B ASP* 1.3 73.8 - - + +
415B GLY* 1.3 65.2 + - - +
417B SER* 3.3 8.1 + - - -
418B TRP* 3.1 32.0 + - + -
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Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLY* 4.0 9.2 - - - -
397B TYR* 3.5 21.4 - - - +
411B SER 2.8 12.7 + - - -
412B ARG 3.3 3.1 + - - -
414B HIS* 1.3 76.6 - - - +
416B ALA* 1.3 62.0 + - - +
418B TRP* 3.3 2.8 + - - +
419B PHE* 3.1 27.9 + - - -
438B LEU* 3.6 14.4 - - - -
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Residues in contact with ALA 416 (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 ARG* 2.9 14.6 + - + +
413B ASP* 3.5 12.6 - - - +
414B HIS 3.3 0.2 - - - -
415B GLY* 1.3 75.5 - - - +
417B SER* 1.4 56.6 + - - +
419B PHE* 3.4 1.9 + - - -
420B LYS* 2.8 31.7 + - - +
435B TYR* 3.5 21.7 - - + -
438B LEU* 3.5 27.3 - - + +
439B LEU* 4.9 5.8 - - + -
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Residues in contact with SER 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP 3.0 16.9 + - - -
414B HIS* 3.3 12.3 + - - -
416B ALA* 1.4 75.7 - - - +
418B TRP* 1.3 62.4 + - - +
420B LYS* 3.3 12.2 + - - +
421B LYS* 3.0 28.6 + - - +
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Residues in contact with TRP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ILE* 4.0 24.4 - - + +
379B VAL* 3.6 41.5 - - + -
380B GLN* 3.8 30.3 - - + -
390B TYR* 3.7 33.5 - + - +
393B VAL* 3.5 21.8 - - + -
394B GLY* 3.9 20.6 - - - +
397B TYR* 3.8 22.0 + + - -
414B HIS* 3.1 31.6 + + + +
415B GLY 3.9 0.2 - - - +
417B SER* 1.3 81.7 - - - +
419B PHE* 1.3 63.1 + - - +
421B LYS* 3.3 7.9 + - + +
422B ALA* 3.1 21.3 + - - +
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Residues in contact with PHE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B CYS* 3.5 43.7 - - + -
394B GLY* 3.5 32.5 - - - -
395B ARG* 3.5 9.0 - - + -
398B LYS* 4.4 5.8 - - + -
415B GLY 3.1 23.9 + - - +
416B ALA 3.9 3.1 - - - +
418B TRP* 1.3 72.7 - - - +
420B LYS* 1.3 60.9 + - - +
422B ALA* 3.4 5.4 + - - +
423B PHE* 2.8 30.5 + - - +
430B GLN* 5.5 0.7 - - - -
431B SER* 3.7 17.5 - - - +
434B ASN* 3.5 44.9 - - + -
435B TYR* 3.9 10.5 - - + +
438B LEU* 3.9 18.4 - - + -
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ALA 2.8 21.4 + - - +
417B SER* 3.4 11.4 - - - +
419B PHE* 1.3 71.5 - - - +
421B LYS* 1.3 58.2 + - - +
423B PHE* 3.0 4.7 + - - +
424B GLU* 2.9 64.5 + - + +
435B TYR* 2.9 49.5 + - + +
451B GLU* 5.1 4.6 - - - +
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B TYR* 3.7 37.5 + - + -
417B SER 3.0 13.9 + - - +
418B TRP* 3.6 11.2 - - + +
420B LYS* 1.3 74.5 - - - +
422B ALA* 1.3 58.0 + - - +
424B GLU* 3.4 10.7 + - + +
425B SER* 2.8 50.6 + - - +
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Residues in contact with ALA 422 (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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387B SER* 4.4 7.7 + - - +
390B TYR* 3.6 35.7 - - + -
391B CYS* 4.2 8.7 - - - -
418B TRP 3.1 6.1 + - - +
419B PHE* 3.4 10.3 - - - +
421B LYS* 1.3 79.0 - - - +
423B PHE* 1.3 53.4 + - - +
425B SER* 3.7 0.8 - - - -
426B GLU* 2.7 39.4 + - - +
431B SER* 3.6 17.7 - - - -
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Residues in contact with PHE 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 PHE 2.8 20.4 + - - +
420B LYS* 3.0 8.3 + - - +
422B ALA* 1.3 73.0 - - - +
424B GLU* 1.3 63.3 + - + +
427B PRO* 3.2 37.2 - - + +
428B THR 3.5 17.3 - - - -
431B SER* 3.3 16.2 - - - +
432B GLY* 3.4 24.7 - - - -
435B TYR* 4.6 15.3 - + + -
455B VAL* 4.0 26.2 - - + -
458B LYS* 3.5 47.8 + - + -
459B LEU* 4.5 4.0 - - + -
462B LEU* 4.0 13.5 - - + -
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Residues in contact with GLU 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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420B LYS* 2.9 57.5 + - + +
421B LYS* 4.1 9.9 - - + +
423B PHE* 1.3 81.1 - - + +
425B SER* 1.3 63.7 + - - +
427B PRO* 4.5 4.3 - - - +
435B TYR* 5.8 0.3 - - - -
454B LYS* 5.2 8.9 + - - +
458B LYS* 4.5 13.0 + - - +
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL 4.5 4.7 + - - -
390B TYR* 4.1 19.4 + - - -
421B LYS* 2.8 36.8 + - - +
422B ALA* 3.7 3.4 - - - -
424B GLU* 1.3 78.7 - - - +
426B GLU* 1.3 63.0 + - - +
427B PRO* 4.1 2.5 - - - +
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Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL 5.6 0.2 - - - +
386B ALA* 4.9 4.0 - - - +
387B SER* 4.2 31.2 + - - +
422B ALA 2.7 20.7 + - - +
425B SER* 1.3 80.4 - - - +
427B PRO* 1.3 72.8 - - + +
428B THR* 3.2 26.7 + - + +
431B SER* 4.2 0.3 + - - -
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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
------------------------------------------------------------
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