Contacts of the helix formed by residues 409 - 432 (chain B) in PDB entry 2BTO
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 SER 409 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B LEU* 4.2 3.6 - - - -
407B GLY 3.9 1.3 + - - -
408B MET* 1.3 73.6 - - - +
410B GLU* 1.3 65.5 + - - +
411B GLU* 4.1 6.6 + - - +
412B GLN* 3.0 44.4 + - - +
413B ILE* 3.2 15.1 + - - +
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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
----------------------------------------------------------
394B TRP* 3.8 21.8 - - + -
397B LYS* 4.0 22.5 + - - +
404B LEU* 3.7 26.2 - - + +
409B SER* 1.3 73.3 - - - +
411B GLU* 1.3 60.5 + - - +
413B ILE* 3.5 12.1 + - - +
414B ASN* 3.0 28.9 + - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B SER* 3.3 6.6 + - - +
410B GLU* 1.3 79.1 - - - +
412B GLN* 1.3 58.9 + - - +
414B ASN* 3.2 20.2 - - + +
415B VAL* 3.1 35.9 + - + +
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 6.4 0.2 - - - -
110B LEU* 5.2 6.5 - - - +
407B GLY 4.5 3.4 + - - +
408B MET* 4.0 26.2 - - + +
409B SER* 3.0 40.8 + - - +
411B GLU* 1.3 77.5 + - - +
413B ILE* 1.3 67.9 + - + +
415B VAL* 3.3 14.6 - - + +
416B LEU* 3.3 26.1 + - + +
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Residues in contact with ILE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 4.6 1.3 - - + -
191B PHE* 3.8 21.3 - - + -
390B PHE* 3.5 34.4 - - + -
394B TRP* 3.4 48.0 - - + -
403B TYR* 5.8 3.6 - - + -
404B LEU* 5.6 3.8 - - + -
408B MET* 3.9 26.0 - - + -
409B SER 3.2 19.3 + - - +
410B GLU* 3.7 4.5 - - - +
411B GLU 3.3 0.4 - - - -
412B GLN* 1.3 73.4 - - - +
414B ASN* 1.3 62.5 + - - +
415B VAL 3.2 0.4 - - - -
416B LEU* 3.3 9.8 + - - +
417B ARG* 2.9 27.4 + - - +
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Residues in contact with ASN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TRP* 3.0 28.0 + - - -
397B LYS* 5.2 0.9 + - - +
410B GLU* 3.0 26.6 + - - +
411B GLU* 3.2 24.1 + - + +
413B ILE* 1.3 79.5 - - - +
415B VAL* 1.3 56.9 + - + +
417B ARG* 3.7 7.1 - - - +
418B ALA* 2.8 30.3 + - - +
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLU* 3.1 24.2 + - + +
412B GLN* 3.3 16.6 - - + +
413B ILE 3.2 0.2 - - - -
414B ASN* 1.3 76.3 - - + +
416B LEU* 1.3 55.5 + - + +
418B ALA* 3.3 6.8 + - - +
419B SER* 2.7 35.8 + - - -
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Residues in contact with LEU 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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105B PHE* 5.5 2.5 - - + -
190B VAL* 3.8 7.9 - - - +
191B PHE* 3.8 30.1 - - + +
194B ASN* 3.5 41.6 - - + +
408B MET* 3.6 31.0 - - + -
412B GLN* 3.3 20.8 + - + +
413B ILE* 3.7 6.1 - - - +
414B ASN 3.3 0.4 - - - -
415B VAL* 1.3 78.3 - - + +
417B ARG* 1.3 65.5 + - - +
418B ALA 3.3 0.2 - - - -
419B SER* 3.7 6.1 - - - -
420B ALA* 3.2 22.9 + - - +
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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
----------------------------------------------------------
190B VAL* 4.2 8.9 - - - +
387B CYS* 3.7 33.4 - - - +
390B PHE* 3.6 33.9 - - + -
391B ASP* 2.8 49.1 + - - +
394B TRP* 5.7 2.2 - - + -
413B ILE 2.9 16.5 + - - +
414B ASN* 3.3 8.9 + - - +
416B LEU* 1.3 76.3 - - - +
418B ALA* 1.3 57.5 + - - +
420B ALA* 3.5 2.5 + - - +
421B GLN* 3.0 69.7 + - - +
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ASN 2.8 17.5 + - - +
415B VAL* 3.5 8.1 - - - +
417B ARG* 1.3 75.6 - - - +
419B SER* 1.3 60.6 + - - +
421B GLN* 3.1 10.1 + - - +
422B GLU* 2.9 30.1 + - - +
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Residues in contact with SER 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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194B ASN* 2.5 36.5 + - - +
197B ARG* 3.4 29.8 + - - +
198B ARG* 4.9 2.4 - - - -
415B VAL* 2.7 23.2 + - - -
416B LEU* 3.7 9.9 - - - -
417B ARG 3.4 0.2 - - - -
418B ALA* 1.3 73.0 - - - +
420B ALA* 1.3 61.1 + - - +
422B GLU* 3.3 21.0 + - - +
423B LEU 3.4 3.5 + - - -
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Residues in contact with ALA 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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190B VAL* 4.3 17.9 - - + +
193B LEU* 4.5 23.6 - - + -
194B ASN* 5.8 2.2 - - - +
197B ARG* 5.5 0.7 - - - +
387B CYS* 4.5 11.9 - - - -
416B LEU 3.2 14.2 + - - +
417B ARG* 3.9 5.2 - - - +
419B SER* 1.3 76.3 - - - +
421B GLN* 1.3 61.6 + - - +
423B LEU* 3.1 10.9 + - + +
424B VAL* 3.0 33.1 + - + +
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 5.8 1.4 + - - -
387B CYS* 5.4 0.8 - - - +
417B ARG* 3.0 43.2 + - - +
418B ALA* 3.3 13.9 - - - +
420B ALA* 1.3 78.7 - - - +
422B GLU* 1.3 53.9 + - - +
424B VAL* 4.1 18.6 - - - +
425B GLN* 2.9 38.9 + - + +
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 3.3 30.2 + - - +
198B ARG* 5.0 4.2 + - - -
418B ALA 2.9 10.8 + - - +
419B SER* 3.3 16.8 - - - +
421B GLN* 1.3 76.2 - - - +
423B LEU* 1.3 57.1 + - - +
425B GLN* 3.4 21.8 - - + +
426B SER* 2.8 27.5 + - - -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 5.2 6.7 - - + -
197B ARG* 3.7 38.8 - - + +
268B SER 3.9 16.6 - - - +
270B HIS 5.8 0.2 - - - +
271B PHE* 3.9 28.0 - - + -
383B LEU* 3.5 34.5 - - + -
419B SER 3.4 2.4 + - - +
420B ALA* 3.1 13.4 + - - +
422B GLU* 1.3 78.9 - - - +
424B VAL* 1.3 63.2 + - + +
425B GLN 3.3 0.2 - - - -
426B SER* 3.3 18.6 + - - -
427B TYR* 3.4 30.2 + - + -
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 6.6 0.2 - - + -
380B ALA* 4.3 14.6 - - + +
383B LEU* 3.8 35.4 - - + -
384B ASP* 4.1 23.1 - - - +
387B CYS* 4.7 9.2 - - - -
420B ALA* 3.0 19.9 + - + +
421B GLN* 3.9 20.6 - - - +
423B LEU* 1.3 76.2 - - + +
425B GLN* 1.3 59.6 + - - +
427B TYR* 3.6 4.9 + - - +
428B GLN* 3.3 34.3 + - - +
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Residues in contact with GLN 425 (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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421B GLN* 2.9 27.3 + - + +
422B GLU* 3.4 32.5 + - + +
424B VAL* 1.3 74.1 - - - +
426B SER* 1.3 65.5 + - - +
428B GLN* 3.3 13.8 + - + +
429B VAL* 3.0 33.8 + - + +
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Residues in contact with SER 426 (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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197B ARG* 5.3 4.0 + - - -
268B SER* 4.3 17.1 + - - -
269B LEU* 3.8 21.1 - - - +
422B GLU 2.8 20.5 + - - -
423B LEU* 3.3 13.9 + - - -
425B GLN* 1.3 77.8 - - - +
427B TYR* 1.3 57.3 + - - +
429B VAL* 3.5 6.0 + - - +
430B ALA* 3.1 26.0 + - - +
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Residues in contact with TYR 427 (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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269B LEU* 3.2 33.9 - - + -
271B PHE* 2.9 37.7 + - + -
317B LEU* 4.6 4.5 - - + -
375B ASN* 2.8 29.2 + - - -
376B ASN 3.9 21.1 - - - -
377B THR* 3.4 39.4 - - + +
379B ILE* 3.9 13.2 - - + -
380B ALA* 4.3 8.3 - - + -
383B LEU* 5.2 1.8 - - + -
423B LEU* 3.4 41.4 + - + +
424B VAL* 3.6 4.5 + - - +
425B GLN 3.3 0.4 - - - -
426B SER* 1.3 76.5 - - - +
428B GLN* 1.3 63.1 - - - +
430B ALA* 3.5 2.4 + - + -
431B GLU* 3.4 14.7 + - - +
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Residues in contact with GLN 428 (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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380B ALA* 4.4 13.1 - - + +
384B ASP* 3.8 21.0 + - - -
424B VAL* 3.3 27.4 + - - +
425B GLN* 3.3 13.7 + - - +
427B TYR* 1.3 77.7 - - - +
429B VAL* 1.3 62.5 + - + +
431B GLU* 3.4 13.4 + - - +
432B GLU* 3.2 21.0 + - - +
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Residues in contact with VAL 429 (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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425B GLN* 3.0 29.0 + - + +
426B SER* 3.8 6.5 - - - +
428B GLN* 1.3 75.3 - - + +
430B ALA* 1.3 65.1 + - - +
431B GLU 3.1 1.1 + - - -
432B GLU* 3.4 36.7 + - - +
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Residues in contact with ALA 430 (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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269B LEU* 4.5 17.5 - - + -
317B LEU* 4.4 11.9 - - + -
347B THR* 3.1 28.2 - - + +
350B ILE* 4.6 15.6 - - + +
377B THR* 3.9 12.8 - - + -
426B SER 3.1 16.8 + - - +
427B TYR* 3.7 9.2 - - + +
428B GLN 3.3 0.4 - - - -
429B VAL* 1.3 79.1 - - - +
431B GLU* 1.3 58.3 + - - +
432B GLU 4.8 2.3 - - - +
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Residues in contact with GLU 431 (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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313B GLU 4.6 5.3 - - - +
314B GLY* 3.8 8.1 - - - -
315B ARG* 2.9 44.9 + - + +
377B THR* 3.0 35.9 + - - +
378B GLU* 3.7 17.4 - - - +
427B TYR 3.4 7.6 + - - +
428B GLN* 3.6 12.2 - - - +
429B VAL 3.1 1.0 - - - -
430B ALA* 1.3 79.1 - - - +
432B GLU* 1.3 62.7 + - + +
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Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ARG* 5.3 0.3 + - - -
428B GLN 3.2 16.0 - - - +
429B VAL* 3.4 32.6 + - - +
430B ALA 4.8 1.8 - - - +
431B GLU* 1.3 79.5 - - + +
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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