Contacts of the helix formed by residues 389 - 403 (chain B) in PDB entry 3BYH
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 VAL 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B ASP* 1.3 82.0 + - - +
390B GLU* 1.3 82.9 + - + +
391B THR 3.1 1.8 - - - -
392B CYS* 3.3 19.9 + - + +
393B ARG* 3.4 34.0 + - + +
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASP* 3.2 12.2 + - - -
389B VAL* 1.3 105.4 + - + +
391B THR* 1.3 60.1 + - - +
393B ARG* 3.3 16.3 + - - +
394B ASP* 2.9 42.7 + - - +
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Residues in contact with THR 391 (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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388B ASP* 3.6 20.5 + - - +
390B GLU* 1.3 80.4 - - - +
392B CYS* 1.3 57.1 - - - +
394B ASP* 3.9 7.0 - - - +
395B GLU* 3.0 27.4 + - - +
415B PHE* 3.4 32.6 - - + -
483B LYS* 4.6 12.6 - - + +
487B LEU* 4.4 10.9 - - + +
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Residues in contact with CYS 392 (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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388B ASP 4.2 2.1 + - - +
389B VAL* 3.3 19.3 + - + +
390B GLU 3.2 0.2 - - - -
391B THR* 1.3 81.1 - - - +
393B ARG* 1.3 62.5 + - + +
395B GLU* 3.4 8.8 + - - +
396B ARG* 3.2 20.7 + - - +
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B VAL* 3.6 32.1 + - + +
390B GLU* 3.3 17.4 + - - +
391B THR 3.3 0.2 - - - -
392B CYS* 1.3 78.2 - - + +
394B ASP* 1.3 62.7 + - - +
396B ARG* 3.2 10.4 + - - +
397B CYS* 2.9 28.2 + - - +
603B GLU* 4.6 26.1 + - - -
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Residues in contact with ASP 394 (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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390B GLU* 2.9 30.4 + - - +
391B THR* 4.0 2.0 - - - +
393B ARG* 1.3 75.4 - - - +
395B GLU* 1.3 67.3 + - - +
397B CYS* 4.1 7.8 - - - +
398B TYR* 3.0 47.7 + - + +
487B LEU* 3.8 31.8 - - + +
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Residues in contact with GLU 395 (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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391B THR 3.0 19.0 + - - +
392B CYS* 3.5 10.8 - - - +
393B ARG 3.2 0.2 - - - -
394B ASP* 1.3 76.2 - - - +
396B ARG* 1.3 64.8 + - - +
399B ARG* 3.0 45.5 + - - +
412B ASN 4.1 0.3 - - - +
413B ASN* 3.3 20.2 - - - +
414B VAL* 3.2 45.8 + - + +
415B PHE* 4.0 20.9 - - + -
487B LEU* 4.7 0.6 - - - +
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Residues in contact with ARG 396 (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 CYS 3.2 8.1 + - - +
393B ARG* 3.2 12.2 + - - +
395B GLU* 1.3 87.3 + - - +
397B CYS* 1.3 66.4 + - - +
399B ARG* 3.2 19.6 + - - +
400B LEU* 2.9 33.2 + - + +
597B LEU* 0.8 273.4 - - + +
599B GLU* 3.1 29.1 + - - +
600B ASP* 3.2 24.0 + - - -
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Residues in contact with CYS 397 (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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393B ARG 2.9 17.0 + - - +
394B ASP* 3.6 11.4 - - - +
396B ARG* 1.3 82.2 - - - +
398B TYR* 1.3 69.5 + - + +
400B LEU* 3.3 7.7 + - - +
401B TRP* 3.0 25.5 + - - +
494B MET* 4.0 21.5 - - - -
595B PHE 4.8 0.2 - - - +
600B ASP* 4.8 12.1 - - - +
605B ASN* 3.7 23.8 - - - -
608B MET* 4.3 8.2 - - - +
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Residues in contact with TYR 398 (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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394B ASP* 3.0 49.2 + - + +
397B CYS* 1.3 77.6 - - - +
399B ARG* 1.3 60.9 + - - +
401B TRP* 3.7 8.7 - + - +
402B ILE* 2.9 36.8 + - + +
414B VAL* 4.0 4.9 - - + -
487B LEU* 4.2 18.4 - - + -
490B LEU* 3.8 42.4 - - + -
491B TRP* 3.2 46.7 - - - +
494B MET* 3.8 32.9 - - + -
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Residues in contact with ARG 399 (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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395B GLU* 3.0 49.1 + - - +
396B ARG* 3.4 22.7 - - - +
397B CYS 3.2 0.4 - - - -
398B TYR* 1.3 79.3 - - - +
400B LEU* 1.3 78.8 + - - +
402B ILE* 3.9 1.6 - - - +
403B ASN* 3.2 31.8 + - - +
410B TYR* 5.8 1.2 + - - -
411B VAL* 3.3 31.9 + - + +
412B ASN* 3.3 30.9 + - - +
414B VAL* 3.4 11.4 - - + +
597B LEU* 5.6 1.0 - - - +
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Residues in contact with LEU 400 (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 ARG* 2.9 18.7 + - + +
397B CYS 3.7 4.0 - - - +
399B ARG* 1.3 92.5 - - - +
401B TRP* 1.3 56.2 + - - +
403B ASN* 3.5 6.0 + - + +
404B SER 3.4 1.0 + - - -
588B ARG* 6.2 1.8 - - - +
595B PHE* 1.8 76.1 - - + +
596B LEU* 4.1 0.9 - - - -
597B LEU* 2.2 70.7 - - + +
600B ASP* 4.9 0.9 - - - +
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Residues in contact with TRP 401 (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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397B CYS 3.0 16.7 + - - +
398B TYR* 3.7 11.9 - + - +
399B ARG 3.3 0.2 - - - -
400B LEU* 1.3 77.2 - - - +
402B ILE* 1.3 82.5 + - + +
404B SER* 2.8 21.9 + - - -
405B LEU* 3.2 44.9 - - + +
427B VAL* 3.9 23.3 - - + -
431B VAL* 4.4 2.5 - - + -
490B LEU* 4.3 9.4 - - + -
493B LEU* 3.8 14.6 - - + -
494B MET* 3.5 67.2 + - + +
497B HIS* 4.2 16.2 + - + -
595B PHE* 3.7 8.7 + - - +
608B MET* 4.0 12.8 - - + +
611B ILE* 5.0 17.2 - - + +
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Residues in contact with ILE 402 (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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398B TYR 2.9 28.5 + - - +
399B ARG 3.9 3.4 - - - +
401B TRP* 1.3 91.8 - - + +
403B ASN* 1.3 60.0 + - - +
404B SER 3.1 1.3 + - - -
405B LEU* 3.4 16.9 + - - +
407B ILE* 3.1 36.3 - - + +
411B VAL* 3.8 25.8 - - + -
414B VAL* 4.2 16.4 - - + -
418B VAL* 6.0 3.1 - - + -
423B ILE* 4.1 6.1 - - + -
424B LEU* 5.7 1.8 - - + -
427B VAL* 3.9 24.5 - - + -
490B LEU* 3.9 23.8 - - + -
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Residues in contact with ASN 403 (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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399B ARG* 3.2 18.1 + - - +
400B LEU* 3.9 8.8 - - + +
401B TRP 3.2 0.6 - - - -
402B ILE* 1.3 77.1 - - - +
404B SER* 1.3 49.6 + - - +
405B LEU 3.5 0.7 - - - -
406B GLY* 4.8 2.1 + - - -
407B ILE* 4.4 5.5 - - - +
409B SER 4.1 4.0 + - - -
410B TYR* 3.4 37.7 + - + +
411B VAL* 2.9 55.7 - - - +
595B PHE* 2.4 27.2 - - + -
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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