Contacts of the helix formed by residues 390 - 406 (chain B) in PDB entry 4HNE
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 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B PRO 3.4 19.7 + - - +
387B LYS 3.2 6.8 + - - +
388B ILE 4.9 0.2 - - - -
389B SER* 1.3 78.5 + - - +
391B PRO* 1.4 70.5 - - - +
392B ASN* 3.1 25.3 + - - +
393B PHE* 3.0 28.3 + - + +
394B VAL* 3.2 13.9 + - - +
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Residues in contact with PRO 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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389B SER 3.6 9.8 - - - +
390B ASP* 1.4 91.5 - - - +
392B ASN* 1.3 58.3 + - - +
394B VAL* 3.7 7.5 + - + +
395B LYS* 3.0 38.5 + - + +
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Residues in contact with ASN 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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390B ASP* 3.1 18.1 + - - +
391B PRO* 1.3 77.5 - - - +
393B PHE* 1.3 60.0 + - - +
395B LYS* 3.1 10.7 + - - +
396B ASP* 2.8 38.7 + - - +
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Residues in contact with PHE 393 (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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202B LYS* 3.5 40.1 - - + -
203B LEU* 3.5 33.9 - - + -
387B LYS* 3.2 54.7 - - + +
388B ILE* 4.4 6.5 - - + -
390B ASP* 3.0 14.6 + - + +
392B ASN* 1.3 78.6 - - - +
394B VAL* 1.3 67.6 + - + +
396B ASP* 3.1 12.3 + - - +
397B LEU* 2.9 34.6 + - + +
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Residues in contact with VAL 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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388B ILE* 3.8 31.0 - - + +
390B ASP 3.2 9.4 + - - +
391B PRO* 3.9 9.9 - - + +
393B PHE* 1.3 80.3 - - + +
395B LYS* 1.3 58.7 + - + +
397B LEU* 3.2 9.8 + - + +
398B GLU* 3.1 50.8 + - + +
424B ARG* 4.7 11.9 - - + +
427B ILE* 4.2 30.5 - - + -
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Residues in contact with LYS 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 PRO* 3.0 25.2 + - + +
392B ASN* 3.1 9.6 + - - +
394B VAL* 1.3 74.6 - - + +
396B ASP* 1.3 64.3 + - - +
398B GLU* 3.4 20.3 + - - +
399B GLU* 3.1 22.2 + - - +
424B ARG* 5.7 2.0 - - - +
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Residues in contact with ASP 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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202B LYS* 3.7 20.3 + - - +
392B ASN* 2.8 31.7 + - - +
393B PHE* 3.4 11.4 - - + +
395B LYS* 1.3 71.8 - - - +
397B LEU* 1.3 57.8 + - - +
399B GLU* 3.1 11.1 + - - +
400B ASP* 2.8 34.8 + - - +
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Residues in contact with LEU 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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198B LEU* 3.9 24.0 - - + -
199B VAL* 4.1 21.1 - - + -
202B LYS* 4.3 18.5 - - + +
203B LEU* 5.3 5.4 - - + -
303B ILE* 5.2 3.8 - - + -
388B ILE* 6.1 1.8 - - + -
393B PHE* 2.9 30.4 + - + +
394B VAL* 3.2 13.0 + - + +
396B ASP* 1.3 76.3 - - - +
398B GLU* 1.3 58.2 + - + +
400B ASP* 3.2 6.9 + - - +
401B LEU* 3.0 34.8 + - + +
423B MET* 3.6 28.3 - - + -
427B ILE* 4.8 12.6 - - + -
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Residues in contact with GLU 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 VAL* 3.1 27.2 + - + +
395B LYS* 3.8 18.8 - - - +
397B LEU* 1.3 77.4 - - + +
399B GLU* 1.3 56.8 + - - +
401B LEU* 4.4 2.0 - - - -
402B TYR* 2.9 30.5 + - - +
416B PHE* 3.6 6.1 - - + -
420B ILE* 3.5 36.1 - - + +
423B MET* 5.8 3.6 - - - -
424B ARG* 2.7 48.7 + - + +
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Residues in contact with GLU 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 LYS 3.1 13.6 + - - +
396B ASP* 3.1 16.1 + - - +
398B GLU* 1.3 76.4 - - - +
400B ASP* 1.3 64.6 + - - +
402B TYR* 3.2 16.8 + - - +
403B GLU* 2.9 52.9 + - - +
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Residues in contact with ASP 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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198B LEU* 3.6 30.9 - - + +
202B LYS* 2.8 40.7 + - - +
396B ASP* 2.8 19.5 + - - +
397B LEU* 3.2 6.1 + - - +
399B GLU* 1.3 77.2 - - - +
401B LEU* 1.3 60.5 + - - +
403B GLU* 3.3 10.3 - - - +
404B LEU* 3.3 15.8 + - - +
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Residues in contact with LEU 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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195B GLY* 4.2 19.3 - - - +
198B LEU* 4.3 15.9 - - + -
199B VAL* 4.5 1.6 - - + -
351B PHE* 3.9 24.7 - - + -
397B LEU* 3.0 27.2 + - + +
398B GLU* 3.8 3.6 - - - +
400B ASP* 1.3 73.9 - - - +
402B TYR* 1.3 54.3 + - - +
404B LEU* 2.9 4.9 + - - +
405B PHE* 2.8 52.4 + - + +
416B PHE* 4.0 12.3 - - + -
420B ILE* 4.3 9.4 - - + -
423B MET* 3.7 38.1 - - + -
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Residues in contact with TYR 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 GLU 2.9 19.4 + - - +
399B GLU* 3.4 20.0 - - - +
401B LEU* 1.3 73.6 - - - +
403B GLU* 1.3 65.8 + - - +
404B LEU 3.0 0.3 + - - -
405B PHE 3.1 0.3 + - - -
406B LYS* 2.9 69.1 + - + +
411B PHE* 3.9 20.6 - + - -
413B ARG* 2.8 33.4 + - - -
416B PHE* 3.2 29.0 - + + -
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Residues in contact with GLU 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 GLU* 2.9 33.5 + - - +
400B ASP* 3.3 15.5 - - - +
401B LEU 3.2 0.2 - - - -
402B TYR* 1.3 81.5 - - - +
404B LEU* 1.3 59.8 + - - +
406B LYS* 3.2 37.9 + - - +
407B LYS* 3.6 19.1 - - - +
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Residues in contact with LEU 404 (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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191B LEU* 3.8 15.3 - - + +
194B ALA* 3.9 12.6 - - + -
195B GLY* 3.5 32.5 - - - +
198B LEU* 4.1 14.4 - - + -
212B LYS* 6.0 2.5 - - + -
213B VAL* 4.2 14.1 - - + +
400B ASP 3.3 9.3 + - - +
401B LEU* 2.9 8.4 + - + +
403B GLU* 1.3 78.3 - - - +
405B PHE* 1.3 83.4 + - + +
407B LYS* 3.3 42.1 - - - +
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Residues in contact with PHE 405 (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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188B GLN* 4.5 11.2 - - - +
191B LEU* 3.6 42.3 - - + +
192B SER* 4.7 0.7 - - - -
195B GLY* 4.4 0.4 - - - -
351B PHE* 4.1 29.2 - + + -
401B LEU* 2.8 34.7 + - + +
402B TYR 4.0 1.8 - - - +
404B LEU* 1.3 90.6 - - + +
406B LYS* 1.3 58.4 + - - +
407B LYS 3.1 6.3 + - - -
408B ASP* 3.4 14.9 + - - +
411B PHE* 3.0 29.9 - - + +
416B PHE* 3.8 23.6 - + + -
419B GLN* 3.5 29.2 - - + -
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Residues in contact with LYS 406 (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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402B TYR* 2.9 56.8 + - + +
403B GLU* 3.2 40.1 + - - +
405B PHE* 1.3 77.0 - - - +
407B LYS* 1.3 65.5 + - + +
408B ASP 3.2 8.1 + - - +
411B PHE* 3.6 18.6 - - + +
413B ARG* 5.4 1.6 - - - +
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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