Contacts of the helix formed by residues 390 - 407 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO 3.9 14.2 - - - +
387A LYS 3.2 10.9 + - - +
388A ILE 3.2 1.4 + - - -
389A SER* 1.3 79.8 - - - +
391A PRO* 1.4 74.1 - - - +
392A ASN* 3.1 26.5 + - - +
393A PHE* 3.0 24.3 + - - +
394A VAL* 3.3 12.2 + - - +
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Residues in contact with PRO 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A SER 4.2 4.2 - - - +
390A ASP* 1.4 91.8 - - - +
392A ASN* 1.3 56.7 + - - +
394A VAL* 3.4 10.0 + - + +
395A LYS* 2.7 36.2 + - - +
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Residues in contact with ASN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 3.1 20.0 + - - +
391A PRO* 1.3 80.2 - - - +
393A PHE* 1.3 59.5 + - - +
395A LYS* 3.5 9.4 - - - +
396A ASP* 2.8 32.1 + - - +
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Residues in contact with PHE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 3.6 45.7 + - + -
203A LEU* 3.4 35.4 - - + -
387A LYS* 3.2 51.4 - - + +
388A ILE* 4.3 7.9 - - + -
390A ASP* 3.0 12.9 + - - +
392A ASN* 1.3 76.0 - - - +
394A VAL* 1.3 58.9 + - + +
396A ASP* 3.1 6.4 + - - +
397A LEU* 2.7 49.3 + - + +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 3.6 29.8 - - - +
390A ASP 3.3 15.4 + - - +
391A PRO* 3.7 9.0 - - + +
393A PHE* 1.3 78.4 - - + +
395A LYS* 1.3 56.1 + - - +
397A LEU* 3.8 6.9 - - - +
398A GLU* 3.1 28.8 + - + +
420A ILE* 6.5 0.2 - - + -
423A MET* 5.3 4.8 - - + +
424A ARG* 4.3 26.0 - - + +
427A ILE* 3.8 30.5 - - + -
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO 2.7 21.5 + - - +
392A ASN* 3.5 12.6 - - - +
394A VAL* 1.3 70.6 - - - +
396A ASP* 1.3 60.9 + - - +
398A GLU* 3.3 31.0 + - - +
399A GLU* 3.0 55.0 + - - +
424A ARG* 4.9 4.5 - - - +
453A THR* 6.2 1.8 - - - +
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 3.5 26.6 + - - +
392A ASN 2.8 19.7 + - - +
393A PHE* 3.4 4.9 - - - +
395A LYS* 1.3 75.5 - - - +
397A LEU* 1.3 64.9 + - - +
399A GLU* 3.3 16.7 + - - +
400A ASP* 3.0 34.1 + - - +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 3.9 24.0 - - + -
199A VAL* 4.1 23.3 - - + -
202A LYS* 3.8 25.5 - - + +
203A LEU* 5.3 4.7 - - + -
303A ILE* 5.1 5.8 - - + -
388A ILE* 6.2 0.9 - - + -
393A PHE* 2.7 37.6 + - + +
394A VAL* 3.8 7.2 - - - +
396A ASP* 1.3 72.5 - - - +
398A GLU* 1.3 57.2 + - - +
400A ASP* 3.1 5.4 + - - +
401A LEU* 3.0 28.8 + - + +
423A MET* 3.6 27.8 - - + -
427A ILE* 4.8 11.7 - - + -
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A VAL* 3.1 17.5 + - + +
395A LYS* 3.6 28.9 + - - +
397A LEU* 1.3 79.6 - - - +
399A GLU* 1.3 57.3 + - + +
401A LEU* 3.5 1.9 + - - +
402A TYR* 3.0 26.9 + - - +
416A PHE* 3.6 11.6 - - + -
417A HIS* 4.8 12.3 + - - -
420A ILE* 3.7 41.2 - - + +
423A MET* 4.8 2.7 - - + +
424A ARG* 2.7 35.5 + - - -
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LYS* 3.0 45.1 + - - +
396A ASP* 3.6 17.7 - - - +
398A GLU* 1.3 75.0 - - + +
400A ASP* 1.3 61.8 + - - +
402A TYR* 3.3 12.3 + - + +
403A GLU* 2.9 33.7 + - + +
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.8 24.5 - - + +
202A LYS* 3.2 29.7 - - - +
396A ASP* 3.0 21.7 + - - +
397A LEU 3.1 9.2 + - - +
399A GLU* 1.3 79.1 - - - +
401A LEU* 1.3 62.3 + - - +
403A GLU* 3.2 10.7 + - - +
404A LEU* 3.1 22.0 + - - +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLY* 4.2 16.8 - - - +
198A LEU* 4.3 18.8 - - + -
199A VAL* 4.7 4.5 - - + -
351A PHE* 3.9 29.6 - - + -
397A LEU* 3.0 17.1 + - + +
398A GLU 3.9 4.0 - - - +
400A ASP* 1.3 72.3 - - - +
402A TYR* 1.3 57.1 + - - +
404A LEU* 3.1 3.5 + - + +
405A PHE* 2.8 56.2 + - + +
416A PHE* 4.0 11.9 - - + -
420A ILE* 4.1 9.9 - - + -
423A MET* 3.7 38.1 - - + -
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Residues in contact with TYR 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLU 3.0 15.8 + - - +
399A GLU* 3.4 17.0 - - + +
400A ASP 3.3 0.2 - - - -
401A LEU* 1.3 74.6 - - - +
403A GLU* 1.3 69.9 + - + +
405A PHE 3.2 0.2 + - - -
406A LYS* 2.9 56.5 + - + +
411A PHE* 3.6 28.9 - + - -
413A ARG* 3.0 37.0 + - + -
416A PHE* 3.4 30.8 - + + -
417A HIS* 6.6 0.2 - + - -
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A GLU* 2.9 18.2 + - + +
400A ASP* 3.2 13.9 + - - +
402A TYR* 1.3 81.8 - - + +
404A LEU* 1.3 63.6 + - - +
406A LYS* 3.6 36.4 + - - +
407A LYS* 4.0 11.5 + - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU* 3.5 11.2 - - + +
194A ALA* 3.8 10.3 - - + +
195A GLY* 3.5 37.2 - - - +
198A LEU* 3.8 18.2 - - + -
212A LYS* 6.2 0.2 - - - -
213A VAL* 3.9 28.0 - - + +
400A ASP 3.1 12.7 + - - +
401A LEU* 3.1 6.5 + - + +
403A GLU* 1.3 78.0 - - - +
405A PHE* 1.3 71.8 + - + +
407A LYS* 3.4 38.9 - - + +
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Residues in contact with PHE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLN* 4.9 6.2 + - - +
191A LEU* 3.5 46.4 - - + +
192A SER 5.0 0.4 - - - -
195A GLY* 4.5 0.4 - - - -
351A PHE* 4.2 27.4 - + + -
401A LEU* 2.8 35.6 + - + +
402A TYR 4.0 0.7 - - - +
404A LEU* 1.3 93.3 - - + +
406A LYS* 1.3 63.8 + - - +
408A ASP* 3.3 17.0 + - - +
411A PHE* 3.2 30.6 - - + +
416A PHE* 3.8 26.7 - + + -
419A GLN* 4.0 26.2 - - + -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TYR* 2.9 62.2 + - + +
403A GLU* 3.6 29.3 + - - +
405A PHE* 1.3 74.0 - - - +
407A LYS* 1.3 66.6 + - - +
408A ASP 2.9 11.1 + - - +
411A PHE* 3.8 17.3 - - + +
413A ARG* 5.2 3.1 - - - +
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 6.2 4.5 - - - -
190A TYR* 5.0 2.9 - - + +
191A LEU* 4.9 4.3 - - + -
213A VAL* 4.2 33.9 - - + -
215A TYR* 6.2 0.4 - - - +
403A GLU 4.3 11.1 + - - +
404A LEU* 3.4 36.6 + - + +
406A LYS* 1.3 77.2 - - - +
408A ASP* 1.3 61.6 + - - +
409A PRO* 3.6 5.7 - - - +
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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