Contacts of the helix formed by residues 334 - 347 (chain H) in PDB entry 4HY0
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 LYS 334 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315H ASP* 6.0 0.2 - - - -
317H TRP* 3.5 57.7 - - + +
330H LEU* 2.9 20.0 + - + +
333H GLN* 1.3 76.4 - - + +
335H GLY* 1.3 60.8 + - - +
338H TYR* 3.3 63.3 + - + +
339H ILE* 5.4 0.2 - - + -
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Residues in contact with GLY 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C THR* 4.8 6.1 - - - -
255C ASN* 3.6 8.1 - - - -
330H LEU 3.3 3.6 + - - -
331H LEU* 3.1 27.6 + - - -
332H GLU 5.6 0.2 - - - -
333H GLN 3.6 0.4 - - - -
334H LYS* 1.3 77.4 - - - +
336H GLN* 1.3 65.7 + - - -
337H GLU 3.3 3.3 + - - -
338H TYR 3.3 1.9 + - - -
339H ILE* 3.1 24.6 + - - +
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Residues in contact with GLN 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C THR 4.7 2.1 + - - +
255C ASN* 3.0 22.9 + - - +
256C LEU 4.5 4.5 - - - +
258C ARG* 4.8 1.2 - - - +
302C HIS* 2.8 42.4 + - - +
303C CYS* 3.3 27.5 - - + -
326C GLY* 3.3 29.8 - - - +
327C CYS* 3.9 2.7 - - - -
328C LYS* 3.2 18.6 - - - +
331H LEU* 3.6 3.0 - - + +
335H GLY* 1.3 71.4 - - - +
337H GLU* 1.3 75.5 + - - +
339H ILE* 3.4 1.6 + - - +
340H ASN* 3.0 36.8 + - - +
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Residues in contact with GLU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C THR 4.7 8.0 - - - +
258C ARG* 2.8 44.0 + - - +
303C CYS 4.2 1.7 - - - +
335H GLY 3.3 0.6 - - - -
336H GLN* 1.3 95.6 - - - +
338H TYR* 1.3 62.4 + - - +
340H ASN* 4.2 5.0 + - - +
341H ASN* 2.8 34.2 + - - +
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Residues in contact with TYR 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315H ASP* 4.1 5.2 + - - -
317H TRP* 3.4 22.1 - - - +
318H GLU* 3.1 32.1 + - - +
321H ALA* 4.2 5.8 - - + -
330H LEU* 5.0 0.7 - - + -
334H LYS* 3.3 67.8 + - + +
335H GLY 3.3 2.1 + - - +
337H GLU* 1.3 77.6 - - - +
339H ILE* 1.3 69.8 + - + +
341H ASN* 3.0 4.5 + - - +
342H ILE* 2.9 55.9 + - + +
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Residues in contact with ILE 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C PRO* 4.7 1.1 - - + -
326C GLY* 3.6 20.2 - - - +
321H ALA* 4.4 11.1 - - + +
325H PRO* 3.4 46.9 - - + +
327H CYS 4.9 0.2 - - - +
330H LEU* 3.8 31.4 - - + +
331H LEU* 3.7 36.8 - - + +
335H GLY 3.1 12.5 + - - +
336H GLN 3.8 0.4 - - - +
338H TYR* 1.3 80.8 - - + +
340H ASN* 1.3 58.6 + - - +
342H ILE* 3.4 2.6 + - - +
343H HIS* 2.9 28.1 + - - +
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Residues in contact with ASN 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C CYS* 3.9 21.2 + - - +
324C TYR* 3.2 28.4 - - + +
325C PRO* 3.3 2.1 - - - +
326C GLY 2.8 24.0 + - - -
327C CYS 3.9 15.6 - - - +
336H GLN* 3.0 23.4 + - - +
337H GLU* 4.2 5.2 + - - +
339H ILE* 1.3 78.3 - - - +
341H ASN* 1.3 55.5 + - - +
343H HIS* 3.7 4.6 - - - +
344H LEU* 2.8 43.3 + - + +
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Residues in contact with ASN 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H GLU 2.8 20.7 + - - +
338H TYR* 3.0 6.9 + - - +
340H ASN* 1.3 74.8 - - - +
342H ILE* 1.3 73.5 + - + +
343H HIS 3.1 1.3 - - - -
344H LEU* 3.2 5.7 + - - +
345H THR* 2.9 34.5 + - - -
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Residues in contact with ILE 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318H GLU* 3.8 45.1 - - + +
321H ALA* 4.0 7.6 - - + -
322H LYS* 3.9 23.6 - - + +
338H TYR* 2.9 68.4 + - + +
339H ILE 3.9 2.7 - - - +
341H ASN* 1.3 80.6 - - + +
343H HIS* 1.3 57.3 + - - +
345H THR* 3.4 7.1 + - - +
346H HIS* 2.8 28.2 + - + +
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Residues in contact with HIS 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LYS 3.2 26.1 + - - -
323C TRP* 3.6 24.7 + + - -
325C PRO* 4.0 19.6 - - + +
343C HIS* 3.3 39.4 + + - -
321H ALA 5.2 5.4 + - - +
322H LYS* 5.1 1.8 - - - +
325H PRO* 5.0 2.2 - - + -
339H ILE* 2.9 19.0 + - + +
340H ASN* 3.7 8.5 - - - +
342H ILE* 1.3 79.7 - - - +
344H LEU* 1.3 64.1 + - - +
346H HIS* 3.3 11.2 + + - +
347H SER* 3.1 39.8 + - - -
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Residues in contact with LEU 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TRP* 3.8 23.8 - - + +
324C TYR* 4.2 17.3 - - + -
402C 1AQ 3.6 39.6 - - - +
340H ASN* 2.8 34.6 + - + +
341H ASN* 3.2 7.4 + - - +
343H HIS* 1.3 75.8 - - - +
345H THR* 1.3 60.6 + - - +
347H SER* 3.7 6.5 + - - -
348H LEU* 3.4 29.2 + - + +
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Residues in contact with THR 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318H GLU* 6.1 1.1 - - - +
341H ASN* 2.9 26.2 + - - -
342H ILE* 3.7 7.0 - - - +
344H LEU* 1.3 75.2 - - - +
346H HIS* 1.3 60.6 - - - +
347H SER 3.2 0.4 - - - -
348H LEU* 2.9 38.5 + - + +
349H GLU* 4.0 12.3 - - - +
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Residues in contact with HIS 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C HIS* 4.3 15.5 - + - -
347C SER* 4.8 5.6 + - - -
322H LYS* 3.2 54.3 + - + +
323H TRP* 4.1 27.8 - + - -
342H ILE* 2.8 23.5 + - + +
343H HIS* 3.3 12.8 + + - +
345H THR* 1.3 75.0 - - - +
347H SER* 1.3 61.9 - - - +
349H GLU* 3.0 30.1 + - + +
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Residues in contact with SER 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TRP* 4.1 19.3 - - - -
350C GLU* 6.1 0.9 - - - -
402C 1AQ 5.3 12.4 - - - +
343H HIS* 3.1 33.7 + - - -
344H LEU* 3.9 8.5 - - - -
345H THR 3.2 0.4 - - - -
346H HIS* 1.3 79.6 - - - +
348H LEU* 1.3 57.2 + - - +
349H GLU 3.2 7.5 + - - +
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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