Contacts of the helix formed by residues 315 - 324 (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 ASP 315 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H GLN* 4.1 13.8 + - - +
310H TRP* 4.5 0.7 - - - -
313H SER 3.9 0.9 + - - +
314H GLU* 1.3 73.4 - - - +
316H PRO* 1.3 80.1 - - - +
317H TRP* 3.6 18.3 + - - +
318H GLU* 3.7 28.7 - - + +
319H GLN* 3.0 27.7 + - - +
334H LYS* 6.0 0.2 - - - -
338H TYR* 4.1 12.5 + - - -
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Residues in contact with PRO 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H VAL* 6.4 1.1 - - + -
280H ASN 6.3 0.2 - - - +
283H GLN* 3.9 17.5 - - + +
284H LEU* 3.5 48.9 - - + +
287H ALA* 3.5 18.6 - - + -
289H PHE* 3.9 5.5 - - + -
310H TRP* 4.0 13.0 - - + -
314H GLU 3.7 7.2 - - - +
315H ASP* 1.3 89.3 - - - +
317H TRP* 1.3 57.8 - - + +
319H GLN* 2.8 2.9 + - - +
320H HIS* 2.6 38.7 + - - +
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Residues in contact with TRP 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H GLN* 4.9 13.0 + - - -
286H ARG* 3.2 35.2 - - + +
287H ALA* 3.8 26.9 - - + +
315H ASP* 3.6 16.8 + - - +
316H PRO* 1.3 79.0 - - + +
318H GLU* 1.3 60.9 + - - +
320H HIS* 3.5 5.5 - - - +
321H ALA* 3.2 22.5 + - - +
329H TYR* 4.0 6.1 - + - -
330H LEU* 3.8 22.4 - - + +
333H GLN* 3.5 39.9 - - + -
334H LYS* 3.5 39.2 - - + +
338H TYR* 3.4 18.0 + - + +
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Residues in contact with GLU 318 (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* 3.5 26.1 + - + +
316H PRO 3.0 1.4 - - - -
317H TRP* 1.3 77.6 - - - +
319H GLN* 1.3 64.2 + - - +
321H ALA* 3.1 4.2 + - - +
322H LYS* 2.8 36.7 + - + +
338H TYR* 3.1 13.9 + - - +
342H ILE* 3.8 26.7 - - + +
345H THR* 6.1 1.2 - - - +
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Residues in contact with GLN 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H LEU* 3.6 22.8 - - + +
310H TRP* 3.8 17.3 - - + -
314H GLU* 4.0 18.3 + - + +
315H ASP 3.0 19.1 + - - +
316H PRO 2.8 6.0 + - - +
318H GLU* 1.3 81.4 + - - +
320H HIS* 1.3 67.3 + - - +
322H LYS* 3.5 26.2 + - - +
323H TRP* 3.2 34.0 + - - +
402H 1AQ 3.0 37.5 + - + +
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Residues in contact with HIS 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H ALA* 3.3 20.1 + - - +
289H PHE* 3.2 25.2 - + + -
300H CYS* 3.5 18.8 - - + +
303H CYS* 3.3 5.9 - - - -
307H LEU* 4.1 3.9 - - - +
316H PRO 2.6 19.7 + - - +
317H TRP* 3.5 9.9 - - - +
319H GLN* 1.3 72.6 - - - +
321H ALA* 1.3 53.0 + - - +
324H TYR* 2.8 51.9 + + + +
327H CYS* 3.6 6.6 - - - +
329H TYR* 5.0 1.3 - + - -
330H LEU* 4.0 17.9 - - + +
401H ZN 2.2 38.3 - - - -
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Residues in contact with ALA 321 (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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343C HIS* 5.2 0.2 + - - -
317H TRP 3.2 12.5 + - - +
318H GLU 3.1 4.9 + - - +
320H HIS* 1.3 77.6 - - - +
322H LYS* 1.3 65.8 + - - +
323H TRP 3.3 0.4 + - - -
325H PRO* 3.8 20.4 - - - +
330H LEU* 3.7 22.9 - - + -
338H TYR* 4.2 13.2 - - + -
339H ILE* 4.4 16.1 - - + +
342H ILE* 4.0 18.4 - - + +
343H HIS* 5.2 4.9 + - - +
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Residues in contact with LYS 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C HIS* 2.9 23.1 + - - -
318H GLU* 2.8 18.4 + - + +
319H GLN* 3.2 30.5 + - - +
321H ALA* 1.3 78.7 - - - +
323H TRP* 1.3 84.1 + - + +
342H ILE* 4.0 10.3 - - + -
343H HIS* 5.1 1.2 - - - +
346H HIS* 3.2 49.8 - - + +
349H GLU* 4.9 15.9 + - - +
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Residues in contact with TRP 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ASN* 4.3 0.3 - - - +
343C HIS* 3.2 23.7 - + - -
344C LEU* 4.0 10.2 - - + +
347C SER* 3.7 23.1 - - - -
348C LEU* 5.9 2.7 - - + -
307H LEU* 3.6 23.3 - - + -
319H GLN* 3.2 26.4 + - - +
322H LYS* 1.3 102.3 - - + +
324H TYR* 1.3 84.4 - - + +
325H PRO* 3.5 6.0 - - - +
346H HIS* 4.1 22.2 - + - -
402H 1AQ 3.6 65.2 + - + -
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Residues in contact with TYR 324 (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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340C ASN* 3.3 20.6 - - + +
344C LEU* 4.5 14.8 - - + -
345E THR* 5.4 8.8 + - - -
289H PHE* 5.9 1.8 - + - -
303H CYS* 4.1 15.3 - - + -
305H GLY* 3.5 27.1 - - - -
306H GLY* 2.6 38.5 + - - -
307H LEU* 3.9 15.0 - - + -
320H HIS* 2.8 41.1 + + + +
323H TRP* 1.3 93.3 - - + +
325H PRO* 1.3 61.3 - - - +
326H GLY 3.1 7.3 + - - -
327H CYS 3.5 8.3 + - - -
330H LEU* 3.8 1.7 - - - +
402H 1AQ 3.0 23.2 + - - +
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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