Contacts of the helix formed by residues 335 - 346 (chain C) 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 GLY 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C LEU 3.9 0.2 + - - -
331C LEU* 3.1 25.2 + - - -
332C GLU 4.7 0.4 + - - -
333C GLN 3.9 0.2 - - - -
334C LYS* 1.3 81.5 - - - +
336C GLN* 1.3 65.7 + - - -
337C GLU* 3.3 2.9 - - - -
338C TYR 3.5 0.5 + - - -
339C ILE* 3.4 22.3 + - - +
254H THR 6.2 1.1 - - - -
255H ASN* 3.4 13.9 - - - -
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Residues in contact with GLN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LEU* 3.7 6.5 - - + +
335C GLY* 1.3 69.6 - - - -
337C GLU* 1.3 76.9 + - - +
339C ILE* 3.3 1.6 + - - +
340C ASN* 2.9 39.3 + - - +
255H ASN* 3.4 20.4 + - - +
256H LEU 5.1 2.1 - - - +
258H ARG* 5.5 0.7 - - - +
302H HIS* 2.8 40.9 + - - +
303H CYS* 3.7 18.1 - - - -
326H GLY* 3.3 27.8 - - - +
327H CYS* 3.9 4.6 - - - +
328H LYS* 3.0 24.0 - - - +
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Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C GLY 3.3 0.6 - - - -
336C GLN* 1.3 95.1 + - - +
338C TYR* 1.3 66.4 + - - +
340C ASN* 4.8 0.9 - - - +
341C ASN* 2.8 28.8 + - - +
337E GLU* 3.8 22.4 - - + +
338E TYR* 3.6 33.7 - - - +
341E ASN* 3.8 12.9 + - + +
255H ASN* 5.4 1.4 - - - +
258H ARG* 2.7 39.8 + - - +
303H CYS 4.3 2.6 - - - +
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Residues in contact with TYR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ASP* 4.3 4.3 + - - -
317C TRP* 3.3 16.3 - - + +
318C GLU* 3.1 31.5 + - - +
321C ALA* 4.0 20.0 - - + -
330C LEU* 4.7 2.0 - - + -
334C LYS* 3.7 56.2 + - + +
335C GLY 3.5 2.9 + - - +
336C GLN 3.4 0.4 - - - -
337C GLU* 1.3 78.3 - - - +
339C ILE* 1.3 70.2 + - + +
341C ASN* 3.5 0.5 + - - +
342C ILE* 3.2 39.7 + - + +
258D ARG* 3.5 31.7 + - - -
337E GLU* 3.3 36.7 - - + +
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ALA* 4.4 8.1 - - + +
325C PRO* 3.5 41.3 - - + +
330C LEU* 3.8 33.4 - - + +
331C LEU* 3.8 30.1 - - + +
334C LYS* 5.2 0.4 - - + -
335C GLY 3.4 15.2 + - - +
336C GLN 3.3 5.8 + - - +
337C GLU 3.2 0.6 - - - -
338C TYR* 1.3 83.1 - - + +
340C ASN* 1.3 59.4 + - - +
342C ILE* 3.2 5.0 + - - +
343C HIS* 2.9 26.5 + - - +
325H PRO* 4.6 2.0 - - + -
326H GLY* 3.9 19.3 - - - +
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Residues in contact with ASN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C GLN* 2.9 25.7 + - - +
337C GLU* 4.8 0.4 - - - +
339C ILE* 1.3 73.6 - - - +
341C ASN* 1.3 58.5 + - - +
343C HIS* 4.3 2.7 - - - -
344C LEU* 2.8 43.0 + - + +
341E ASN* 4.0 13.9 - - - +
303H CYS* 4.3 13.1 + - - +
323H TRP 4.3 1.1 - - - +
324H TYR* 3.3 36.6 - - + +
325H PRO* 3.4 6.1 - - - +
326H GLY* 3.2 33.5 + - - +
327H CYS 4.2 1.0 - - - +
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Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C GLU 2.8 25.0 + - - +
338C TYR 3.7 3.8 - - - +
340C ASN* 1.3 73.4 - - - +
342C ILE* 1.3 63.7 + - + +
344C LEU* 3.7 5.2 + - - +
345C THR* 3.1 29.3 + - - +
258D ARG* 5.2 1.3 - - - +
337E GLU* 3.1 47.9 + - - +
340E ASN* 4.3 8.1 - - - +
341E ASN* 2.7 37.8 + - - +
344E LEU* 4.8 9.2 - - + +
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Residues in contact with ILE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C GLU* 4.1 17.9 - - + +
321C ALA* 3.9 9.9 - - + -
322C LYS* 3.8 29.8 - - + +
338C TYR* 3.2 55.7 + - + +
339C ILE 3.7 6.1 - - - +
341C ASN* 1.3 77.3 - - + +
343C HIS* 1.3 67.0 + - - +
345C THR* 3.1 5.1 + - - -
346C HIS* 3.0 44.5 + - + +
258D ARG* 4.0 17.3 - - - +
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Residues in contact with HIS 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C ALA 5.3 6.0 + - - +
322C LYS* 5.2 3.9 + - - +
325C PRO* 4.9 1.4 - - - +
339C ILE* 2.9 17.5 + - + +
340C ASN* 3.8 7.2 - - - +
342C ILE* 1.3 79.8 - - - +
344C LEU* 1.3 66.8 + - + +
345C THR 3.2 0.2 + - - -
346C HIS* 3.6 2.3 + - - -
347C SER* 3.2 27.9 + - - -
322H LYS 2.9 23.7 + - - -
323H TRP* 3.2 37.4 - + - -
325H PRO* 3.9 17.2 - - + +
343H HIS* 3.3 40.9 + + - -
346H HIS* 4.3 10.2 + + - -
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Residues in contact with LEU 344 (chain C).
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* 2.8 38.5 + - + +
341C ASN* 3.9 6.1 - - - +
343C HIS* 1.3 75.3 - - + +
345C THR* 1.3 62.3 + - - +
347C SER* 3.6 14.1 + - - -
348C LEU* 4.4 4.0 + - - +
341E ASN* 5.5 4.7 - - - +
344E LEU* 5.1 19.1 - - + -
345E THR* 5.8 4.9 - - - +
348E LEU* 5.1 8.1 - - + -
323H TRP* 4.0 21.1 - - + +
324H TYR* 4.5 14.4 - - + -
402H 1AQ 3.5 44.5 - - - +
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Residues in contact with THR 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ASN* 3.1 19.2 + - - +
342C ILE* 3.1 5.4 + - - -
344C LEU* 1.3 75.0 - - - +
346C HIS* 1.3 70.3 + - + +
347C SER 3.2 6.1 + - - -
348C LEU* 4.5 1.0 + - - +
349C GLU* 3.8 15.9 + - - +
324D TYR* 5.4 7.5 + - - +
403D 1AQ 3.2 47.2 - - + +
344E LEU* 4.3 16.6 - - - +
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Residues in contact with HIS 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU* 3.4 31.8 + - + +
322C LYS* 3.7 43.5 - - + -
342C ILE* 3.0 32.1 + - + +
343C HIS* 3.9 3.1 - - - +
345C THR* 1.3 98.2 - - + +
347C SER* 1.3 60.6 + - - +
348C LEU 3.8 0.2 - - - -
349C GLU* 3.6 23.3 + - - +
350C GLU* 3.9 18.6 + - + +
403D 1AQ 3.6 15.0 - + - -
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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