Contacts of the helix formed by residues 335 - 347 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330F LEU 3.9 0.2 + - - -
331F LEU* 3.0 18.4 + - - -
334F LYS* 1.3 79.2 - - - +
336F GLN* 1.3 65.6 - - - -
337F GLU 3.5 1.8 - - - -
338F TYR 3.5 1.0 + - - -
339F ILE* 3.2 25.3 + - - +
254G THR 6.1 0.9 - - - -
255G ASN* 3.3 19.9 - - - +
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Residues in contact with GLN 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F LEU* 4.3 1.1 - - + -
335F GLY* 1.3 69.4 - - - -
337F GLU* 1.3 69.8 + - - +
339F ILE* 3.2 2.1 + - - +
340F ASN* 2.7 48.7 + - - +
255G ASN* 3.2 22.7 + - - +
256G LEU 4.6 3.5 - - - +
258G ARG* 5.0 1.6 - - - +
302G HIS* 2.9 38.8 + - - +
303G CYS* 3.4 25.1 - - + +
326G GLY* 3.7 20.2 - - - +
327G CYS* 4.0 1.4 - - - +
328G LYS* 3.1 28.4 - - - +
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Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F GLY 3.5 0.2 - - - -
336F GLN* 1.3 87.6 + - - +
338F TYR* 1.3 58.8 + - - +
340F ASN* 4.4 6.5 - - + +
341F ASN* 2.7 50.8 + - - +
254G THR 5.6 1.7 - - - +
258G ARG* 2.9 46.0 + - - +
303G CYS 4.2 5.2 - - - +
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Residues in contact with TYR 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F ASP* 4.0 2.3 + - - -
317F TRP* 3.2 12.0 - - - +
318F GLU* 3.2 30.2 + - - +
321F ALA* 3.9 12.3 - - + -
330F LEU* 4.8 2.7 - - + -
334F LYS* 3.5 61.0 + - + +
335F GLY 3.5 3.0 + - - +
336F GLN 3.2 0.6 - - - -
337F GLU* 1.3 79.5 - - - +
339F ILE* 1.3 72.6 + - + +
341F ASN* 3.6 5.1 - - - +
342F ILE* 3.2 47.4 + - + +
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Residues in contact with ILE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F ALA* 4.6 6.9 - - + +
325F PRO* 3.4 48.5 - - + +
330F LEU* 4.0 19.1 - - + +
331F LEU* 3.5 50.7 - - + +
335F GLY 3.2 9.8 + - - +
336F GLN 3.2 5.2 + - - +
338F TYR* 1.3 84.7 - - + +
340F ASN* 1.3 59.4 + - - +
342F ILE* 3.3 2.8 + - - +
343F HIS* 2.9 26.3 + - - +
325G PRO* 4.8 1.1 - - + -
326G GLY* 3.8 16.4 - - - +
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Residues in contact with ASN 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F GLN* 2.7 37.4 + - - +
337F GLU* 4.2 4.4 - - + +
339F ILE* 1.3 70.0 - - - +
341F ASN* 1.3 64.7 + - - +
343F HIS* 3.9 4.2 - - - +
344F LEU* 3.0 31.4 + - + +
303G CYS* 4.3 13.5 + - - +
323G TRP 4.6 0.2 - - - +
324G TYR* 3.3 32.5 - - + +
325G PRO* 3.5 2.4 - - - +
326G GLY* 3.0 35.6 + - - -
327G CYS 4.0 2.0 - - - +
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Residues in contact with ASN 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F GLU* 2.7 37.8 + - - +
338F TYR* 3.6 6.0 + - - +
340F ASN* 1.3 72.8 - - - +
342F ILE* 1.3 61.8 - - + +
344F LEU* 3.2 8.3 + - - +
345F THR* 2.9 32.6 + - - +
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Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F GLU* 3.8 29.6 - - + +
321F ALA* 3.7 9.0 - - + -
322F LYS* 3.7 35.4 - - + +
338F TYR* 3.2 58.2 + - + +
339F ILE 3.7 2.9 - - - +
341F ASN* 1.3 82.8 - - + +
343F HIS* 1.3 58.5 + - - +
345F THR* 3.2 7.8 + - + +
346F HIS* 2.9 28.9 + - + +
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Residues in contact with HIS 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F ALA 5.7 1.1 + - - +
325F PRO* 5.3 2.5 - - + -
339F ILE 2.9 16.1 + - - +
340F ASN* 3.9 3.8 - - - +
342F ILE* 1.3 78.3 - - - +
344F LEU* 1.3 62.7 + - + +
346F HIS* 3.5 1.1 + - - +
347F SER* 2.9 50.2 + - - -
402F ZN 2.5 32.8 - - - -
322G LYS 2.9 18.7 + - - -
323G TRP* 3.3 27.6 + + - -
325G PRO* 3.3 25.2 - - + +
343G HIS* 3.9 0.6 + - - -
346G HIS* 4.0 6.7 - + - -
402G ZN 2.4 32.2 - - - -
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Residues in contact with LEU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F ASN* 3.0 24.4 + - + +
341F ASN* 3.4 8.1 - - - +
343F HIS* 1.3 81.9 - - + +
345F THR* 1.3 60.6 + - - +
347F SER* 3.4 11.0 - - - +
348F LEU* 3.3 25.2 - - + +
323G TRP* 3.7 23.6 - - + +
324G TYR* 4.5 15.9 - - + -
403G 1AQ 3.6 45.3 - - - +
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Residues in contact with THR 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F ASN 2.9 17.4 + - - -
342F ILE* 3.6 9.4 - - + +
343F HIS 3.2 0.4 - - - -
344F LEU* 1.3 75.6 - - - +
346F HIS* 1.3 62.4 + - - +
347F SER 3.2 0.2 - - - -
348F LEU* 3.0 29.7 + - + +
349F GLU* 3.5 5.0 + - - +
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Residues in contact with HIS 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F LYS* 4.1 34.3 - - + +
323F TRP* 3.7 17.8 - + - -
342F ILE* 2.9 16.6 + - + +
343F HIS* 3.9 2.5 + - - +
345F THR* 1.3 73.0 - - - +
347F SER* 1.3 64.2 + - - +
348F LEU 3.0 4.5 - - - -
349F GLU* 2.9 45.4 + - - +
402F ZN 3.0 20.3 - - - -
343G HIS* 3.7 24.0 - + - -
346G HIS* 4.7 10.8 - + - -
347G SER* 3.9 13.9 + - - -
350G GLU* 5.1 3.9 + - - +
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Residues in contact with SER 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F HIS* 2.9 41.4 + - - -
344F LEU* 3.4 12.9 - - - +
345F THR 3.2 0.2 - - - -
346F HIS* 1.3 78.8 - - - +
348F LEU* 1.3 60.1 + - - +
349F GLU 4.8 1.9 - - - +
323G TRP* 4.1 9.9 - - - -
346G HIS* 4.0 11.6 + - - -
350G GLU* 3.9 21.3 - - - +
403G 1AQ 4.1 19.1 - - - +
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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