Contacts of the helix formed by residues 335 - 348 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A LEU 3.8 1.6 + - - -
331A LEU* 2.9 23.6 + - - -
332A GLU 4.8 0.4 - - - -
334A LYS* 1.3 77.5 - - - +
336A GLN* 1.3 66.6 + - - -
337A GLU 3.3 2.9 + - - -
338A TYR 3.4 2.5 + - - -
339A ILE* 3.2 24.1 + - - +
254B THR 5.8 2.2 - - - -
255B ASN* 3.3 10.5 - - - -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.5 2.3 - - + +
335A GLY* 1.3 70.0 - - - -
337A GLU* 1.3 69.6 + - - +
339A ILE* 3.2 3.1 + - - +
340A ASN* 2.9 39.8 + - - +
255B ASN* 3.2 25.6 + - - +
256B LEU 4.7 4.6 + - - -
258B ARG* 5.1 2.4 - - - +
302B HIS* 2.8 54.7 + - - -
303B CYS* 3.3 15.4 + - + +
326B GLY* 3.1 30.5 - - - +
327B CYS* 4.0 1.3 - - - -
328B LYS* 3.7 14.3 - - - +
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Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLY* 3.3 1.4 - - - -
336A GLN* 1.3 93.6 + - - +
338A TYR* 1.3 57.2 + - - +
340A ASN* 4.8 2.0 - - - -
341A ASN* 2.9 32.1 + - - +
258B ARG* 2.9 42.1 + - - +
303B CYS 4.4 2.6 - - - +
337G GLU* 3.8 17.7 - - + +
338G TYR* 3.4 41.8 - - + +
341G ASN* 3.7 14.2 + - - +
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Residues in contact with TYR 338 (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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315A ASP* 3.8 5.7 + - - -
317A TRP* 3.4 25.1 - - - +
318A GLU* 3.4 14.4 + - - +
321A ALA* 3.9 12.8 - - + -
330A LEU* 4.7 2.0 - - + -
334A LYS* 3.4 65.9 + - + +
335A GLY 3.4 2.5 + - - +
336A GLN 3.3 0.2 - - - -
337A GLU* 1.3 77.5 - - - +
339A ILE* 1.3 70.6 + - + +
341A ASN* 3.4 2.8 + - - +
342A ILE* 3.2 52.5 + - + +
258F ARG* 3.9 20.6 - - + -
337G GLU* 3.6 31.5 - - + +
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Residues in contact with ILE 339 (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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321A ALA* 4.8 7.4 - - + +
325A PRO* 3.5 46.9 - - + +
327A CYS 5.0 0.2 - - - +
330A LEU* 3.9 21.8 - - + -
331A LEU* 3.7 42.0 - - + +
335A GLY 3.3 15.7 - - - +
336A GLN 3.2 6.3 + - - +
338A TYR* 1.3 82.8 - - + +
340A ASN* 1.3 65.8 + - - +
341A ASN 3.1 0.5 + - - -
342A ILE* 3.2 3.8 + - - +
343A HIS* 3.0 21.3 + - - +
325B PRO* 4.7 0.7 - - + -
326B GLY* 3.8 15.0 - - - +
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Residues in contact with ASN 340 (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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336A GLN* 2.9 24.1 + - - +
337A GLU* 5.2 1.4 - - - +
339A ILE* 1.3 76.2 - - - +
341A ASN* 1.3 57.9 + - - +
343A HIS* 3.6 5.3 - - - +
344A LEU* 2.8 43.2 + - + +
303B CYS* 4.1 26.1 + - - +
324B TYR* 3.5 30.6 - - + +
325B PRO* 3.6 1.8 - - - +
326B GLY* 2.9 30.5 + - - -
341G ASN* 4.0 14.8 + - - +
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Residues in contact with ASN 341 (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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337A GLU 2.9 21.6 + - - +
338A TYR 3.4 6.3 - - - +
340A ASN* 1.3 76.4 - - - +
342A ILE* 1.3 57.7 + - - +
344A LEU* 3.4 5.4 + - - +
345A THR* 3.0 32.4 + - - -
258F ARG* 2.8 29.2 + - - +
337G GLU* 4.1 9.4 + - + +
340G ASN* 3.9 24.9 - - - +
341G ASN* 2.8 26.5 - - - +
344G LEU* 5.0 8.1 - - - +
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Residues in contact with ILE 342 (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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318A GLU* 4.1 20.9 - - + +
321A ALA* 4.0 8.1 - - + -
322A LYS* 3.8 37.7 - - + +
338A TYR* 3.2 61.9 + - + +
339A ILE 3.9 2.9 - - - +
341A ASN* 1.3 76.7 - - - +
343A HIS* 1.3 60.2 + - - +
345A THR* 3.3 6.6 + - + +
346A HIS* 2.8 29.9 + - + +
258F ARG* 3.4 27.1 - - - +
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA 5.4 1.1 + - - +
325A PRO* 5.3 2.9 - - + -
339A ILE 3.0 15.6 + - - +
340A ASN* 3.6 4.3 - - - +
342A ILE* 1.3 79.4 - - - +
344A LEU* 1.3 60.0 + - + +
346A HIS* 3.7 0.5 - - - +
347A SER* 2.6 46.5 + - - -
402A ZN 2.4 37.4 - - - -
322B LYS 3.0 17.7 + - - -
323B TRP* 3.1 29.4 + + - -
325B PRO* 3.6 20.7 - - + +
343B HIS* 3.9 0.6 + - - -
346B HIS* 3.7 15.5 - + - -
402B ZN 2.6 32.4 - - - -
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Residues in contact with LEU 344 (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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340A ASN* 2.8 30.2 + - + +
341A ASN* 3.6 6.5 - - - +
343A HIS* 1.3 83.2 - - + +
345A THR* 1.3 61.2 + - - +
347A SER* 3.4 8.6 - - - +
348A LEU* 3.1 27.1 - - + +
323B TRP* 3.7 24.2 - - + +
324B TYR* 4.4 14.6 - - + -
403B 1AQ 3.6 39.5 - - - +
341G ASN* 5.8 3.6 - - - +
344G LEU* 4.5 23.3 - - + -
348G LEU* 5.8 3.6 - - + -
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 5.6 5.6 - - - +
341A ASN* 3.0 22.2 + - - -
342A ILE* 3.6 7.6 - - + +
344A LEU* 1.3 73.2 - - - +
346A HIS* 1.3 70.7 + - - +
348A LEU* 3.0 30.7 + - - +
349A GLU* 5.4 1.6 - - - -
299F LYS* 5.8 4.3 - - - +
304F GLY 5.8 3.8 - - - +
306F GLY 5.9 2.6 + - - +
324F TYR* 4.8 14.1 + - - +
403F 1AQ 3.4 30.2 - - + +
344G LEU* 4.8 10.2 - - - +
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Residues in contact with HIS 346 (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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322A LYS* 3.6 41.0 + - + +
323A TRP* 3.8 19.7 - + - -
342A ILE* 2.8 22.1 + - + +
343A HIS* 3.7 2.4 + - - +
345A THR* 1.3 73.0 - - - +
347A SER* 1.3 69.1 + - - +
348A LEU 2.9 1.4 + - - -
349A GLU* 3.1 35.5 + - + +
402A ZN 2.8 28.1 - - - -
343B HIS* 3.7 15.7 - + - -
346B HIS* 5.3 5.4 - + - -
347B SER* 3.9 13.4 - - - -
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Residues in contact with SER 347 (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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343A HIS* 2.6 44.9 + - - -
344A LEU* 3.4 11.1 - - - -
345A THR 3.2 0.2 + - - -
346A HIS* 1.3 78.6 - - - +
348A LEU* 1.3 61.9 + - - +
349A GLU 3.3 7.3 + - - +
323B TRP* 4.6 11.6 - - - -
346B HIS* 3.9 16.5 + - - -
403B 1AQ 5.9 2.5 - - - -
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Residues in contact with LEU 348 (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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344A LEU* 3.1 28.3 - - + +
345A THR* 3.0 13.8 + - - +
346A HIS 3.4 1.3 - - - -
347A SER* 1.3 75.6 - - - +
349A GLU* 1.3 57.3 + - - +
403B 1AQ 4.1 26.0 - - + -
403F 1AQ 3.2 83.9 - - + +
344G LEU* 6.2 3.1 - - + -
348G LEU* 6.4 0.2 - - + -
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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