Contacts of the helix formed by residues 327 - 347 (chain B) 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 CYS 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 4.3 0.6 - - - +
336A GLN* 4.0 1.3 - - - -
340A ASN* 4.3 2.2 + - - +
300B CYS* 3.4 11.2 - - - -
302B HIS* 3.8 1.1 - - - -
303B CYS* 3.6 22.7 - - + -
320B HIS* 3.5 3.8 - - - +
324B TYR 3.6 4.6 + - - +
325B PRO 3.4 4.3 - - - +
326B GLY* 1.3 77.8 - - - +
328B LYS* 1.3 60.0 + - - +
329B TYR* 3.6 18.6 - - - -
330B LEU* 3.6 20.3 - - + +
331B LEU* 3.1 24.6 + - - +
401B ZN 2.2 37.0 - - - -
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Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LYS* 6.3 0.2 - - - +
331A LEU* 3.6 23.8 - - + +
332A GLU* 4.9 12.9 + - - +
336A GLN* 3.7 11.3 + - - +
255B ASN* 3.3 40.3 - - + +
302B HIS* 3.6 26.7 - - + +
326B GLY 3.5 3.4 + - - -
327B CYS* 1.3 71.1 - - - +
329B TYR* 1.3 61.1 + - - +
331B LEU* 3.2 1.4 + - + +
332B GLU* 2.9 53.3 + - + +
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ALA 6.1 0.2 - - - -
268B ARG* 3.6 13.0 + - - -
286B ARG* 2.7 29.6 + - - -
287B ALA 4.0 8.1 - - - -
288B GLY* 3.6 15.7 - - - -
300B CYS* 4.9 0.4 - - - -
301B PHE* 3.5 27.8 - + - -
302B HIS* 3.7 30.5 + - + +
317B TRP* 3.7 12.8 - + - -
320B HIS* 4.7 4.7 - + - -
327B CYS* 3.4 4.0 - - - -
328B LYS* 1.3 78.1 - - - +
330B LEU* 1.3 63.7 + - - +
332B GLU* 3.9 10.1 - - - +
333B GLN* 3.0 60.7 + - + +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 3.4 44.2 - - + +
320B HIS* 4.2 12.6 - - + +
321B ALA* 3.6 30.7 - - + +
324B TYR 3.7 17.3 - - - +
325B PRO 4.2 4.0 - - - +
327B CYS* 3.6 18.9 + - + +
329B TYR* 1.3 80.6 - - - +
331B LEU* 1.3 54.4 + - - +
334B LYS* 2.7 45.6 + - + +
338B TYR* 4.7 1.1 - - + -
339B ILE* 3.7 24.0 - - + -
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASN* 3.2 17.1 + - - +
326A GLY 3.2 23.8 - - - +
328A LYS* 3.6 34.3 - - + -
331A LEU* 3.5 28.0 - - + -
325B PRO 5.7 0.2 - - - +
327B CYS 3.1 15.1 + - - +
328B LYS* 3.2 4.7 + - + +
330B LEU* 1.3 80.7 - - - +
332B GLU* 1.3 59.4 + - + +
335B GLY* 2.8 32.3 + - - +
336B GLN* 3.6 25.8 - - + +
339B ILE* 3.8 15.0 - - + -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASN* 4.1 12.3 + - - +
328A LYS* 6.3 0.9 - - - +
302B HIS* 6.0 1.3 - - - -
328B LYS* 2.9 46.1 + - + +
329B TYR* 3.9 10.5 - - - +
331B LEU* 1.3 75.6 - - - +
333B GLN* 1.3 71.7 + - - +
335B GLY 4.9 0.3 + - - -
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 3.5 25.6 - - + -
329B TYR* 3.0 62.0 + - + +
330B LEU 3.9 0.2 - - - +
332B GLU* 1.3 88.5 + - - +
334B LYS* 1.3 64.6 + - - +
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Residues in contact with LYS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 3.5 62.6 - - + +
330B LEU* 2.7 21.5 + - + +
333B GLN* 1.3 80.6 - - - +
335B GLY* 1.3 58.1 + - - +
338B TYR* 3.4 58.6 + - + +
256E LEU* 5.7 11.5 + - - +
257E PRO 5.9 1.4 + - - -
258E ARG* 6.1 2.2 - - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 5.5 6.7 - - - -
255A ASN* 3.2 17.3 - - - -
330B LEU 3.7 1.6 + - - -
331B LEU* 2.8 25.8 + - - -
332B GLU 4.7 0.4 - - - -
333B GLN 3.9 0.2 - - - -
334B LYS* 1.3 75.8 - - - +
336B GLN* 1.3 66.4 + - - -
337B GLU 3.5 2.0 + - - -
338B TYR 3.6 0.2 + - - -
339B ILE* 3.3 22.9 + - - +
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A THR 5.0 3.5 + - - +
255A ASN* 3.2 20.2 + - - +
256A LEU 4.3 4.7 - - - +
258A ARG* 5.1 1.9 - - - +
302A HIS* 2.6 56.2 + - - +
303A CYS* 3.5 13.3 - - + +
326A GLY* 3.6 19.1 - - - +
327A CYS* 3.9 2.4 - - - +
328A LYS* 3.1 21.6 - - + +
331B LEU* 3.6 7.5 - - + +
335B GLY* 1.3 68.5 - - - -
337B GLU* 1.3 81.8 + - - +
339B ILE* 3.1 3.3 + - - +
340B ASN* 2.9 34.6 + - - +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR 4.5 13.0 + - - +
258A ARG* 2.6 39.5 + - - +
303A CYS 4.4 3.3 - - - +
335B GLY 3.5 0.4 - - - -
336B GLN* 1.3 86.6 + - - +
338B TYR* 1.3 57.7 + - - +
340B ASN* 3.7 1.5 - - - +
341B ASN* 2.8 34.1 + - - +
337D GLU* 3.5 17.5 - - + -
338D TYR* 3.5 35.8 - - + +
341D ASN* 3.8 15.5 - - - +
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Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASP* 4.9 1.4 + - - -
317B TRP* 3.4 11.9 - - - +
318B GLU* 3.3 25.8 + - - +
321B ALA* 3.9 12.8 - - + -
330B LEU* 4.7 1.3 - - + -
334B LYS* 3.4 67.1 + - + +
335B GLY 3.6 2.3 + - - +
336B GLN 3.3 0.6 - - - -
337B GLU* 1.3 76.3 - - - +
339B ILE* 1.3 68.9 + - + +
341B ASN* 3.3 1.4 + - - +
342B ILE* 3.1 47.3 + - + +
337D GLU* 3.6 28.8 - - + +
258E ARG* 3.8 29.7 + - + +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A PRO* 4.8 0.7 - - + -
326A GLY* 3.7 17.7 - - - +
321B ALA* 4.7 7.8 - - + +
325B PRO* 3.4 46.2 - - + +
330B LEU* 3.7 32.1 - - + +
331B LEU* 3.8 35.2 - - + +
335B GLY 3.3 7.4 + - - +
336B GLN 3.1 7.4 + - - +
338B TYR* 1.3 84.9 - - + +
340B ASN* 1.3 59.4 + - - +
342B ILE* 3.5 2.4 + - - +
343B HIS* 3.0 25.8 + - - +
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Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A CYS* 4.0 25.9 + - - +
324A TYR* 3.3 25.5 - - + +
325A PRO* 3.4 2.3 - - - +
326A GLY* 2.8 34.2 + - - -
327A CYS 4.1 1.4 - - - +
336B GLN* 2.9 22.8 + - - +
337B GLU* 4.0 2.6 - - - +
339B ILE* 1.3 76.6 - - - +
341B ASN* 1.3 56.2 + - - +
343B HIS* 3.7 4.0 - - - +
344B LEU* 2.9 47.3 + - + +
341D ASN* 4.2 9.8 + - - +
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B GLU 2.8 18.7 + - - +
338B TYR 3.6 1.3 - - - +
340B ASN* 1.3 75.2 - - - +
342B ILE* 1.3 62.4 + - - +
344B LEU* 3.6 4.4 + - - +
345B THR* 3.1 30.3 + - - -
337D GLU* 3.6 18.5 + - + +
340D ASN* 3.8 14.9 + - - +
341D ASN* 2.6 36.1 - - - +
344D LEU* 6.0 2.6 - - - +
258E ARG* 2.6 35.0 + - - +
303E CYS 5.0 0.7 - - - +
324E TYR* 6.1 0.7 - - - -
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B GLU* 3.6 26.0 - - + +
321B ALA* 3.7 10.5 - - + -
322B LYS* 3.9 35.2 - - + +
338B TYR* 3.1 56.6 + - + +
339B ILE 3.9 3.1 - - - +
341B ASN* 1.3 74.0 - - - +
343B HIS* 1.3 60.9 + - - +
345B THR* 3.2 6.9 + - + -
346B HIS* 3.0 28.1 + - + +
258E ARG* 3.9 21.8 - - - +
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Residues in contact with HIS 343 (chain B).
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 3.1 17.9 + - - -
323A TRP* 3.2 26.8 + - - -
325A PRO* 3.4 21.4 - - + +
343A HIS* 3.9 0.6 + + - -
346A HIS* 3.7 14.2 - + - -
402A ZN 2.6 31.6 - - - -
321B ALA 5.5 0.7 - - - +
325B PRO* 5.3 2.0 - - + -
339B ILE 3.0 19.1 + - - +
340B ASN* 3.7 4.0 - - - +
341B ASN 3.3 0.2 - - - -
342B ILE* 1.3 78.3 - - - +
344B LEU* 1.3 70.4 + - + +
346B HIS* 3.7 1.4 - - - +
347B SER* 3.0 41.9 + - - -
402B ZN 2.5 35.6 - - - -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A TRP* 3.3 27.4 - - + +
324A TYR* 3.9 26.2 - - + -
403A 1AQ 4.4 34.0 - - - +
340B ASN* 2.9 34.4 + - + +
341B ASN* 3.9 5.6 - - - +
342B ILE 3.4 0.2 - - - -
343B HIS* 1.3 86.9 - - + +
345B THR* 1.3 57.7 + - - +
347B SER* 4.0 9.3 - - - +
348B LEU* 3.6 22.9 - - - +
341D ASN* 5.4 6.7 - - - +
344D LEU* 5.7 5.4 - - + +
345D THR* 6.2 0.4 - - - +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASN* 3.1 19.3 + - - -
342B ILE* 3.2 12.1 + - + +
343B HIS 3.0 0.8 - - - -
344B LEU* 1.3 77.8 - - - +
346B HIS* 1.3 68.2 + - - +
347B SER 3.1 1.1 - - - -
348B LEU* 2.9 16.5 + - - +
349B GLU* 4.2 0.8 - - - +
258E ARG* 5.3 4.8 + - - +
299E LYS* 5.5 7.0 - - - +
304E GLY 5.5 6.5 - - - +
306E GLY 6.1 1.1 - - - +
324E TYR* 5.4 9.7 + - - +
403E 1AQ 3.4 41.2 - - + +
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Residues in contact with HIS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A HIS* 3.7 23.3 - + - -
346A HIS* 5.3 4.3 - + - -
347A SER* 3.9 17.9 + - - -
322B LYS* 4.0 40.2 - - + +
323B TRP* 3.8 21.3 - + - -
342B ILE* 3.0 17.5 + - + +
343B HIS* 3.7 6.1 + + - +
345B THR* 1.3 76.7 - - - +
347B SER* 1.3 62.0 + - - +
349B GLU* 2.9 34.6 - - + +
402B ZN 3.0 19.2 - - - -
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Residues in contact with SER 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A TRP* 4.1 13.6 - - - -
346A HIS* 3.9 12.7 - - - -
403A 1AQ 5.1 7.4 - - - -
343B HIS* 3.0 38.6 + - - -
344B LEU* 4.0 12.5 - - - +
345B THR 3.1 0.4 - - - -
346B HIS* 1.3 81.7 - - - +
348B LEU* 1.3 54.2 + - - +
349B GLU* 2.7 17.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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