Contacts of the helix formed by residues 327 - 343 (chain B) in PDB entry 3G76
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
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300B CYS* 4.2 0.4 - - - -
302B HIS* 4.5 0.9 - - - -
303B CYS* 3.5 24.3 - - - +
320B HIS* 3.5 1.3 - - - -
324B TYR* 3.4 18.3 + - - +
325B PRO 3.1 6.5 - - - +
326B GLY* 1.3 78.9 - - - +
328B LYS* 1.3 65.4 - - - +
329B TYR* 3.5 9.6 - - - -
330B LEU* 3.4 26.0 - - + +
331B LEU* 3.5 18.0 + - - +
502B ZN 2.4 35.9 - - - -
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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
----------------------------------------------------------
255B ASN* 3.2 36.8 - - - +
302B HIS* 4.2 8.3 + - + +
303B CYS* 5.3 0.2 - - - +
326B GLY 3.3 19.9 + - - +
327B CYS* 1.3 73.9 - - - +
329B TYR* 1.3 56.5 + - - +
330B LEU 3.2 1.3 - - - -
331B LEU* 3.0 24.1 + - + +
332B GLU* 2.7 34.7 + - - +
336B GLN* 5.8 2.9 - - - +
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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
----------------------------------------------------------
268B ARG* 3.6 12.4 + - - -
286B ARG 2.8 21.9 + - - -
287B ALA 3.4 27.8 - - - -
288B GLY* 3.7 6.3 - - - -
300B CYS* 4.7 1.3 - - - -
301B PHE* 3.5 30.3 - + - -
302B HIS* 3.8 31.4 + + + -
317B TRP* 4.2 6.3 - + - -
320B HIS* 4.7 6.3 - + - -
327B CYS* 3.5 2.7 - - - -
328B LYS* 1.3 76.6 - - - +
330B LEU* 1.3 69.4 + - - +
332B GLU* 3.8 17.2 - - - +
333B GLN* 3.1 59.6 + - + +
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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* 3.7 36.6 - - + +
320B HIS* 4.0 10.3 - - + +
321B ALA* 3.7 31.9 - - + +
324B TYR 3.2 25.6 - - - +
325B PRO* 4.0 7.2 - - + +
327B CYS* 3.4 17.9 - - + +
329B TYR* 1.3 80.6 - - - +
331B LEU* 1.3 57.2 + - - +
333B GLN 3.5 0.9 + - - -
334B LYS* 2.8 39.5 + - + +
338B TYR* 5.0 2.0 - - + -
339B ILE* 3.5 32.0 - - + +
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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
----------------------------------------------------------
327B CYS 3.5 13.0 - - - +
328B LYS* 3.0 31.0 + - + +
330B LEU* 1.3 78.5 - - - +
332B GLU* 1.3 64.0 + - - +
333B GLN 3.3 0.2 - - - -
335B GLY* 2.8 29.2 + - - +
336B GLN* 3.3 59.5 - - + +
339B ILE* 3.9 10.3 - - + -
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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
----------------------------------------------------------
328B LYS 2.7 18.0 + - - +
329B TYR* 3.8 15.7 - - - +
330B LEU 3.4 0.2 - - - -
331B LEU* 1.3 77.5 - - + +
333B GLN* 1.3 98.5 + - - +
334B LYS 3.7 0.2 + - - -
335B GLY 4.8 0.7 + - - -
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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
----------------------------------------------------------
286B ARG 4.7 2.9 - - - +
317B TRP* 3.9 19.9 - - + -
329B TYR* 3.1 49.7 + - + +
330B LEU 4.3 0.2 - - - +
332B GLU* 1.3 108.0 + - - +
334B LYS* 1.3 71.5 + - - +
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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 59.1 - - + +
330B LEU* 2.8 19.0 + - + +
332B GLU 3.4 0.4 + - - -
333B GLN* 1.3 89.0 + - - +
335B GLY* 1.3 63.9 + - - +
338B TYR* 3.3 61.5 + - + +
339B ILE* 5.2 0.2 - - + -
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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
----------------------------------------------------------
331B LEU* 2.8 32.3 + - - -
332B GLU 4.7 0.8 + - - -
334B LYS* 1.3 77.3 - - - +
336B GLN* 1.3 65.1 + - - -
337B GLU 3.3 2.6 + - - -
338B TYR 3.5 4.7 + - - -
339B ILE* 3.5 14.9 + - - +
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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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325B PRO 5.5 3.0 + - - -
328B LYS* 5.8 3.0 - - - +
331B LEU* 3.3 32.4 - - + +
335B GLY* 1.3 69.7 - - - -
337B GLU* 1.3 63.9 + - + +
339B ILE* 3.5 10.7 + - - +
340B ASN* 2.9 66.4 + - - +
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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
----------------------------------------------------------
335B GLY 3.3 0.8 - - - -
336B GLN* 1.3 77.1 - - + +
338B TYR* 1.3 65.5 + - - +
340B ASN* 4.3 8.1 - - - +
341B ASN* 2.8 40.7 + - - +
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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* 4.5 2.3 + - - -
317B TRP* 3.6 22.6 - - + +
318B GLU* 3.5 31.2 + - + +
321B ALA* 4.7 3.8 - - + -
330B LEU* 5.0 1.8 - - + -
334B LYS* 3.3 66.0 + - + +
335B GLY 3.5 2.9 + - - +
336B GLN 3.2 0.6 - - - -
337B GLU* 1.3 77.9 - - - +
339B ILE* 1.3 75.4 + - + +
341B ASN* 3.1 11.0 + - + +
342B ILE* 3.1 41.2 + - + +
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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
----------------------------------------------------------
321B ALA* 4.0 18.3 - - + +
325B PRO* 3.5 41.5 - - + +
330B LEU* 3.5 36.3 - - + +
331B LEU* 3.9 27.4 - - + -
335B GLY 3.5 17.5 - - - +
336B GLN* 3.5 11.6 + - - +
338B TYR* 1.3 76.9 - - + +
340B ASN* 1.3 58.1 + - - +
342B ILE* 3.0 5.6 + - - +
343B HIS* 2.7 38.4 + - + +
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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
----------------------------------------------------------
336B GLN* 2.9 52.7 + - - +
337B GLU* 3.8 10.2 - - - +
338B TYR 3.3 0.2 - - - -
339B ILE* 1.3 74.7 - - - +
341B ASN* 1.3 67.2 + - - +
343B HIS* 3.0 16.3 + - - +
344B LEU* 3.2 24.5 + - + +
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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 31.7 + - - +
338B TYR* 3.1 6.5 + - + +
340B ASN* 1.3 79.3 - - - +
342B ILE* 1.3 68.7 + - + +
344B LEU* 3.2 26.5 + - - +
345B THR* 4.6 2.9 + - - -
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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
----------------------------------------------------------
318B GLU* 3.6 44.9 - - + +
321B ALA* 4.3 4.9 - - + -
322B LYS* 3.9 24.6 - - + +
338B TYR* 3.1 46.2 - - + +
339B ILE 3.0 7.7 + - - +
341B ASN* 1.3 78.4 - - + +
343B HIS* 1.3 59.8 + - - +
344B LEU 2.8 10.7 + - - -
345B THR* 3.1 21.4 + - - +
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Residues in contact with HIS 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ALA 3.4 22.4 - - - -
322B LYS* 3.5 19.9 + - + -
325B PRO* 3.5 29.2 - - + +
339B ILE* 2.7 21.3 + - + +
340B ASN* 3.0 10.7 + - - +
342B ILE* 1.3 72.5 - - - +
344B LEU* 1.3 61.0 + - + +
345B THR 3.1 7.0 + - - -
346B HIS 4.8 1.3 + - - -
347B SER* 4.1 33.7 + - - -
348B LEU* 4.5 8.9 - - + +
352B LEU* 5.9 5.2 - - + -
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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
------------------------------------------------------------
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