Contacts of the helix formed by residues 327 - 350 (chain B) in PDB entry 3GSB
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 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN 3.7 0.6 + - - -
326B PRO* 1.3 73.5 - - - +
328B THR* 1.3 61.7 + - - +
329B TYR 3.8 0.7 - - - -
330B GLU* 3.4 26.8 + - - +
331B TYR* 3.1 24.8 + - - +
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Residues in contact with THR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU 3.8 6.8 + - - -
323B LEU* 3.2 44.0 + - + +
325B GLN* 3.2 15.2 + - - +
326B PRO 3.4 1.3 + - - -
327B GLY* 1.3 76.1 - - - +
329B TYR* 1.3 87.7 + - + +
330B GLU* 3.1 5.0 + - - -
331B TYR* 3.3 6.4 + - - +
332B LEU* 3.4 10.0 + - + +
412B LEU* 3.5 34.0 - - + +
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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
----------------------------------------------------------
71B ILE* 4.5 6.5 - - + -
251B PHE* 2.6 33.5 + - - -
252B ARG* 3.8 17.9 - - - -
253B ILE 4.2 7.4 - - - +
254B ALA* 4.1 7.0 - - - -
255B TYR* 3.6 38.1 - + + -
323B LEU* 3.6 29.9 - - + +
328B THR* 1.3 95.2 - - + +
330B GLU* 1.3 68.4 + - - +
332B LEU* 3.9 10.5 - - + +
333B ASP* 3.1 25.3 + - - +
360B SER* 4.1 10.6 + - - +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLY* 3.4 29.8 + - - +
328B THR 3.1 1.3 + - - -
329B TYR* 1.3 82.3 + - - +
331B TYR* 1.3 58.0 - - - +
332B LEU 3.2 0.3 + - - -
333B ASP* 3.3 7.0 + - - +
334B GLN* 2.9 29.6 + - - +
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLY 3.1 15.5 + - - +
328B THR 3.3 5.4 + - - +
330B GLU* 1.3 80.1 - - - +
332B LEU* 1.3 59.0 + - + +
334B GLN* 3.4 19.0 + - - +
335B ILE* 3.1 52.4 + - + +
411B SER 4.2 1.1 - - - -
412B LEU* 4.2 30.6 + - + -
414B HIS 2.7 29.6 + - - -
415B THR* 3.6 14.2 - - - +
416B GLU* 3.7 18.4 + - - -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.0 27.4 - - + -
252B ARG* 4.4 1.6 - - + +
328B THR* 3.4 11.6 + - + +
329B TYR* 3.9 18.6 - - + +
330B GLU 3.2 0.6 - - - -
331B TYR* 1.3 74.0 - - + +
333B ASP* 1.3 68.4 + - - +
335B ILE* 4.0 4.0 - - + -
336B THR* 2.8 30.5 + - - -
360B SER* 3.9 14.8 - - - +
361B GLY* 3.7 18.2 - - - +
410B THR* 3.3 24.0 - - + +
411B SER* 3.6 24.9 - - - +
412B LEU* 3.9 14.8 - - + +
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LYS* 5.6 5.4 + - - -
329B TYR 3.1 16.4 + - - +
330B GLU* 3.7 4.9 - - - +
332B LEU* 1.3 78.9 - - - +
334B GLN* 1.3 63.8 + - - +
336B THR* 4.0 0.5 - - - -
337B LYS* 3.1 32.2 + - - +
358B GLN* 3.6 12.3 + - - +
359B VAL* 4.5 2.1 - - - +
360B SER* 3.1 30.9 + - - +
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU 2.9 16.9 + - - +
331B TYR* 3.6 25.5 - - - +
332B LEU 3.1 0.2 - - - -
333B ASP* 1.3 78.3 - - - +
335B ILE* 1.3 60.2 + - - +
337B LYS* 4.1 3.6 - - - +
338B ARG* 3.6 18.0 + - - +
416B GLU* 3.9 19.9 + - - +
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR* 3.1 49.4 + - + +
332B LEU* 3.6 6.5 - - - +
334B GLN* 1.3 71.5 - - + +
336B THR* 1.3 68.1 + - - +
337B LYS 3.1 2.0 + - - -
338B ARG* 3.2 8.3 + - - +
339B LEU* 3.0 24.4 + - - +
410B THR* 3.9 13.5 - - + +
411B SER 3.6 17.7 - - - +
414B HIS* 3.7 18.4 - - + +
416B GLU* 3.7 30.3 - - - +
419B ILE* 3.9 25.3 - - + +
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Residues in contact with THR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU 2.8 20.6 + - - -
335B ILE* 1.3 77.4 - - - +
337B LYS* 1.3 56.6 + - - +
339B LEU* 4.0 5.8 - - + +
340B SER* 2.9 31.2 + - - -
358B GLN* 3.4 22.4 - - + -
360B SER 3.2 20.6 - - - +
361B GLY* 3.2 16.8 - - - -
362B MET 3.9 10.5 - - - +
363B PHE* 4.1 15.5 - - + -
410B THR* 3.3 18.1 + - - +
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Residues in contact with LYS 337 (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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333B ASP* 3.1 25.2 + - - +
334B GLN* 4.1 4.5 - - - +
336B THR* 1.3 73.8 - - - +
338B ARG* 1.3 60.4 + - - +
339B LEU 3.1 1.6 - - - -
340B SER* 4.3 0.2 - - - -
341B ASP* 2.8 60.0 + - - +
358B GLN* 3.5 23.5 - - + +
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLN 3.6 11.1 + - - +
335B ILE* 3.2 9.2 + - - +
337B LYS* 1.3 78.2 - - - +
339B LEU* 1.3 56.2 + - - +
341B ASP* 4.2 3.6 - - - +
342B GLY* 3.0 25.1 + - - -
416B GLU* 2.7 59.6 + - - +
419B ILE* 3.6 25.6 - - + +
420B ASP* 2.6 38.1 + - - -
423B LEU* 3.8 8.0 - - + +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 4.5 12.8 - - + -
335B ILE 3.0 16.1 + - - +
336B THR* 4.0 7.0 - - - +
338B ARG* 1.3 76.2 - - - +
340B SER* 1.3 61.0 + - - +
342B GLY* 3.2 0.7 + - - -
343B LEU* 2.9 49.0 + - + +
363B PHE* 4.0 33.7 - - + -
410B THR* 5.6 2.9 - - - +
419B ILE* 3.7 25.6 - - + +
422B THR* 4.0 26.5 - - + -
423B LEU* 3.6 24.0 - - + -
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B THR 2.9 20.9 + - - -
337B LYS* 3.7 2.4 - - - +
339B LEU* 1.3 78.4 - - - +
341B ASP* 1.3 69.6 + - - +
343B LEU* 3.5 10.3 + - - +
344B LEU* 3.2 29.6 + - - +
357B GLY* 4.1 18.5 + - - -
358B GLN* 3.6 23.5 - - - +
363B PHE* 4.8 7.2 - - - -
364B GLY 5.8 1.3 - - - -
365B PHE* 5.1 1.1 - - - -
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Residues in contact with ASP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LYS* 2.8 51.5 + - - +
338B ARG* 4.2 3.1 - - - +
340B SER* 1.3 80.6 + - - +
342B GLY* 1.3 68.3 + - - +
344B LEU* 3.0 11.5 + - - +
345B ALA* 2.8 25.7 + - - +
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Residues in contact with GLY 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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338B ARG 3.0 16.0 + - - -
339B LEU 3.2 0.2 + - - -
341B ASP* 1.3 77.2 - - - +
343B LEU* 1.3 62.7 + - - +
345B ALA* 3.4 5.6 + - - +
346B ILE* 3.2 26.9 + - - +
423B LEU* 3.4 26.9 - - - -
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 2.9 43.4 + - + +
340B SER* 3.7 6.7 - - - +
341B ASP 3.2 0.2 - - - -
342B GLY* 1.3 77.1 - - - +
344B LEU* 1.3 63.4 + - - +
345B ALA 3.1 1.0 + - - -
346B ILE* 3.2 5.9 + - - +
347B ALA* 3.2 18.2 + - - +
363B PHE* 4.3 16.4 - - + -
365B PHE* 3.7 33.2 - - + -
389B PHE* 5.7 4.3 - - + -
393B MET* 5.0 4.9 - - + -
400B LEU* 6.3 2.0 - - + -
422B THR* 4.9 6.3 - - + -
423B LEU* 3.7 9.6 - - + -
426B ALA* 3.7 27.8 - - + -
430B MET* 3.7 10.1 - - + +
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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
----------------------------------------------------------
340B SER* 3.2 18.1 + - - +
341B ASP* 3.0 14.6 + - - +
343B LEU* 1.3 79.2 - - - +
345B ALA* 1.3 59.3 + - - +
347B ALA* 3.7 1.9 + - - +
348B GLN* 2.8 34.4 + - - +
354B ALA* 4.4 4.7 - - + +
355B CYS* 3.7 27.8 - - - +
356B GLY* 3.8 22.9 - - - +
357B GLY* 5.0 0.4 - - - +
365B PHE* 3.2 31.9 - - + -
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Residues in contact with ALA 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 ASP 2.8 19.7 + - - +
342B GLY* 3.7 7.0 - - - +
344B LEU* 1.3 70.5 - - - +
346B ILE* 1.3 67.4 + - + +
348B GLN* 3.0 18.2 + - - +
349B GLU* 3.1 14.2 + - - +
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Residues in contact with ILE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLY* 3.2 20.8 + - - +
343B LEU* 3.7 5.4 - - - +
345B ALA* 1.3 78.3 - - + +
347B ALA* 1.3 59.5 + - - +
349B GLU* 3.5 8.6 + - - +
350B THR* 2.8 33.7 + - + +
423B LEU* 3.2 35.9 - - + +
426B ALA* 3.5 34.3 - - + +
427B ARG* 3.5 37.7 - - + +
430B MET* 4.0 13.9 - - + -
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Residues in contact with ALA 347 (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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343B LEU 3.2 12.0 + - - +
344B LEU 3.8 8.7 - - - +
345B ALA 3.1 0.6 - - - -
346B ILE* 1.3 75.4 - - - +
348B GLN* 1.3 67.5 + - - +
350B THR* 3.1 11.7 + - - -
352B HIS* 3.0 44.0 + - + +
354B ALA* 4.1 18.6 - - + -
365B PHE* 4.4 1.3 - - + -
367B PHE* 5.6 0.4 - - + -
430B MET* 3.8 17.9 - - + +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 2.8 30.7 + - - +
345B ALA* 3.0 11.3 + - - +
347B ALA* 1.3 83.8 - - - +
349B GLU* 1.3 61.3 + - + +
350B THR 3.5 0.3 + - - -
351B GLY* 3.7 8.5 + - - -
352B HIS 4.3 8.1 + - - +
353B ALA* 4.9 2.9 - - - -
354B ALA 4.8 16.7 + - - +
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA 3.1 12.3 + - - +
346B ILE* 3.9 12.1 - - - +
348B GLN* 1.3 78.5 - - - +
350B THR* 1.3 65.3 + - + +
351B GLY 3.4 0.7 - - - -
427B ARG* 3.3 37.8 + - - -
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Residues in contact with THR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 2.8 31.3 + - + +
347B ALA* 3.1 6.0 + - - -
349B GLU* 1.3 88.2 - - + +
351B GLY* 1.3 59.4 + - - +
352B HIS* 3.0 39.9 + - - -
427B ARG* 5.1 2.2 - - + +
430B MET* 3.7 12.7 - - + +
431B SER* 3.7 24.2 - - - +
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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
------------------------------------------------------------
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