Contacts of the helix formed by residues 322 - 345 (chain B) in PDB entry 1G1E
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 PRO 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B GLN 4.9 2.4 - - - +
320B GLY* 3.4 9.0 - - - +
321B GLN* 1.3 91.0 - - - +
323B ASP* 1.3 67.0 + - - +
324B ILE 3.3 0.2 - - - -
325B TYR* 4.7 5.2 - - + +
326B LYS* 3.0 43.0 + - + +
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Residues in contact with ASP 323 (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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321B GLN* 3.0 16.1 + - - +
322B PRO* 1.3 88.1 - - - +
324B ILE* 1.3 51.8 + - + +
326B LYS* 4.7 2.2 - - - -
327B ALA* 2.7 39.7 + - - +
365B LEU* 4.3 3.0 - - + +
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Residues in contact with ILE 324 (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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314B ILE* 4.9 0.9 - - + -
318B PHE* 3.0 58.3 - - + -
321B GLN* 3.0 38.5 + - + +
323B ASP* 1.3 75.7 - - + +
325B TYR* 1.3 57.0 + - - +
328B PHE* 2.7 37.1 + - - +
365B LEU* 3.3 46.2 - - + +
366B PHE* 4.2 1.8 - - + -
369B GLN* 5.2 1.3 - - - +
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Residues in contact with TYR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.1 34.5 + - + +
19A LEU* 3.9 1.2 - - - +
20A GLU* 3.8 18.4 - - + -
311B VAL* 3.1 23.9 - - + +
314B ILE* 4.0 10.8 - - + -
315B LYS* 3.2 72.3 - - + +
318B PHE* 4.8 5.1 - - + +
321B GLN 3.3 11.1 + - - +
322B PRO* 4.2 5.4 - - + +
324B ILE* 1.3 80.4 - - - +
326B LYS* 1.3 68.9 + - + +
328B PHE* 3.5 5.3 + + + +
329B LEU* 3.1 36.7 + - + +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 4.8 13.4 + - - -
322B PRO* 3.0 31.4 + - + +
323B ASP* 4.3 2.7 - - - +
325B TYR* 1.3 82.7 - - + +
327B ALA* 1.3 62.7 + - - +
329B LEU* 3.3 14.8 + - + +
330B GLU* 2.9 33.4 + - + +
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Residues in contact with ALA 327 (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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323B ASP 2.7 23.2 + - - +
324B ILE 3.7 2.2 - - - +
326B LYS* 1.3 75.6 - - - +
328B PHE* 1.3 51.4 + - - +
330B GLU* 3.0 10.4 + - - +
331B ILE* 2.7 43.1 + - + +
365B LEU* 3.9 18.8 - - + -
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Residues in contact with PHE 328 (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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12A LEU* 3.8 9.0 - - + -
310B TYR* 4.0 3.6 - + - -
311B VAL* 5.9 3.8 - - + -
314B ILE* 3.5 21.3 - - + -
324B ILE* 2.7 24.4 + - + +
325B TYR* 3.7 6.7 - + + +
327B ALA* 1.3 71.2 - - - +
329B LEU* 1.3 73.0 + - + +
331B ILE* 3.1 21.6 + - - +
332B LEU* 3.2 35.0 + - + +
362B VAL* 3.4 27.6 - - + -
365B LEU* 3.4 8.4 - - + +
366B PHE* 3.4 34.3 - + + -
376B PHE* 3.3 28.7 - + - -
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Residues in contact with LEU 329 (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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12A LEU* 5.2 0.7 - - + +
13A LEU* 2.9 38.0 - - + +
16A ALA* 3.5 35.7 - - + -
17A ASP* 4.8 5.4 - - - +
20A GLU* 4.1 10.8 - - - +
311B VAL* 5.3 4.5 - - + -
325B TYR* 3.1 27.6 + - + +
326B LYS* 3.6 15.5 - - + +
328B PHE* 1.3 84.1 - - + +
330B GLU* 1.3 59.1 + - + +
332B LEU* 3.2 1.6 + - + -
333B HIS* 2.8 38.0 + - + +
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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
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326B LYS* 2.9 26.1 + - + +
327B ALA* 3.4 10.1 - - - +
329B LEU* 1.3 76.8 - - + +
331B ILE* 1.3 51.1 + - - +
333B HIS* 3.7 14.3 - - - +
334B THR* 2.7 44.3 + - - +
337B LYS* 4.9 9.7 + - - -
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Residues in contact with ILE 331 (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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327B ALA* 2.7 30.9 + - + +
328B PHE* 3.1 7.8 + - - +
330B GLU* 1.3 75.5 - - + +
332B LEU* 1.3 64.7 + - - +
334B THR* 3.3 16.4 + - - -
335B TYR* 3.4 5.5 + - - +
353B LEU* 3.9 5.0 - - - +
357B GLU 4.0 1.6 - - - +
358B VAL* 3.0 44.6 - - + +
361B GLN* 3.0 55.9 - - + +
362B VAL* 3.2 15.0 - - + +
365B LEU* 3.7 16.6 - - + -
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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
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9A ILE* 3.5 23.4 - - + +
12A LEU* 3.5 19.1 - - + -
13A LEU* 3.1 40.6 - - + +
328B PHE* 3.2 35.2 + - + +
329B LEU* 4.7 0.4 - - + -
331B ILE* 1.3 75.7 - - + +
333B HIS* 1.3 59.2 + - - +
335B TYR* 2.9 21.9 + - - +
336B GLN 2.9 11.1 + - - -
358B VAL* 3.2 29.6 - - + -
362B VAL* 4.6 0.2 - - + -
376B PHE* 3.6 19.3 - - + -
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Residues in contact with HIS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 5.9 1.8 - - + -
13A LEU* 3.3 35.7 - - + +
14A GLU* 5.6 1.1 - - + -
17A ASP* 5.1 6.6 + - - -
329B LEU* 2.8 37.2 + - + +
330B GLU* 3.7 18.4 - - - +
332B LEU* 1.3 77.5 - - - +
334B THR* 1.3 56.2 + - - +
336B GLN* 2.9 24.5 + - + +
337B LYS* 2.8 40.8 + - + +
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Residues in contact with THR 334 (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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330B GLU* 2.7 30.3 + - - +
331B ILE* 3.4 5.6 - - - -
332B LEU 3.1 0.2 - - - -
333B HIS* 1.3 72.9 - - - +
335B TYR* 1.3 62.9 + - - +
337B LYS* 3.4 18.5 + - - +
338B GLU* 2.8 45.1 + - - +
353B LEU* 2.9 36.8 - - + -
361B GLN* 5.9 2.9 - - - +
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Residues in contact with TYR 335 (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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6A ARG* 3.4 22.6 + - + -
8A ASN* 4.7 3.9 + - - -
9A ILE* 2.9 27.6 - - + -
331B ILE 3.4 0.2 + - - -
332B LEU 2.9 10.0 + - - +
334B THR* 1.3 79.1 - - - +
336B GLN* 1.3 61.2 + - - +
337B LYS 3.4 0.2 + - - -
338B GLU* 3.4 10.9 + - - +
339B GLN* 3.1 35.9 + - + +
353B LEU* 3.0 18.9 - - + +
354B THR* 3.2 19.3 - - - -
355B GLU* 3.1 47.7 + - - +
358B VAL* 3.2 34.5 - - + -
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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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9A ILE* 3.4 20.6 - - + -
10A GLN* 3.3 36.7 - - + +
13A LEU* 4.4 0.9 - - + -
332B LEU 2.9 6.2 + - - +
333B HIS* 2.9 47.6 + - - +
335B TYR* 1.3 77.0 - - - +
337B LYS* 1.3 91.5 + - - +
339B GLN* 3.3 15.3 + - - +
340B ARG* 3.2 29.7 + - - +
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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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330B GLU* 4.9 9.2 + - - -
333B HIS* 2.8 35.2 + - + +
334B THR* 3.6 22.4 + - - +
336B GLN* 1.3 90.2 - - - +
338B GLU* 1.3 60.3 + - - +
340B ARG* 2.7 30.1 + - + +
341B ASN* 2.7 26.1 + - - +
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Residues in contact with GLU 338 (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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334B THR* 2.8 40.4 + - - +
335B TYR 3.4 8.7 + - - +
337B LYS* 1.3 86.0 - - - +
339B GLN* 1.3 62.5 + - - +
341B ASN* 3.1 15.7 + - - +
342B ALA* 3.0 21.5 + - - +
349B TYR* 3.8 11.7 - - - +
351B PRO* 3.8 20.0 - - + +
352B ALA* 3.2 33.5 - - + +
353B LEU* 3.4 15.2 - - + +
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Residues in contact with GLN 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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6A ARG* 3.2 44.2 + - - +
9A ILE* 4.0 4.4 - - - +
10A GLN* 5.4 2.2 + - - -
335B TYR* 3.1 44.7 - - + +
336B GLN* 3.3 12.4 - - - +
337B LYS 3.1 0.6 - - - -
338B GLU* 1.3 77.3 - - + +
340B ARG* 1.3 91.5 + - - +
342B ALA* 3.4 7.4 + - - +
343B LYS* 3.4 15.4 + - - +
351B PRO* 5.1 7.6 - - + -
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Residues in contact with ARG 340 (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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6A ARG 5.9 2.0 - - - +
10A GLN* 4.4 15.8 + - - +
336B GLN* 3.2 34.3 + - - +
337B LYS* 2.7 17.8 + - + +
339B GLN* 1.3 109.1 + - - +
341B ASN* 1.3 63.1 + - - +
343B LYS* 3.1 16.5 + - - +
344B GLU* 3.0 37.6 + - + +
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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 LYS* 2.7 38.0 + - - +
338B GLU* 3.1 21.1 + - - +
340B ARG* 1.3 74.1 - - - +
342B ALA* 1.3 63.0 + - - +
344B GLU* 3.1 17.5 + - - +
345B ALA* 3.0 23.4 + - - +
349B TYR* 3.5 29.8 + - + +
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Residues in contact with ALA 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 GLU 3.0 10.4 + - - +
339B GLN* 3.6 10.3 - - - +
340B ARG 3.3 0.2 - - - -
341B ASN* 1.3 75.9 - - - +
343B LYS* 1.3 62.1 + - - +
345B ALA* 3.4 5.7 + - - +
347B GLY* 3.4 25.8 + - - +
349B TYR* 3.2 36.9 - - + +
351B PRO* 4.6 9.6 - - + -
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Residues in contact with LYS 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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339B GLN 3.4 8.3 + - - +
340B ARG* 3.1 20.5 + - - +
342B ALA* 1.3 76.9 - - - +
344B GLU* 1.3 65.9 + - + +
346B GLY* 3.0 16.4 + - - -
347B GLY* 5.3 0.7 - - - +
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Residues in contact with GLU 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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340B ARG* 3.0 33.6 + - + +
341B ASN* 3.1 16.1 + - - +
343B LYS* 1.3 77.5 - - + +
345B ALA* 1.3 60.2 + - - +
346B GLY* 3.1 1.8 + - - -
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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
----------------------------------------------------------
341B ASN 3.0 10.8 + - - +
342B ALA 3.7 2.9 - - - +
343B LYS 3.2 0.2 - - - -
344B GLU* 1.3 75.5 - - - +
346B GLY* 1.3 56.4 + - - +
347B GLY 3.3 4.0 + - - +
348B ASN* 4.4 13.9 + - - +
349B TYR* 3.3 36.1 - - + -
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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
------------------------------------------------------------
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