Contacts of the helix formed by residues 323 - 345 (chain A) in PDB entry 2GLQ
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 ARG 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLY 3.0 13.3 + - - +
321A GLU* 3.0 38.1 + - + +
322A SER* 1.3 77.3 - - - +
324A ALA* 1.3 65.2 + - - +
325A TYR 3.0 2.5 - - - +
326A ARG* 2.9 51.3 + - + +
327A ALA 3.1 8.8 + - - -
393A TYR* 4.0 0.2 - - - -
417A PRO 4.5 3.1 - - - +
418A GLU* 2.9 34.5 + - - +
419A TYR 3.5 18.6 - - - +
420A ARG* 3.4 41.7 - - + +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 1.3 71.5 - - - +
325A TYR* 1.3 57.4 + - - +
327A ALA* 4.3 5.8 - - - -
328A LEU* 2.8 35.1 + - + +
362A PHE* 3.8 12.1 - - + -
375A PHE* 3.9 2.7 - - + -
391A LEU* 3.7 24.2 - - + -
393A TYR* 3.5 16.0 + - - +
421A GLN* 2.9 31.5 + - - +
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Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 6.1 0.4 - - + -
59A LYS* 5.3 8.5 + - - -
278A ILE* 4.0 19.0 - - + +
323A ARG* 3.0 2.1 - - + +
324A ALA* 1.3 77.9 - - - +
326A ARG* 1.3 52.6 + - - +
328A LEU* 4.1 0.5 - - - +
329A THR* 2.8 58.1 + - + +
375A PHE* 3.6 43.9 - + + -
415A GLY 3.9 21.5 - - - -
416A SER 4.2 5.4 - - - +
417A PRO* 3.7 48.5 - - + +
419A TYR 5.3 1.8 + - - +
421A GLN* 4.6 2.7 - - - +
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 3.8 37.8 - - + -
278A ILE* 4.0 19.0 - - + +
279A HIS* 3.7 19.6 - - - -
318A GLY* 4.0 4.7 - - - -
321A GLU* 2.8 29.8 + - - -
323A ARG* 2.9 33.1 + - + +
325A TYR* 1.3 75.2 - - - +
327A ALA* 1.3 65.2 + - - +
329A THR* 3.3 5.8 + - - -
330A GLU* 3.0 30.4 + - - +
417A PRO 3.3 17.4 + - - +
418A GLU* 3.0 35.2 + - - +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 3.5 26.9 - - + +
318A GLY* 3.8 3.2 - - - -
319A HIS* 3.2 47.1 - - + +
323A ARG 3.1 7.1 + - - +
324A ALA 3.2 4.5 + - - +
326A ARG* 1.3 78.5 - - - +
328A LEU* 1.3 58.0 + - - +
330A GLU* 3.4 3.5 + - - +
331A THR* 2.8 30.7 + - - -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.8 36.1 - - + +
51A ALA* 3.8 31.6 - - + +
52A ALA* 3.9 9.8 - - + +
55A LEU* 3.8 16.2 - - + -
319A HIS* 4.9 2.7 - - + -
324A ALA* 2.8 22.2 + - + +
325A TYR 4.4 0.7 - - - +
327A ALA* 1.3 71.5 - - - +
329A THR* 1.3 64.0 + - - +
331A THR* 3.2 4.8 + - - -
332A ILE* 3.1 25.3 + - - +
362A PHE* 4.4 11.7 - - + -
374A ILE* 4.2 8.7 - - + -
375A PHE* 4.1 23.1 - - + -
391A LEU* 4.3 9.0 - - + -
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.3 13.7 - - + -
59A LYS* 4.8 15.9 - - - +
276A TYR* 6.2 0.2 - - - +
277A GLU* 5.0 6.7 - - - +
278A ILE* 3.8 21.7 - - + +
325A TYR* 2.8 48.6 + - + +
326A ARG* 3.3 11.1 + - - -
328A LEU* 1.3 75.5 - - - +
330A GLU* 1.3 67.2 + - - +
332A ILE* 3.4 8.3 + - + +
333A MET* 3.2 21.3 + - - +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 4.5 15.1 + - - +
275A LYS 5.0 1.6 - - - +
276A TYR* 3.5 28.0 - - + +
277A GLU* 2.8 39.2 + - - +
278A ILE 4.6 0.3 + - - -
312A GLY* 5.4 2.6 - - - -
314A ARG* 3.8 23.1 + - - +
315A ILE* 3.6 21.2 - - + +
326A ARG 3.0 22.2 + - - +
327A ALA 3.7 2.9 - - - +
329A THR* 1.3 79.6 + - - +
331A THR* 1.3 57.6 + - - +
333A MET* 3.3 7.7 + - - +
334A PHE* 3.0 28.6 + - - +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.9 29.6 - - + -
48A THR* 3.4 19.4 - - + +
49A VAL* 5.1 1.6 - - - -
52A ALA* 3.5 25.4 - - + -
69A LEU* 6.0 1.6 - - + -
71A MET* 5.0 5.4 - - + -
315A ILE* 3.5 15.5 - - - +
327A ALA 2.8 18.5 + - - -
328A LEU* 3.2 9.6 + - - -
330A GLU* 1.3 75.1 - - - +
332A ILE* 1.3 59.5 + - - +
334A PHE* 3.2 3.6 + - - +
335A ASP* 2.9 27.8 + - + +
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Residues in contact with ILE 332 (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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52A ALA* 4.1 9.9 - - + +
55A LEU* 3.6 39.3 - - + -
56A LYS* 3.8 43.7 - - + +
59A LYS* 4.2 14.8 - - + -
69A LEU* 5.7 1.1 - - + -
328A LEU 3.1 10.1 + - - +
329A THR* 3.7 9.9 - - + +
331A THR* 1.3 74.4 - - - +
333A MET* 1.3 57.9 + - - +
335A ASP* 3.2 8.0 + - - +
336A ASP* 2.8 43.6 + - - +
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Residues in contact with MET 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 3.7 43.1 - - + +
280A ARG* 4.9 1.1 - - - +
287A SER* 3.8 15.3 - - - +
288A LEU* 3.9 19.5 - - + +
289A MET* 3.8 37.7 - - + -
329A THR 3.2 12.7 + - - +
330A GLU* 3.8 11.4 - - - +
331A THR 3.3 0.2 - - - -
332A ILE* 1.3 73.3 - - - +
334A PHE* 1.3 61.3 + - - +
336A ASP* 3.2 16.8 + - - +
337A ALA* 2.9 25.6 + - - +
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Residues in contact with PHE 334 (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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39A PHE* 3.6 27.8 - + + -
40A LEU 3.5 23.6 - - - -
41A GLY* 3.3 20.9 - - - -
44A MET* 3.7 31.9 - - + -
71A MET* 4.2 2.5 - - + -
288A LEU* 3.9 15.0 - - + +
310A VAL* 4.0 5.2 - - + -
312A GLY* 3.5 25.1 - - - -
315A ILE* 4.2 8.5 - - + -
330A GLU 3.0 13.9 + - - +
331A THR* 3.3 9.9 - - - +
333A MET* 1.3 76.9 - - - +
335A ASP* 1.3 62.4 + - - +
337A ALA* 3.1 5.7 + - - +
338A ILE* 3.0 40.4 + - + +
354A VAL* 4.0 7.2 - - + -
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Residues in contact with ASP 335 (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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56A LYS* 2.6 25.4 + - - +
69A LEU* 3.5 18.3 - - + +
70A ALA* 2.9 20.0 + - - +
71A MET* 3.1 44.1 + - + +
331A THR* 2.9 14.5 + - + +
332A ILE* 3.5 9.6 - - - +
334A PHE* 1.3 77.3 - - - +
336A ASP* 1.3 56.8 + - - +
338A ILE* 3.2 11.4 + - - +
339A GLU* 3.0 27.5 + - - +
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Residues in contact with ASP 336 (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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56A LYS* 2.8 36.0 + - - +
289A MET* 3.8 22.4 - - - +
332A ILE* 2.8 28.6 + - - +
333A MET* 3.2 25.0 + - - +
335A ASP* 1.3 73.1 - - - +
337A ALA* 1.3 55.8 + - - +
339A GLU* 3.4 13.4 + - - +
340A ARG* 3.0 28.2 + - - +
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Residues in contact with ALA 337 (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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39A PHE* 4.5 2.5 - - - -
288A LEU* 4.0 14.1 - - + -
289A MET* 3.9 18.3 - - - +
292A THR* 3.8 29.8 + - + -
310A VAL* 4.8 3.8 - - + -
333A MET 2.9 12.0 + - - +
334A PHE* 3.1 8.9 + - + +
336A ASP* 1.3 72.8 - - - +
338A ILE* 1.3 60.3 + - + +
340A ARG* 3.3 2.0 + - - +
341A ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 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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39A PHE* 3.6 31.9 - - + -
70A ALA* 4.3 11.2 - - + -
71A MET* 3.9 18.2 - - + +
74A PHE* 3.8 35.6 - - + -
334A PHE* 3.0 42.4 + - + +
335A ASP* 3.2 8.0 + - - +
337A ALA* 1.3 74.2 - - - +
339A GLU* 1.3 64.0 + - - +
341A ALA* 3.3 3.1 + - - +
342A GLY* 3.0 20.6 + - - -
354A VAL* 3.7 20.9 - - + -
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Residues in contact with GLU 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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56A LYS* 4.6 7.5 + - - +
60A LYS* 5.6 3.3 + - - -
70A ALA* 3.8 21.0 - - + +
335A ASP 3.0 13.4 + - - +
336A ASP* 3.5 20.7 - - - +
338A ILE* 1.3 77.3 - - - +
340A ARG* 1.3 63.2 + - - +
342A GLY* 3.2 4.4 + - - -
343A GLN* 3.2 34.3 + - + +
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Residues in contact with ARG 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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289A MET* 3.6 33.9 - - + +
292A THR* 5.5 1.8 - - - +
293A GLU* 2.9 44.7 + - + +
336A ASP 3.0 17.4 + - - +
337A ALA* 3.6 3.8 - - - +
339A GLU* 1.3 75.3 - - - +
341A ALA* 1.3 65.9 + - - +
343A GLN* 2.9 51.1 + - - +
344A LEU* 3.2 36.3 + - + +
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Residues in contact with ALA 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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37A ILE* 4.6 7.6 - - + -
39A PHE* 3.5 33.9 - - + -
292A THR* 4.1 6.4 + - - +
296A LEU* 4.0 24.9 - - + -
308A LEU* 5.8 0.7 - - + -
337A ALA 2.9 13.1 + - - +
338A ILE 3.3 0.6 + - - +
340A ARG* 1.3 75.8 - - - +
342A GLY* 1.3 60.1 + - - +
344A LEU 3.2 0.9 + - - -
345A THR* 2.8 32.4 + - - +
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Residues in contact with GLY 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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338A ILE 3.0 13.8 + - - -
339A GLU* 3.2 5.8 + - - -
340A ARG 3.2 0.6 - - - -
341A ALA* 1.3 76.5 - - - +
343A GLN* 1.3 57.8 + - - +
345A THR* 3.0 23.2 - - - +
442A ARG* 6.2 4.0 - - - -
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Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 3.2 22.8 + - + +
340A ARG* 2.9 52.2 + - - +
342A GLY* 1.3 79.6 - - - +
344A LEU* 1.3 61.4 + - - +
345A THR 3.4 2.1 + - - +
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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
----------------------------------------------------------
293A GLU* 3.7 40.2 - - + +
296A LEU* 4.1 27.6 - - + +
297A ARG* 6.2 1.3 - - + -
300A SER* 6.0 2.4 - - - -
340A ARG* 3.2 42.6 + - + +
341A ALA 3.2 4.9 + - - +
343A GLN* 1.3 79.3 - - - +
345A THR* 1.3 64.3 + - - +
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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
----------------------------------------------------------
35A ASN* 5.3 1.1 - - - +
37A ILE* 4.2 12.9 - - + +
296A LEU* 4.3 11.7 - - + -
306A PHE* 4.0 28.3 - - + -
341A ALA 2.8 20.8 + - - +
342A GLY* 3.0 21.8 - - - +
343A GLN 4.4 2.1 - - - +
344A LEU* 1.3 83.9 - - - +
346A SER* 1.3 60.5 + - - +
347A GLU 4.1 0.9 + - - -
350A THR* 3.8 22.3 - - - +
352A SER* 5.0 2.3 + - - -
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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