Contacts of the helix formed by residues 297 - 320 (chain A) in PDB entry 3GEB
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 ASP 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA* 3.9 0.4 - - - +
296A LYS* 1.3 76.1 - - - +
298A THR* 1.3 61.9 + - - +
299A THR* 3.3 15.4 + - - -
300A THR* 2.6 42.1 + - - +
301A SER* 3.2 24.3 + - - -
420A LEU* 4.4 1.3 - - - +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLY* 4.6 3.8 - - - +
291A ALA* 3.9 16.2 - - + -
292A SER 4.9 0.9 - - - +
296A LYS 3.4 4.2 + - - +
297A ASP* 1.3 72.9 + - - +
299A THR* 1.3 70.4 + - - +
300A THR 3.2 0.2 - - - -
301A SER* 3.3 7.4 + - - -
302A VAL* 3.0 28.4 + - - +
412B GLN* 5.0 2.0 + - - +
415B ALA* 3.2 38.4 - - + +
416B GLU* 4.1 18.6 - - - +
419B ALA* 4.0 17.3 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASP* 3.3 14.1 + - - -
298A THR* 1.3 82.0 + - - +
300A THR* 1.3 58.7 + - - +
303A ARG* 3.1 21.1 + - + +
412B GLN* 2.8 39.7 - - + +
416B GLU* 5.9 2.6 - - - +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASP* 2.6 34.8 + - - +
298A THR 3.2 0.2 - - - -
299A THR* 1.3 72.9 - - - +
301A SER* 1.3 65.7 + - - +
303A ARG* 3.7 26.3 + - - +
304A ILE* 3.0 41.5 + - + +
416A GLU* 4.8 2.5 - - - +
420A LEU* 4.1 9.4 - - + -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER 4.3 2.3 + - - -
285A LEU* 2.8 45.2 + - - +
288A GLY* 4.8 2.6 - - - -
291A ALA* 3.9 21.0 + - - +
297A ASP 3.2 16.9 + - - -
298A THR* 3.4 7.0 - - - -
300A THR* 1.3 80.5 - - - +
302A VAL* 1.3 57.4 + - - +
304A ILE* 3.8 2.0 - - - +
305A GLY 2.9 22.5 + - - -
420A LEU* 3.9 16.6 - - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU 3.6 15.3 - - - +
286A LEU* 4.0 8.7 - - + +
298A THR 3.0 16.1 + - - +
301A SER* 1.3 73.7 - - - +
303A ARG* 1.3 66.8 + - - +
305A GLY* 4.3 0.4 - - - +
306A LEU* 3.0 43.7 + - + +
408B GLU 4.8 0.7 - - - +
411B LEU* 3.9 35.9 - - + +
412B GLN* 3.5 30.5 - - - +
415B ALA* 3.9 11.9 - - + -
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Residues in contact with ARG 303 (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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299A THR* 3.1 19.3 + - + +
300A THR* 3.3 21.5 + - - +
302A VAL* 1.3 75.9 - - - +
304A ILE* 1.3 71.2 + - - +
306A LEU* 3.5 6.1 + - - +
307A MET* 3.1 52.8 + - + +
416A GLU* 2.4 44.5 + - - -
412B GLN* 4.3 2.2 + - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.2 3.8 - - + -
300A THR* 3.0 33.9 + - + +
301A SER* 3.8 4.3 - - - +
303A ARG* 1.3 89.6 - - - +
305A GLY* 1.3 65.6 + - - +
307A MET* 3.2 3.8 + - - +
308A MET* 3.0 21.9 + - + +
413A LEU* 3.6 25.2 - - + +
416A GLU* 3.5 39.5 - - + +
417A LEU* 3.9 31.2 - - + +
420A LEU* 4.1 12.6 - - + -
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Residues in contact with GLY 305 (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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282A PHE* 3.6 9.8 - - - -
285A LEU* 3.9 18.4 - - - +
286A LEU* 3.3 22.6 - - - +
301A SER 2.9 16.4 + - - -
302A VAL 3.3 0.4 + - - -
304A ILE* 1.3 76.1 - - - +
306A LEU* 1.3 56.1 + - - +
308A MET* 3.4 1.5 + - - -
309A GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 306 (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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286A LEU* 3.4 7.6 - - + +
302A VAL* 3.0 34.5 + - + +
303A ARG* 3.8 5.6 - - - +
305A GLY* 1.3 72.4 - - - +
307A MET* 1.3 61.2 + - + +
309A GLU* 3.3 13.8 + - - +
310A GLU* 2.9 29.1 + - - +
407B ARG* 3.5 28.9 - - - +
408B GLU* 3.6 37.7 - - + +
411B LEU* 3.9 14.6 - - + -
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Residues in contact with MET 307 (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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303A ARG* 3.1 51.9 + - + +
304A ILE 3.2 2.9 + - - +
306A LEU* 1.3 76.9 - - + +
308A MET* 1.3 63.0 + - - +
310A GLU* 3.5 6.1 + - - +
311A MET* 3.1 27.6 + - + +
409A THR* 5.7 4.7 - - - +
413A LEU* 3.6 29.6 - - + -
416A GLU* 5.0 3.6 - - - +
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.8 10.8 - - + -
285A LEU* 5.8 0.4 - - + -
304A ILE* 3.0 12.3 + - + +
305A GLY* 3.6 8.1 - - - +
307A MET* 1.3 73.3 - - - +
309A GLU* 1.3 68.5 + - - +
311A MET* 2.9 27.8 + - - +
312A ILE* 2.8 68.2 + - + +
410A TRP* 5.1 1.3 - - - -
413A LEU* 3.7 11.6 - - + +
414A ARG* 5.3 4.0 - - - -
417A LEU* 4.2 13.5 - - + -
460A LEU* 3.8 23.3 - - + +
461A TYR* 3.3 37.5 - - + +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.7 20.6 - - + -
286A LEU* 3.9 12.6 - - - +
305A GLY 3.0 15.2 + - - +
306A LEU* 3.4 18.2 - - - +
308A MET* 1.3 79.2 - - - +
310A GLU* 1.3 61.4 + - - +
312A ILE* 3.1 11.1 + - - +
313A PHE* 3.1 47.6 + - + -
407B ARG* 2.9 42.7 + - - -
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Residues in contact with GLU 310 (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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306A LEU 2.9 16.5 + - - +
307A MET* 3.7 7.6 - - - +
309A GLU* 1.3 75.9 + - - +
311A MET* 1.3 61.0 + - + +
313A PHE* 4.0 5.1 - - - +
314A ASN* 3.0 46.3 + - + +
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Residues in contact with MET 311 (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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307A MET 3.1 12.5 + - - +
308A MET* 2.9 17.7 + - - +
310A GLU* 1.3 79.9 - - + +
312A ILE* 1.3 63.7 + - - +
314A ASN* 3.9 4.1 - - - +
315A LEU* 3.0 27.2 + - - +
402A ILE* 5.9 1.7 - - - +
406A LYS* 4.8 8.3 - - + +
409A THR* 4.3 11.4 - - - -
410A TRP* 3.5 50.7 - - + -
413A LEU* 3.3 30.1 - - + -
460A LEU* 3.5 13.1 - - + +
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Residues in contact with ILE 312 (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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282A PHE* 3.8 29.2 - - + -
308A MET* 2.8 44.0 + - + +
309A GLU* 3.5 6.3 - - - +
311A MET* 1.3 78.3 - - - +
313A PHE* 1.3 75.6 + - + +
315A LEU 3.6 0.2 + - - -
316A ALA* 3.0 21.1 + - - +
453A PRO* 3.8 24.9 - - + +
456A ALA* 3.2 13.2 - - + +
457A LYS* 3.8 30.1 - - + -
460A LEU* 3.4 11.4 - - + -
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Residues in contact with PHE 313 (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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282A PHE* 5.8 2.7 - + - -
309A GLU* 3.1 50.9 + - + +
310A GLU* 4.4 5.2 - - - +
312A ILE* 1.3 84.6 - - + +
314A ASN* 1.3 61.3 + - - +
316A ALA* 3.6 3.0 - - + +
317A ASP* 2.8 41.5 + - - +
322A PHE* 4.2 22.2 - + + -
453A PRO* 4.1 26.5 - - + -
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Residues in contact with ASN 314 (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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310A GLU* 3.0 40.9 + - + +
311A MET* 3.9 5.4 - - - +
313A PHE* 1.3 75.6 - - - +
315A LEU* 1.3 59.4 + - - +
317A ASP* 3.9 4.2 - - - -
318A THR* 2.8 49.0 + - - +
406A LYS* 3.0 34.5 + - + +
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Residues in contact with LEU 315 (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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311A MET 3.0 17.9 + - - +
312A ILE 3.8 2.2 - - - +
314A ASN* 1.3 77.8 - - - +
316A ALA* 1.3 56.4 + - - +
318A THR* 4.7 0.2 - - - -
319A HIS* 2.8 35.8 + - + +
320A LEU* 3.4 24.9 + - + -
398A VAL* 4.8 6.1 - - + -
401A LEU* 4.6 14.1 - - + -
402A ILE* 3.4 34.1 - - + -
456A ALA* 3.4 27.6 - - + +
459A LEU* 4.8 5.8 - - + -
460A LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 316 (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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312A ILE 3.0 20.1 + - - +
313A PHE* 3.6 9.9 - - + +
314A ASN 3.2 0.2 - - - -
315A LEU* 1.3 81.2 - - - +
317A ASP* 1.3 57.0 + - - +
320A LEU* 3.1 27.4 + - - -
322A PHE* 3.1 36.5 + - + +
452A ILE* 4.0 11.9 - - + -
453A PRO* 4.6 7.2 - - + -
456A ALA* 4.2 7.2 - - + -
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Residues in contact with ASP 317 (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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313A PHE* 2.8 30.0 + - - +
314A ASN* 4.0 4.2 - - - +
316A ALA* 1.3 73.0 - - - +
318A THR* 1.3 67.2 + - - +
319A HIS 3.6 0.2 + - - -
321A PHE* 4.2 9.9 + - - -
322A PHE* 3.4 29.9 + - - +
323A ASN* 3.5 26.4 + - + +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASN* 2.8 35.0 + - - +
315A LEU* 4.7 0.2 - - - -
317A ASP* 1.3 81.1 - - - +
319A HIS* 1.3 87.7 + - + +
321A PHE 5.4 0.2 + - - -
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Residues in contact with HIS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASN* 6.1 0.2 - - - -
315A LEU* 2.8 23.0 + - + +
318A THR* 1.3 101.6 - - + +
320A LEU* 1.3 75.7 + - + +
321A PHE* 3.6 13.9 + - - -
386A ARG* 5.7 0.2 - - - +
390A MET* 4.0 28.0 - - + +
401A LEU* 3.1 46.2 + - + -
402A ILE* 4.4 16.6 - - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.4 33.0 - - + +
316A ALA* 3.1 7.8 + - - +
319A HIS* 1.3 95.0 - - + +
321A PHE* 1.3 73.7 + - - +
322A PHE 3.0 3.9 + - - -
325A LEU* 3.4 14.2 - - - +
387A VAL* 3.9 22.6 - - + +
390A MET* 4.3 20.6 - - + -
391A TYR 5.9 0.2 - - - +
401A LEU* 5.3 3.6 - - + -
452A ILE* 3.4 39.4 - - + +
455A LEU* 4.6 8.7 - - + -
456A ALA* 4.0 11.0 - - + +
459A LEU* 5.1 7.0 - - + -
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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