Contacts of the helix formed by residues 301 - 324 (chain A) in PDB entry 1YC9
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 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.1 30.1 + - + +
299A GLY 3.2 0.6 - - - -
300A HIS* 1.3 74.7 - - - +
302A ALA* 1.3 65.5 + - - +
303A ASP* 2.7 42.9 + - - +
304A ILE* 3.3 17.6 + - + +
305A THR* 3.1 25.1 + - - -
390A THR 5.0 0.2 + - - -
393A GLN* 4.9 1.8 - - - +
394A ALA* 3.5 33.0 + - - +
397A GLU* 2.9 32.7 + - - -
473A HIS* 4.2 6.0 + - - -
474A ALA* 2.9 38.7 + - - +
475A LEU 4.1 7.6 - - - +
476A GLY* 4.2 6.1 - - - +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.1 33.0 - - + +
177A GLU* 5.9 0.2 - - - -
179A VAL* 4.2 13.5 - - + -
180A ALA* 3.9 19.1 - - + +
300A HIS 3.1 8.3 + - - +
301A ARG* 1.3 72.7 - - - +
303A ASP* 1.3 57.9 + - - +
305A THR* 3.5 8.8 - - - -
306A ALA* 2.8 31.2 + - - +
476A GLY* 5.3 2.1 + - - +
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 6.2 1.1 - - - -
180A ALA* 4.9 9.5 - - + +
301A ARG* 2.7 51.5 + - - +
302A ALA* 1.3 78.6 - - - +
304A ILE* 1.3 63.7 + - - +
306A ALA* 3.5 5.3 + - - +
307A ALA* 3.0 29.1 + - - +
390A THR* 3.5 21.4 + - + +
393A GLN* 6.2 0.2 - - - +
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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
----------------------------------------------------------
298A LEU* 3.9 22.2 - - + +
301A ARG* 3.3 26.4 + - + +
303A ASP* 1.3 82.7 + - - +
305A THR* 1.3 61.7 + - - +
307A ALA* 3.3 2.4 + - - +
308A ARG* 2.8 29.6 + - + +
387A TYR* 3.7 27.4 - - + +
390A THR* 3.7 25.6 - - + +
391A LEU* 4.2 17.0 - - + +
394A ALA* 3.8 21.3 - - + -
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA 5.3 0.4 - - - +
176A ALA* 4.0 12.3 - - + -
299A GLY 4.7 7.8 + - - -
301A ARG 3.1 15.5 + - - -
302A ALA* 3.5 10.3 - - - -
304A ILE* 1.3 78.7 - - - +
306A ALA* 1.3 62.9 + - - +
308A ARG* 3.2 10.1 + - + +
309A TRP* 3.0 48.0 + - + +
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Residues in contact with ALA 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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173A ALA* 3.5 36.3 - - + +
176A ALA* 4.0 2.2 - - + -
177A GLU* 3.9 17.0 - - + +
302A ALA 2.8 17.6 + - - +
303A ASP* 3.8 6.3 - - - +
305A THR* 1.3 74.9 - - - +
307A ALA* 1.3 57.6 + - - +
309A TRP 3.2 1.7 + - - -
310A ARG* 3.0 39.2 + - - +
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Residues in contact with ALA 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 ASP 3.0 18.0 + - - +
304A ILE 3.9 3.6 - - - +
306A ALA* 1.3 72.9 - - - +
308A ARG* 1.3 65.5 + - - +
310A ARG* 3.8 7.9 - - - +
311A ALA* 3.0 24.4 + - - +
383A ALA 4.5 2.8 - - - +
386A GLN* 4.6 4.0 - - + +
387A TYR* 3.8 30.7 - - + +
390A THR* 4.1 12.3 - - - +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 2.8 14.7 + - + +
305A THR* 3.2 14.4 - - + +
307A ALA* 1.3 76.3 - - - +
309A TRP* 1.3 70.3 + - + +
311A ALA* 3.2 7.4 + - - +
312A GLU* 3.0 20.5 + - + +
387A TYR* 3.6 30.7 + - + -
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Residues in contact with TRP 309 (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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168A THR 5.8 0.2 - - - -
169A SER* 3.3 50.8 - - - +
172A ALA* 3.5 34.0 + - + +
173A ALA* 3.9 4.3 - - + -
305A THR* 3.0 39.6 + - + +
306A ALA 3.2 6.5 + - - +
308A ARG* 1.3 85.9 - - + +
310A ARG* 1.3 57.9 + - - +
312A GLU* 3.3 17.8 + - + +
313A ALA* 2.9 23.4 + - - +
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Residues in contact with ARG 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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170A GLU* 2.8 33.8 + - - +
173A ALA* 3.8 18.2 - - + +
174A ALA* 4.4 6.9 - - - +
177A GLU* 2.5 45.4 + - - -
306A ALA* 3.0 25.3 + - - +
307A ALA* 3.8 7.3 - - - +
308A ARG 3.2 0.4 - - - -
309A TRP* 1.3 76.1 - - - +
311A ALA* 1.3 56.8 + - - +
313A ALA* 3.3 7.8 + - - +
314A ALA* 2.9 28.8 + - - +
379A ARG* 4.1 21.8 + - - +
383A ALA* 4.1 5.8 - - + +
386A GLN* 6.1 0.2 - - - +
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Residues in contact with ALA 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 ALA 3.0 13.8 + - - +
308A ARG* 3.2 9.4 + - - +
310A ARG* 1.3 74.9 - - - +
312A GLU* 1.3 62.8 + - - +
314A ALA* 3.3 0.9 + - - +
315A ALA* 2.9 23.6 + - - +
380A TYR* 3.6 8.4 - - + -
383A ALA* 3.8 31.1 - - + +
384A VAL* 4.3 15.3 - - + +
387A TYR* 4.9 4.3 - - + -
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Residues in contact with GLU 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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165A VAL* 5.0 4.0 - - + -
169A SER* 3.8 16.4 - - - +
308A ARG* 3.0 12.4 + - + +
309A TRP* 3.3 24.0 + - + +
311A ALA* 1.3 76.4 - - - +
313A ALA* 1.3 61.2 + - - +
315A ALA* 3.2 12.6 + - - +
316A GLN* 3.0 47.1 + - + +
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Residues in contact with ALA 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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166A ALA* 3.6 34.8 - - + +
169A SER* 3.9 4.5 - - - -
170A GLU* 3.7 22.2 - - + +
309A TRP 2.9 14.2 + - - +
310A ARG 3.4 8.3 - - - +
312A GLU* 1.3 73.9 - - - +
314A ALA* 1.3 58.4 + - - +
316A GLN* 3.1 6.8 + - - +
317A GLN* 3.0 34.8 + - - +
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Residues in contact with ALA 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 ARG 2.9 17.5 + - - +
311A ALA 3.6 4.3 - - - +
313A ALA* 1.3 74.1 - - - +
315A ALA* 1.3 62.9 + - - +
317A GLN* 3.2 15.9 + - - +
318A VAL* 3.1 24.4 + - - +
376A ALA 4.6 1.6 - - - +
379A ARG* 4.1 13.0 - - + +
380A TYR* 3.6 30.9 - - - +
383A ALA* 4.0 11.4 - - + -
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Residues in contact with ALA 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 ALA 2.9 13.6 + - - +
312A GLU* 3.2 22.0 + - - +
314A ALA* 1.3 74.4 - - - +
316A GLN* 1.3 62.9 + - - +
318A VAL* 3.1 16.7 + - - +
319A GLY* 3.2 9.0 + - - -
380A TYR* 3.5 24.3 - - + +
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Residues in contact with GLN 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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162A ALA* 3.4 42.4 - - - +
165A VAL* 3.5 34.9 - - + +
166A ALA* 3.9 7.6 - - + +
312A GLU* 3.0 33.5 + - - +
313A ALA 3.3 8.1 - - - +
315A ALA* 1.3 75.6 - - - +
317A GLN* 1.3 58.4 + - - +
319A GLY* 3.0 5.1 + - - +
320A ILE* 2.9 30.0 + - - +
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Residues in contact with GLN 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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166A ALA* 4.2 16.0 - - + +
170A GLU* 5.1 5.7 + - - +
313A ALA* 3.0 20.1 + - - +
314A ALA* 3.2 21.9 + - - +
316A GLN* 1.3 75.0 - - - +
318A VAL* 1.3 62.3 + - - +
320A ILE* 3.4 18.0 + - + +
321A ALA* 3.1 22.9 + - - +
376A ALA* 3.8 12.6 - - + +
379A ARG* 4.2 19.4 - - + +
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Residues in contact with VAL 318 (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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314A ALA 3.1 12.0 + - - +
315A ALA* 3.1 9.2 + - - +
317A GLN* 1.3 75.9 - - - +
319A GLY* 1.3 63.6 + - - +
321A ALA* 3.2 3.3 + - - +
322A GLN* 3.0 43.3 + - - +
373A LEU* 4.2 10.5 - - + -
376A ALA* 3.4 35.7 - - - +
377A GLU* 3.9 12.6 - - + -
380A TYR* 3.8 17.3 - - + -
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Residues in contact with GLY 319 (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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159A LYS* 5.8 0.4 - - - -
162A ALA* 5.0 5.4 - - - -
315A ALA 3.2 8.4 + - - -
316A GLN* 3.0 9.8 + - - -
318A VAL* 1.3 74.7 - - - +
320A ILE* 1.3 63.9 + - - +
322A GLN* 3.3 14.9 + - - +
323A ALA* 2.9 24.3 + - - +
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Residues in contact with ILE 320 (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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159A LYS* 3.6 37.8 - - + +
162A ALA* 3.8 6.7 - - + +
163A ALA* 3.7 29.8 - - + +
166A ALA* 5.1 1.1 - - + -
316A GLN 2.9 12.9 + - - +
317A GLN* 3.5 30.7 - - + +
318A VAL 3.3 0.2 - - - -
319A GLY* 1.3 75.0 - - - +
321A ALA* 1.3 64.8 + - - +
323A ALA* 3.1 3.7 + - - +
324A GLN* 3.1 39.0 + - - +
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Residues in contact with ALA 321 (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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317A GLN 3.1 13.6 + - - +
318A VAL 3.2 7.8 + - - +
320A ILE* 1.3 77.5 - - - +
322A GLN* 1.3 63.6 + - - +
324A GLN* 3.4 27.1 + - - +
325A PHE* 3.5 16.3 - - - -
369A LEU 4.9 1.2 - - - +
372A GLN* 4.1 4.0 - - + +
373A LEU* 3.7 35.7 - - + +
376A ALA* 3.9 9.2 - - + -
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Residues in contact with GLN 322 (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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318A VAL* 3.0 32.1 + - - +
319A GLY* 3.6 16.4 - - - +
321A ALA* 1.3 77.5 - - - +
323A ALA* 1.3 61.4 + - - +
325A PHE* 3.2 23.0 + - - +
326A TYR* 3.5 17.4 - - + -
373A LEU* 3.8 19.6 - - + +
377A GLU* 5.4 2.6 + - - -
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Residues in contact with ALA 323 (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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157A TRP* 4.2 21.6 - - + +
159A LYS* 3.8 33.6 + - + +
319A GLY 2.9 17.2 + - - +
320A ILE 3.1 6.0 + - - +
322A GLN* 1.3 73.2 - - - +
324A GLN* 1.3 59.3 + - - +
325A PHE 3.1 0.4 - - - -
326A TYR* 3.0 35.8 + - - +
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 4.0 22.7 - - + +
320A ILE* 3.1 29.8 + - - +
321A ALA* 3.6 19.0 - - - +
322A GLN 3.2 0.6 - - - -
323A ALA* 1.3 77.8 - - - +
325A PHE* 1.3 59.4 + - - +
326A TYR 3.2 4.3 + - - +
362A PRO* 3.7 12.0 - - - +
369A LEU* 3.6 32.1 - - + +
372A GLN* 2.9 31.7 + - - +
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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