Contacts of the helix formed by residues 289 - 308 (chain A) in PDB entry 5A19
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 LYS 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LYS* 4.1 9.3 - - - +
54A VAL 3.5 25.0 + - - +
55A ALA* 4.1 14.2 - - - +
70A GLU 5.5 0.8 + - - -
133A GLY* 5.0 11.7 - - - -
134A ASP* 5.5 5.2 - - + +
285A LYS* 3.8 31.9 - - + -
286A ASP* 2.8 42.8 + - - +
287A TYR 3.9 2.0 - - - -
288A THR* 1.3 80.1 + - - +
290A VAL* 1.3 59.2 + - - +
291A ASP* 3.1 6.5 - - + +
292A ARG* 2.9 21.1 + - - +
293A SER* 3.4 6.9 + - - -
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Residues in contact with VAL 290 (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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132A ALA* 4.1 17.7 - - + -
134A ASP* 3.8 27.7 - - + +
135A GLN 5.3 0.2 - - - -
138A MET* 3.5 22.4 - - + +
288A THR 3.0 11.5 + - - +
289A LYS* 1.3 66.6 - - - +
291A ASP* 1.3 66.6 + - - +
292A ARG 3.1 0.2 - - - -
293A SER* 3.4 16.8 - - - +
294A ALA* 3.0 34.5 + - + +
320A TYR* 3.8 28.3 - - + -
357A PRO* 4.2 15.9 - - + -
360A ILE* 5.7 0.7 - - + -
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Residues in contact with ASP 291 (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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134A ASP* 5.1 10.0 - - - +
135A GLN 5.0 5.7 - - - +
136A GLY* 5.1 2.1 - - - -
137A LEU 4.9 2.6 - - - +
138A MET* 3.8 19.8 - - - +
280A GLY* 3.5 26.7 + - - +
281A ALA 3.5 16.2 - - - +
282A PHE* 3.3 10.7 - - - -
285A LYS* 2.9 24.9 + - + +
289A LYS* 3.1 5.6 - - - +
290A VAL* 1.3 78.4 - - - +
292A ARG* 1.3 57.8 + - - +
295A ALA* 3.3 22.9 - - - +
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Residues in contact with ARG 292 (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 ASP* 2.7 43.0 + - - -
42A LEU* 3.3 21.0 - - - +
282A PHE* 3.1 43.4 + - + +
283A SER* 3.8 0.8 - - - +
284A GLY 3.8 0.4 - - - +
285A LYS* 3.4 18.5 + - + +
286A ASP 4.9 3.1 - - - +
287A TYR* 6.1 0.4 - - - -
289A LYS 2.9 10.5 + - - +
291A ASP* 1.3 79.1 - - - +
293A SER* 1.3 65.6 + - - +
295A ALA* 3.2 3.3 + - - +
296A TYR* 2.9 56.9 + - + +
371A TYR* 3.2 24.1 - - - -
374A THR* 2.9 21.4 + - - -
379A HIS* 3.7 6.1 - - - -
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 2.9 31.2 + - - +
289A LYS 3.4 1.6 + - - -
290A VAL* 3.4 18.2 - - - +
292A ARG* 1.3 80.5 - - - +
294A ALA* 1.3 60.6 + - - +
296A TYR* 3.4 5.7 + - - +
297A ALA* 3.0 27.5 + - - +
357A PRO* 4.7 4.4 - - - +
360A ILE* 3.6 15.5 - - - +
366A LEU* 3.7 27.6 - - - -
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Residues in contact with ALA 294 (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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138A MET* 4.0 8.1 - - - -
290A VAL* 3.0 21.3 + - + +
293A SER* 1.3 75.8 + - - +
295A ALA* 1.3 60.5 + - - +
297A ALA* 3.8 7.3 - - - +
298A ALA* 2.9 29.5 + - - +
318A VAL* 4.1 6.3 - - + +
320A TYR* 3.4 41.1 - - + +
360A ILE* 4.3 4.3 - - + -
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Residues in contact with ALA 295 (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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138A MET* 4.0 15.7 - - + +
139A PHE 4.3 11.8 - - - +
282A PHE* 3.6 23.8 - - + -
290A VAL 3.6 2.8 + - - -
291A ASP 3.3 21.3 - - - +
292A ARG 3.2 1.7 + - - +
294A ALA* 1.3 75.8 - - - +
296A TYR* 1.3 65.2 + - - +
298A ALA* 3.3 5.2 + - - +
299A ARG* 3.0 24.6 + - - +
380A PHE* 4.1 5.7 - - + -
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Residues in contact with TYR 296 (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* 4.1 10.3 - + - -
292A ARG* 2.9 56.2 + - + -
293A SER* 3.5 9.2 - - - +
294A ALA 3.3 0.2 - - - -
295A ALA* 1.3 77.4 - - - +
297A ALA* 1.3 56.7 - - - +
299A ARG* 3.4 5.2 - - - +
300A TRP 3.1 21.5 + - - -
364A LEU* 4.1 12.3 - - + -
366A LEU* 4.2 9.6 - - + -
371A TYR* 4.2 9.4 - + - -
374A THR* 3.7 5.9 + - - +
379A HIS* 2.7 42.1 + - + -
380A PHE* 3.8 19.1 - + - -
387A TRP* 3.3 56.7 - + + +
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Residues in contact with ALA 297 (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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293A SER 3.0 17.6 + - - +
294A ALA* 3.8 4.9 - - - +
296A TYR* 1.3 75.0 - - - +
298A ALA* 1.3 60.4 + - - +
300A TRP* 3.1 15.2 + - + +
301A VAL* 2.8 33.0 + - - +
355A LEU* 4.0 15.0 - - + -
360A ILE* 3.9 31.2 - - + -
364A LEU* 3.9 6.0 - - + +
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Residues in contact with ALA 298 (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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139A PHE 4.0 3.8 - - - -
140A GLY* 3.5 26.7 - - - +
294A ALA 2.9 19.5 + - - +
295A ALA* 3.3 3.3 + - - +
297A ALA* 1.3 75.9 - - - +
299A ARG* 1.3 58.1 + - - +
301A VAL* 3.4 8.4 + - - +
302A ALA* 2.9 29.6 + - - +
316A VAL* 4.1 18.1 - - + +
318A VAL* 4.7 13.5 - - + -
355A LEU* 5.5 2.4 - - - +
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Residues in contact with ARG 299 (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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140A GLY* 3.7 3.9 - - - -
141A TYR 2.8 27.7 + - - -
142A ALA* 3.6 8.5 - - - +
148A GLU 2.8 28.3 + - - -
149A CYS* 3.0 19.8 + - - +
150A MET* 3.7 18.8 - - - +
271A TYR* 3.4 25.4 - - - +
295A ALA 3.0 11.6 + - - +
296A TYR 3.4 9.6 - - - +
298A ALA* 1.3 75.5 - - - +
300A TRP* 1.3 54.0 + - - +
302A ALA* 3.7 1.9 - - - +
303A LYS* 2.7 52.5 + - - +
380A PHE* 3.5 26.7 - - + +
381A GLY 3.9 0.2 - - - +
387A TRP* 4.2 8.3 - - + +
388A GLU* 2.9 33.9 + - - +
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Residues in contact with TRP 300 (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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296A TYR 3.1 13.1 + - - +
297A ALA* 3.1 22.0 + - + +
299A ARG* 1.3 76.0 - - - +
301A VAL* 1.3 53.3 + - - +
303A LYS* 3.9 2.0 - - + +
304A SER* 2.6 41.1 + - - -
353A PHE* 3.8 23.1 - + - -
355A LEU* 5.8 1.8 - - + -
360A ILE* 6.0 2.7 - - + -
363A ASP* 3.7 41.7 - - + -
364A LEU* 3.8 20.9 - - + -
386A PRO 3.9 3.1 + - - -
387A TRP* 3.5 27.4 - - + +
389A VAL 2.9 30.2 + - - -
390A PRO* 4.5 0.7 - - + -
391A LYS* 3.6 43.1 - - + +
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Residues in contact with VAL 301 (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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297A ALA 2.8 21.0 + - - +
298A ALA* 3.6 10.5 - - - +
300A TRP* 1.3 73.0 - - - +
302A ALA* 1.3 62.0 + - - +
304A SER* 3.2 3.8 + - - -
305A LEU* 3.0 26.7 + - + +
316A VAL* 4.1 19.1 - - + -
349A VAL* 3.7 35.9 - - + -
353A PHE* 3.7 40.6 - - + -
355A LEU* 4.3 15.5 - - + -
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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
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140A GLY 4.0 2.7 - - - -
141A TYR* 3.6 34.8 - - - +
142A ALA* 3.7 2.7 - - - -
298A ALA 2.9 18.6 + - - +
299A ARG 3.7 2.7 - - - +
301A VAL* 1.3 74.5 - - - +
303A LYS* 1.3 63.7 + - - +
305A LEU* 3.4 2.2 + - - -
306A VAL* 3.2 20.4 + - - +
314A VAL* 3.4 27.5 - - + +
316A VAL* 4.0 8.9 - - + +
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Residues in contact with LYS 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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142A ALA* 3.8 7.1 - - - +
148A GLU* 3.9 15.9 + - - +
149A CYS* 4.1 17.9 - - + -
299A ARG* 2.7 40.2 + - - +
300A TRP* 4.0 4.7 - - - +
302A ALA* 1.3 74.2 - - - +
304A SER* 1.3 55.7 + - - +
306A VAL* 3.4 1.0 + - - +
307A LYS* 2.9 56.2 + - + +
381A GLY 6.0 0.2 - - - -
387A TRP 4.6 0.7 - - - +
388A GLU* 2.7 63.6 + - - +
390A PRO* 4.7 7.4 - - + -
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Residues in contact with SER 304 (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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300A TRP* 2.6 25.3 + - - -
301A VAL 3.2 4.7 + - - -
303A LYS* 1.3 75.5 - - - +
305A LEU* 1.3 58.9 + - - +
307A LYS* 4.5 0.2 - - - +
308A GLY* 3.0 26.0 + - - -
353A PHE* 3.8 15.4 - - - -
390A PRO* 3.7 12.8 - - - +
391A LYS* 2.9 39.4 + - - +
393A LEU* 3.9 13.8 - - - +
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Residues in contact with LEU 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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301A VAL* 3.0 25.2 + - + +
302A ALA* 3.7 6.5 - - - +
303A LYS 3.3 0.2 - - - -
304A SER* 1.3 77.8 - - - +
306A VAL* 1.3 58.1 + - - +
308A GLY 3.7 0.5 + - - -
309A GLY 3.6 1.9 + - - -
310A LEU* 3.1 54.0 + - + +
311A CYS* 3.5 16.6 + - - -
314A VAL* 4.0 25.1 - - + -
316A VAL* 4.7 0.9 - - + -
332A ILE* 4.4 12.1 - - + -
345A LEU* 4.6 12.8 - - + +
348A ILE* 4.7 4.5 - - + -
349A VAL* 4.1 27.1 - - + -
353A PHE* 5.9 1.3 - - + -
393A LEU* 3.9 11.9 - - + -
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Residues in contact with VAL 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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142A ALA* 3.8 18.4 - - + +
144A ASP* 4.0 16.2 - - + +
149A CYS* 3.8 24.7 - - - -
302A ALA 3.2 16.8 + - - +
303A LYS 4.0 2.7 - - - +
305A LEU* 1.3 74.2 - - - +
307A LYS* 1.3 61.1 + - + +
309A GLY* 2.9 21.5 + - - -
311A CYS* 3.4 20.1 - - - +
312A ARG 3.9 25.1 - - - +
313A ARG 4.1 0.4 - - - +
314A VAL* 3.9 13.2 - - + -
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Residues in contact with LYS 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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147A GLU* 2.8 35.2 + - - +
149A CYS* 3.7 21.8 - - - -
303A LYS* 2.9 36.3 + - + +
306A VAL* 1.3 72.8 - - + +
308A GLY* 1.3 58.5 + - - +
309A GLY 3.2 1.3 + - - -
390A PRO* 3.8 30.7 - - + -
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Residues in contact with GLY 308 (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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304A SER 3.0 19.9 + - - -
305A LEU 4.1 0.9 - - - -
306A VAL 3.2 0.6 - - - -
307A LYS* 1.3 75.1 - - - +
309A GLY* 1.3 58.9 + - - +
310A LEU* 3.3 8.4 + - - +
390A PRO* 5.9 0.2 - - - +
393A LEU* 5.6 5.2 - - - -
395A TYR* 4.2 15.1 + - - -
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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
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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