Contacts of the helix formed by residues 296 - 318 (chain E) in PDB entry 1SZP
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 LEU 296 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E PHE 5.4 1.0 - - - -
295E GLU* 1.4 71.8 - - - +
297E SER* 1.3 73.3 + - - +
298E ALA 2.5 1.6 + - - -
299E ARG* 2.4 41.5 + - - +
300E GLN* 3.7 8.7 - - + -
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Residues in contact with SER 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E GLU 2.8 9.1 + - - -
296E LEU* 1.3 77.2 - - - +
298E ALA* 1.3 63.4 + - - -
300E GLN* 2.3 37.5 + - - +
301E MET* 2.9 11.2 + - - +
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Residues in contact with ALA 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E PHE* 6.2 1.6 - - - -
295E GLU* 3.1 10.2 + - + +
296E LEU 2.5 5.3 + - - +
297E SER* 1.3 78.1 + - - +
299E ARG* 1.3 63.7 + - - +
301E MET* 3.1 8.0 + - - +
302E HIS* 3.0 25.4 + - - +
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Residues in contact with ARG 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E MET* 4.3 18.3 - - - +
286E TYR* 4.0 30.0 + - + +
287E ARG* 4.8 18.9 - - - +
290E PHE* 3.9 38.0 + - - +
295E GLU 4.8 0.2 - - - -
296E LEU* 2.4 29.4 + - - +
298E ALA* 1.3 75.6 - - - +
300E GLN* 1.3 67.1 + - - +
301E MET 2.9 1.4 + - - -
302E HIS* 3.3 7.2 + - - +
303E LEU* 3.1 25.3 + - + +
346E GLY* 3.9 26.5 - - - +
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Residues in contact with GLN 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E LEU* 3.2 4.6 + - + -
297E SER* 2.3 34.4 + - - +
299E ARG* 1.3 78.2 - - + +
301E MET* 1.3 58.0 + - - +
303E LEU* 4.3 2.7 - - - -
304E ALA* 3.8 8.5 + - - +
346E GLY* 6.2 2.2 - - - +
349E ILE* 3.3 34.4 - - + +
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Residues in contact with MET 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E SER* 2.9 8.5 + - - +
298E ALA* 3.6 10.1 - - - +
299E ARG 3.0 0.2 - - - -
300E GLN* 1.3 77.1 - - - +
302E HIS* 1.3 67.9 + - - +
303E LEU 2.8 2.7 + - - -
304E ALA* 3.0 6.2 + - - +
305E LYS* 3.0 29.4 + - - +
308E ARG* 5.1 1.0 + - - +
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Residues in contact with HIS 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E ALA* 4.0 16.7 + - + -
256E ASP* 4.1 26.7 + - - +
259E LEU* 3.9 26.2 - - + +
286E TYR* 3.7 26.1 + + + -
298E ALA 3.0 16.3 + - - +
299E ARG* 3.7 7.2 - - - +
301E MET* 1.3 76.2 - - - +
303E LEU* 1.3 62.9 + - - +
305E LYS* 3.5 12.9 - - + +
306E PHE* 3.4 12.5 + - - +
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Residues in contact with LEU 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E VAL* 3.8 27.8 - - + -
283E MET* 2.9 34.1 - - + -
286E TYR* 3.7 20.4 - - + -
299E ARG* 3.1 16.7 + - + +
300E GLN* 4.4 4.5 - - - +
301E MET 2.8 3.6 + - - -
302E HIS* 1.3 71.8 - - - +
304E ALA* 1.3 70.2 + - - +
306E PHE* 2.7 21.8 + - + +
307E MET* 3.3 14.2 + - + -
346E GLY* 3.7 20.0 - - - +
349E ILE* 4.1 17.0 - - + -
350E MET* 4.5 2.2 - - - -
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E GLN 3.8 11.3 + - - +
301E MET* 3.0 9.8 + - - +
303E LEU* 1.3 79.7 - - - +
305E LYS* 1.3 53.2 + - - +
306E PHE 2.6 12.3 + - - -
307E MET* 3.0 6.6 + - - +
308E ARG* 2.7 44.0 + - - +
349E ILE* 3.6 22.3 - - + +
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Residues in contact with LYS 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E LEU* 4.5 17.8 - - + +
301E MET* 3.0 12.9 + - - +
302E HIS* 3.5 19.1 - - + +
304E ALA* 1.3 81.1 - - - +
306E PHE* 1.3 54.6 + - - +
308E ARG* 3.8 25.9 - - - +
309E ALA* 3.3 21.5 + - - +
312E ARG* 4.7 6.3 + - - +
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Residues in contact with PHE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ILE* 5.6 0.9 - - + -
258E GLN* 2.9 57.2 - - + -
259E LEU* 3.9 16.4 - - + -
262E LEU* 3.5 22.7 - - + -
279E VAL* 4.3 10.3 - - + -
282E VAL* 3.7 23.1 - - + -
286E TYR* 3.9 13.5 - - - +
302E HIS 3.4 7.8 + - - +
303E LEU* 2.7 14.8 + - + +
304E ALA 2.6 3.6 + - - -
305E LYS* 1.3 71.1 - - - +
307E MET* 1.3 60.1 + - + +
308E ARG 2.6 14.5 + - - -
309E ALA* 2.9 2.5 + - - +
310E LEU* 2.8 49.3 + - + +
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Residues in contact with MET 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ILE* 3.5 37.8 - - + +
182E GLU* 6.2 0.7 - - + -
282E VAL* 4.6 9.9 - - - -
303E LEU* 3.3 16.8 + - + +
304E ALA* 3.0 10.5 + - - +
306E PHE* 1.3 78.7 - - - +
308E ARG* 1.3 61.1 + - + +
310E LEU* 4.1 17.0 - - - -
311E GLN* 3.3 18.0 + - - +
323E VAL* 4.9 3.8 - - + -
349E ILE* 4.3 11.9 - - + +
350E MET* 3.4 45.1 - - + +
353E SER* 3.0 40.8 + - - +
354E SER* 4.3 3.4 - - - -
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Residues in contact with ARG 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E MET* 5.1 0.6 + - - +
304E ALA* 2.7 26.5 + - - +
305E LYS* 3.8 38.5 - - - +
306E PHE 2.6 3.8 + - - -
307E MET* 1.3 70.7 - - + +
309E ALA* 1.3 57.3 + - - +
311E GLN* 2.6 32.0 + - + +
312E ARG* 2.8 27.2 + - - +
353E SER* 5.5 4.5 - - - -
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Residues in contact with ALA 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E LEU* 4.2 8.7 - - + -
262E LEU* 4.0 20.2 - - + -
305E LYS 3.3 11.9 + - - +
306E PHE 2.9 9.5 + - - +
308E ARG* 1.3 74.0 - - - +
310E LEU* 1.3 64.2 + - - +
312E ARG* 3.1 28.5 + - - +
313E LEU* 3.0 27.2 + - + +
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Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ILE* 3.9 12.1 - - + -
262E LEU* 3.8 26.8 - - + +
277E ILE* 4.7 6.3 - - + -
279E VAL* 4.0 16.6 - - + -
306E PHE* 2.8 45.3 + - + +
307E MET* 4.3 11.0 - - - -
309E ALA* 1.3 74.7 - - - +
311E GLN* 1.3 65.8 + - - +
312E ARG 3.0 0.5 + - - -
313E LEU* 3.1 14.9 + - - +
314E ALA* 3.2 10.9 + - - +
321E VAL* 3.9 21.3 - - + +
323E VAL* 3.9 27.6 - - + -
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Residues in contact with GLN 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E GLY 3.9 11.1 + - - -
179E SER* 4.3 3.5 - - - -
180E ILE* 4.0 29.9 + - + +
307E MET 3.3 12.7 + - - +
308E ARG* 2.6 17.7 + - + +
310E LEU* 1.3 73.9 - - - +
312E ARG* 1.3 68.1 + - - +
314E ALA* 3.0 9.8 + - - +
315E ASP* 2.7 29.9 + - - +
353E SER* 4.5 11.2 - - - +
355E THR* 4.8 6.4 - - - +
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Residues in contact with ARG 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E TYR* 5.0 20.2 - - + -
305E LYS* 4.7 6.1 + - - +
308E ARG* 2.8 21.9 + - - +
309E ALA* 3.2 36.6 - - - +
311E GLN* 1.3 76.1 - - - +
313E LEU* 1.3 55.0 + - + +
314E ALA 2.7 0.7 + - - -
315E ASP* 2.4 40.0 + - - +
316E GLN* 2.9 20.5 + - - +
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Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.8 40.6 - - + +
266E ALA* 4.1 14.6 - - + -
269E MET* 3.8 22.2 - - + -
277E ILE* 3.9 17.7 - - + -
309E ALA* 3.0 15.0 + - + +
310E LEU* 3.6 8.5 - - - +
312E ARG* 1.3 76.8 - - + +
314E ALA* 1.3 57.1 + - - +
316E GLN* 3.8 14.5 - - - +
317E PHE* 3.0 52.3 + - + +
319E VAL* 3.8 4.1 - - - +
321E VAL* 5.5 0.2 - - + -
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Residues in contact with ALA 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E GLY* 3.5 32.5 - - - +
179E SER* 4.3 4.9 - - - +
180E ILE 5.2 0.2 - - - +
310E LEU 3.2 6.8 + - - +
311E GLN* 3.0 16.1 + - - +
312E ARG 2.7 5.1 + - - -
313E LEU* 1.3 76.7 - - - +
315E ASP* 1.3 55.4 + - - +
318E GLY* 2.8 28.9 + - - -
319E VAL* 3.9 13.4 - - - +
321E VAL* 4.3 15.9 - - + -
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Residues in contact with ASP 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E GLU* 4.6 3.8 - - - +
112E TYR* 4.3 24.0 + - + +
178E GLY 4.5 4.6 - - - +
311E GLN* 2.7 34.9 + - - +
312E ARG* 2.4 27.2 + - - +
314E ALA* 1.3 69.8 - - - +
316E GLN* 1.3 62.0 + - - +
317E PHE 3.3 0.7 + - - -
318E GLY* 4.0 3.3 + - - -
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Residues in contact with GLN 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E MET* 4.4 6.6 - - - -
105E HIS* 4.4 10.1 - - - +
106E THR* 3.7 29.4 + - - +
108E GLU* 4.1 28.0 - - + +
109E ALA* 4.2 21.8 + - - +
112E TYR* 4.3 9.7 - - + -
266E ALA* 4.7 6.3 - - - +
312E ARG* 2.9 24.7 + - - +
313E LEU* 3.8 19.8 + - - +
315E ASP* 1.3 72.2 - - - +
317E PHE* 1.3 86.5 + - + +
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Residues in contact with PHE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E MET* 4.4 23.4 + - + +
105E HIS* 5.2 0.7 - - + -
106E THR* 3.9 16.2 - - - -
266E ALA* 3.7 14.8 - - - -
269E MET* 3.0 59.5 - - + -
270E SER* 3.8 4.7 - - - -
274E PHE 4.9 4.4 - - - +
313E LEU* 3.0 35.7 + - + +
316E GLN* 1.3 104.8 - - + +
318E GLY* 1.3 59.8 + - - +
319E VAL* 2.9 21.2 + - + +
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Residues in contact with GLY 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E THR* 3.5 10.9 + - - -
178E GLY* 3.3 10.0 + - - -
314E ALA 2.8 16.2 + - - -
315E ASP 4.0 3.6 + - - -
316E GLN 3.9 0.2 - - - -
317E PHE* 1.3 76.9 - - - +
319E VAL* 1.3 71.0 + - - +
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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
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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