Contacts of the helix formed by residues 309 - 329 (chain E) in PDB entry 5U07
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 GLY 309 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308E ASP* 1.3 87.8 + - - +
310E TYR* 1.3 64.3 + - - -
311E THR* 3.3 4.7 + - - -
312E LEU* 4.0 8.6 + - - +
313E ARG* 4.0 11.3 - - - +
31I GLY 4.1 2.9 + - - -
301I GLU* 3.8 24.8 + - - -
302I THR* 4.2 18.0 - - - +
303I ALA 5.0 2.2 - - - +
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Residues in contact with TYR 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E HIS* 3.3 54.9 - + + +
196E GLY 5.2 1.4 + - - -
230E THR* 3.6 18.6 - - + -
304E LEU* 3.8 27.6 + - + +
305E TYR 3.8 4.2 + - - -
306E GLY* 3.0 40.6 + - - -
308E ASP 3.2 5.1 + - - -
309E GLY* 1.3 71.2 - - - -
311E THR* 1.3 65.8 + - - +
312E LEU 3.4 0.2 - - - -
313E ARG* 3.9 9.4 - - - +
314E ALA* 2.8 26.4 + - - +
31I GLY* 3.8 4.3 - - - -
32I GLY* 3.7 29.0 - - - -
301I GLU* 4.1 14.5 + - - +
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Residues in contact with THR 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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9E ILE* 5.3 2.0 - - - +
11E THR* 4.7 2.5 - - - -
230E THR* 5.0 6.5 - - - +
282E ASP* 2.9 37.4 + - - +
309E GLY 4.8 0.7 - - - -
310E TYR* 1.3 77.4 - - - +
312E LEU* 1.3 73.0 + - + +
314E ALA* 3.6 4.3 - - - +
315E CYS* 3.0 31.3 + - - -
341E GLU* 4.1 9.7 + - - +
298I PRO 5.6 2.2 - - - +
301I GLU* 4.2 25.4 - - + +
302I THR* 4.5 17.9 - - + -
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Residues in contact with LEU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ASP* 6.1 0.9 - - - +
309E GLY 4.0 5.5 + - - +
310E TYR 3.4 0.2 - - - -
311E THR* 1.3 85.8 - - + +
313E ARG* 1.3 65.5 + - + +
315E CYS* 3.3 4.6 + - + +
316E GLN* 3.0 52.3 + - + +
341E GLU* 4.4 26.7 - - + +
343E LYS* 4.6 20.6 - - + -
344E THR* 4.1 13.5 - - - +
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Residues in contact with ARG 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E LEU* 4.0 33.6 - - + +
305E TYR* 4.4 13.3 - - - +
306E GLY* 3.7 35.6 + - - +
308E ASP* 4.8 16.6 + - - +
309E GLY 4.0 13.9 - - - +
310E TYR* 3.4 10.1 + - - +
311E THR 3.3 0.6 - - - -
312E LEU* 1.3 79.6 - - + +
314E ALA* 1.3 58.1 + - - +
316E GLN* 3.4 11.8 + - - +
317E GLU* 3.0 42.3 + - + +
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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
----------------------------------------------------------
9E ILE* 4.4 17.3 - - + -
194E VAL* 4.4 19.3 - - + -
230E THR* 5.0 1.3 - - - +
300E PHE* 3.9 23.0 - - + -
304E LEU* 4.5 3.3 - - - +
310E TYR* 2.8 20.0 + - + +
311E THR* 3.6 4.0 - - - +
313E ARG* 1.3 73.9 - - - +
315E CYS* 1.3 65.9 + - - +
317E GLU* 3.2 4.7 + - - +
318E LEU* 2.9 24.8 + - - +
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Residues in contact with CYS 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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9E ILE* 4.9 10.8 - - - -
282E ASP* 5.1 1.8 - - - -
283E LEU* 3.6 35.4 - - + +
311E THR* 3.0 26.1 + - - +
312E LEU* 3.7 6.1 - - + +
314E ALA* 1.3 77.8 - - - +
316E GLN* 1.3 62.2 + - - +
318E LEU* 3.3 5.5 + - - +
319E ASN* 2.9 22.3 + - - +
341E GLU* 3.0 34.8 - - - +
346E LEU* 3.9 11.1 - - + +
349E LEU* 5.4 0.3 - - - +
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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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312E LEU* 3.0 47.6 + - + +
313E ARG* 3.8 11.4 - - - +
314E ALA 3.3 0.2 - - - -
315E CYS* 1.3 75.5 - - - +
317E GLU* 1.3 60.2 + - + +
319E ASN* 3.2 9.6 + - - +
320E ASN* 2.9 28.1 + - - +
344E THR* 3.8 21.4 + - + +
346E LEU* 4.4 7.4 - - + -
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Residues in contact with GLU 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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299E ALA* 4.6 12.7 - - + +
300E PHE* 4.3 14.6 - - + -
304E LEU* 4.8 19.5 - - + +
313E ARG* 3.0 33.8 + - + +
314E ALA* 3.2 5.8 + - - +
316E GLN* 1.3 74.5 - - - +
318E LEU* 1.3 66.3 + - - +
320E ASN* 2.5 39.1 + - - +
321E TYR* 3.0 10.2 + - - +
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E HIS* 4.6 7.2 - - + -
8E ALA 5.6 0.2 - - - +
9E ILE* 4.4 12.3 - - + -
232E TYR* 3.9 31.0 - - + -
283E LEU* 4.5 11.2 - - + -
285E HIS* 4.8 4.5 - - + -
296E PHE* 3.8 26.0 - - + -
299E ALA* 5.0 2.5 - - - -
300E PHE* 4.3 14.5 - - + -
314E ALA 2.9 15.6 + - - +
315E CYS* 3.8 6.1 - - - +
317E GLU* 1.3 78.2 - - - +
319E ASN* 1.3 57.3 + - - +
321E TYR* 4.0 4.5 - - - +
322E ALA* 2.9 30.8 + - - +
349E LEU* 3.7 34.1 - - + -
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Residues in contact with ASN 319 (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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315E CYS 2.9 6.4 + - - +
316E GLN* 3.3 9.7 + - - +
317E GLU 3.1 0.2 - - - -
318E LEU* 1.3 74.5 - - - +
320E ASN* 1.3 67.3 + - - +
322E ALA* 3.0 5.9 + - - +
323E GLU* 2.9 22.7 + - - +
344E THR* 5.0 3.4 - - - +
346E LEU* 3.3 51.0 - - + +
347E ALA* 3.8 4.0 - - - +
348E ALA* 3.1 26.3 + - - +
349E LEU* 4.4 7.4 + - + +
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Residues in contact with ASN 320 (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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316E GLN 2.9 17.8 + - - +
317E GLU* 2.5 34.5 + - - +
319E ASN* 1.3 73.7 - - - +
321E TYR* 1.3 82.2 + - - +
323E GLU* 2.8 40.3 - - - +
324E ARG* 3.0 10.2 + - - +
343F LYS* 5.4 7.7 - - - +
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Residues in contact with TYR 321 (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 SER 4.7 1.0 + - - -
296E PHE* 3.9 31.0 - + - -
298E PRO* 3.6 26.2 - - + +
299E ALA* 3.5 34.8 - - + -
317E GLU 3.0 14.2 + - - +
318E LEU* 4.0 2.2 - - - +
320E ASN* 1.3 89.0 + - - +
322E ALA* 1.3 58.9 + - - +
324E ARG* 3.3 4.9 + - + +
325E LEU* 2.9 60.7 + - + +
279F THR* 5.2 0.7 - - - +
280F LEU 4.5 5.2 + - - -
282F ASP* 3.7 9.3 + - - -
340F VAL* 4.5 26.2 - - + +
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Residues in contact with ALA 322 (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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285E HIS* 5.7 0.2 - - - +
296E PHE* 4.2 22.9 - - + -
318E LEU 2.9 19.8 + - - +
319E ASN 3.5 3.1 - - - +
321E TYR* 1.3 78.2 - - - +
323E GLU* 1.3 62.2 + - - +
325E LEU* 3.3 2.7 + - - +
326E ARG* 2.9 25.7 + - - +
348E ALA* 4.1 7.9 - - + +
349E LEU* 3.5 28.3 - - + -
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Residues in contact with GLU 323 (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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319E ASN* 2.9 11.1 + - - +
320E ASN* 2.8 41.0 - - - +
322E ALA* 1.3 77.0 - - - +
324E ARG* 1.3 69.2 + - + +
326E ARG* 3.0 13.8 - - + +
327E GLU* 2.9 23.7 + - - +
348E ALA* 3.5 22.2 - - + +
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Residues in contact with ARG 324 (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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320E ASN 3.0 16.5 + - - +
321E TYR* 3.8 7.2 - - + +
323E GLU* 1.3 80.4 - - + +
325E LEU* 1.3 58.1 + - - +
327E GLU* 3.3 25.3 + - - +
328E VAL* 2.9 35.8 + - - +
339F THR 3.2 17.2 + - - +
340F VAL* 3.1 40.4 + - + +
342F ASN* 3.9 16.3 + - - +
352F ARG* 3.0 32.7 - - - +
353F TYR 5.3 0.4 + - - -
354F ASP* 4.3 18.8 + - - +
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Residues in contact with LEU 325 (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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294E ILE* 3.6 34.1 - - + -
295E SER 4.9 0.2 - - - +
296E PHE* 3.8 12.8 - - + -
321E TYR* 2.9 54.0 + - + +
322E ALA* 4.0 3.8 - - - +
324E ARG* 1.3 74.6 - - - +
326E ARG* 1.3 60.3 + - - +
328E VAL* 4.3 6.1 - - + +
329E TRP* 2.8 34.6 + - + +
280F LEU* 4.5 26.9 - - + +
281F PRO 5.8 1.1 - - - +
340F VAL* 4.1 20.4 - - + -
356F TYR* 6.0 0.4 - - + -
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Residues in contact with ARG 326 (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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322E ALA 2.9 17.0 + - - +
323E GLU* 3.0 25.3 - - - +
325E LEU* 1.3 77.4 - - - +
327E GLU* 1.3 69.0 + - - +
329E TRP 3.6 14.8 - - - +
330E PRO* 3.7 9.7 - - - +
331E ASP 4.8 3.1 + - - +
335E ARG* 4.0 39.9 - - - +
347E ALA 5.4 1.2 + - - -
348E ALA* 4.4 23.5 + - + +
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Residues in contact with GLU 327 (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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323E GLU 2.9 12.6 + - - +
324E ARG* 3.5 35.4 - - - +
326E ARG* 1.3 87.5 - - - +
328E VAL* 1.3 63.3 + - - +
329E TRP 3.6 0.2 + - - -
330E PRO* 3.9 7.4 - - - +
354F ASP* 4.1 23.8 - - + +
355F SER* 3.7 12.5 - - - -
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Residues in contact with VAL 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E ARG* 2.9 40.3 + - - +
325E LEU* 4.2 8.1 - - + +
327E GLU* 1.3 74.6 - - - +
329E TRP* 1.3 58.9 + - + +
330E PRO* 3.2 8.0 - - - +
338F ALA* 5.2 0.4 - - + -
339F THR 4.0 13.9 - - - +
340F VAL* 4.2 11.7 - - + -
354F ASP 3.8 15.5 - - - +
355F SER* 3.2 2.1 - - - -
356F TYR* 3.2 67.3 + - + +
357F PRO* 3.8 1.6 - - - +
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Residues in contact with TRP 329 (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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289E ARG* 3.2 26.3 + - - +
291E ASP* 2.3 27.8 + - + -
292E ARG* 4.7 7.0 - - + +
294E ILE* 4.3 7.0 - - + -
325E LEU* 2.8 22.3 + - + +
326E ARG* 3.6 7.6 - - - +
328E VAL* 1.3 73.2 - - + +
330E PRO* 1.3 73.3 + - + +
331E ASP* 3.4 5.1 + - + +
335E ARG* 4.9 0.2 + - - -
261F ARG* 3.8 40.6 - - + -
264F LEU* 4.8 11.2 - - + -
265F SER* 4.0 29.4 - - - -
280F LEU* 3.5 33.4 - - + -
356F TYR* 4.0 28.3 - + + -
357F PRO* 4.7 10.1 - - + -
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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
------------------------------------------------------------
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