Contacts of the helix formed by residues 281 - 302 (chain E) in PDB entry 6DWZ
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 THR 281 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277E SER 3.4 7.8 + - - -
278E PHE 3.1 6.8 + - - +
280E GLU* 1.3 79.3 + - - +
282E PRO* 1.3 61.0 - - - +
283E GLU* 3.1 7.9 - - + -
284E LEU* 2.9 48.9 + - + +
285E ASN* 2.9 9.5 + - - +
405E ASP 4.3 4.5 - - - +
408E LYS* 4.0 17.1 - - - +
409E LEU* 3.6 33.7 + - - +
412E ASN* 3.3 14.9 + - - -
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Residues in contact with PRO 282 (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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279E GLU 3.8 9.4 - - - +
280E GLU* 3.3 9.0 - - - +
281E THR* 1.3 89.5 - - - +
283E GLU* 1.3 58.1 + - + +
284E LEU 3.3 0.2 - - - -
285E ASN* 3.6 14.8 - - + +
286E MET* 3.0 30.8 + - - +
408E LYS* 4.3 8.7 - - - +
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Residues in contact with GLU 283 (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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281E THR* 4.3 7.9 - - + -
282E PRO* 1.3 77.9 - - + +
284E LEU* 1.3 60.6 + - - +
286E MET* 4.0 10.0 - - + +
287E PRO* 3.0 20.0 - - - +
356E ILE* 5.6 0.3 - - - +
405E ASP* 2.9 48.3 + - - +
408E LYS* 3.2 32.1 + - - +
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Residues in contact with LEU 284 (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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278E PHE* 4.4 5.8 - - + -
281E THR* 2.9 19.1 + - + +
283E GLU* 1.3 80.7 - - - +
285E ASN* 1.3 65.8 + - - +
286E MET 3.0 2.0 - - - -
287E PRO* 2.8 18.2 - - + +
288E ILE* 3.1 14.5 + - - +
356E ILE* 3.5 33.4 - - + +
360E MET* 3.6 34.3 - - + +
405E ASP* 4.2 25.6 - - + +
406E ILE* 4.6 5.4 - - + +
409E LEU* 3.8 29.2 - - + -
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Residues in contact with ASN 285 (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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278E PHE* 3.3 38.1 + - - +
279E GLU* 4.0 17.8 + - - +
281E THR 2.9 9.7 + - - -
282E PRO* 3.8 13.8 - - + +
284E LEU* 1.3 73.4 - - - +
286E MET* 1.3 57.0 + - - +
288E ILE* 3.9 20.1 - - - +
289E LEU* 3.0 30.4 + - - +
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Residues in contact with MET 286 (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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282E PRO 3.0 18.6 + - - +
283E GLU* 4.0 12.1 - - + +
284E LEU 3.0 0.6 + - - -
285E ASN* 1.3 75.3 - - - +
287E PRO* 1.3 75.5 - - + +
289E LEU* 3.5 8.6 + - + +
290E ALA* 2.9 26.7 + - + +
351E HIS* 3.9 44.2 - - + -
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Residues in contact with PRO 287 (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 GLU 3.0 25.4 - - - +
284E LEU* 2.8 28.9 - - + +
286E MET* 1.3 88.9 - - + +
288E ILE* 1.3 63.6 + - - +
290E ALA* 2.9 5.4 + - + +
291E CYS* 2.8 28.4 + - - -
351E HIS* 3.8 24.2 - - + +
352E ILE 4.3 12.8 - - - +
353E ASN* 6.2 0.7 - - + -
356E ILE* 4.9 4.7 - - + -
357E ILE* 4.4 14.4 - - + -
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Residues in contact with ILE 288 (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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278E PHE* 3.1 45.5 - - + -
284E LEU 3.1 13.4 + - - +
285E ASN* 3.6 18.6 - - - +
287E PRO* 1.3 75.0 - - - +
289E LEU* 1.3 67.0 + - + +
291E CYS* 3.0 26.3 - - - +
292E LYS* 3.1 19.7 + - + +
314E GLU* 4.9 2.2 - - - +
322E THR* 4.0 26.2 - - + -
325E MET* 4.6 1.7 - - + +
326E LEU* 4.4 12.3 - - + -
357E ILE* 5.2 0.8 - - + +
360E MET* 4.1 15.5 - - - -
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Residues in contact with LEU 289 (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 ASN* 3.0 22.2 + - - +
286E MET* 4.0 8.1 - - + +
288E ILE* 1.3 75.0 - - + +
290E ALA* 1.3 70.4 + - - +
292E LYS* 3.1 29.0 + - + +
293E ASN* 2.7 41.2 + - - +
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Residues in contact with ALA 290 (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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286E MET* 2.9 15.6 + - + +
287E PRO* 2.9 14.5 + - + +
289E LEU* 1.3 83.3 - - - +
291E CYS* 1.3 64.2 + - - +
293E ASN* 3.1 5.4 + - - +
294E ILE* 2.9 27.9 + - + +
348E ARG 4.3 15.5 - - - +
351E HIS* 4.4 14.1 - - + +
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Residues in contact with CYS 291 (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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287E PRO* 2.8 18.5 + - - -
288E ILE 3.0 9.0 - - - +
290E ALA* 1.3 74.8 - - - +
292E LYS* 1.3 65.2 + - - +
294E ILE* 2.8 24.7 + - - +
295E VAL* 2.9 14.7 + - - +
325E MET* 4.0 8.3 - - - -
326E LEU* 3.7 22.9 - - + -
329E ILE* 3.5 34.0 - - + +
333E TRP* 6.4 0.7 - - - -
357E ILE* 4.9 9.9 - - - -
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Residues in contact with LYS 292 (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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288E ILE* 3.1 11.4 + - + +
289E LEU* 3.1 36.1 + - + +
291E CYS* 1.3 78.2 - - - +
293E ASN* 1.3 63.2 + - - +
295E VAL* 3.2 6.7 + - - +
296E LYS* 3.0 25.8 + - - +
313E SER* 5.9 0.4 - - - +
314E GLU* 3.3 48.8 + - + +
316E PRO* 5.2 6.5 - - - +
325E MET* 3.9 21.3 - - + -
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Residues in contact with ASN 293 (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 LEU* 2.7 50.9 + - - +
290E ALA* 3.1 7.9 + - - +
292E LYS* 1.3 77.9 - - - +
294E ILE* 1.3 68.0 + - + +
296E LYS* 2.6 43.4 + - - +
297E TYR* 3.3 20.3 + - - +
348E ARG* 3.6 12.9 + - - +
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Residues in contact with ILE 294 (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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290E ALA* 2.9 21.7 + - + +
291E CYS* 3.1 15.9 - - - +
293E ASN* 1.3 79.2 - - + +
295E VAL* 1.3 64.3 + - - +
297E TYR* 2.9 20.0 + - - +
298E PHE* 3.2 18.8 + - + -
311E LEU* 4.9 4.0 - - + -
329E ILE* 4.7 9.2 - - + -
336E VAL* 4.5 11.9 - - + -
340E LEU* 3.6 26.2 - - + -
348E ARG* 3.1 46.9 - - + +
349E ILE* 5.2 1.6 - - + -
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Residues in contact with VAL 295 (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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291E CYS 2.9 17.0 + - - +
292E LYS 3.3 7.9 - - - +
294E ILE* 1.3 75.8 - - - +
296E LYS* 1.3 58.6 + - - +
297E TYR 2.7 12.0 + - - -
298E PHE* 2.9 14.4 + - - +
299E LYS* 3.1 24.2 + - + +
311E LEU* 4.2 25.1 - - + -
312E LYS 4.3 1.8 - - - +
313E SER* 3.6 37.7 - - - +
325E MET* 4.1 16.2 - - + -
329E ILE* 3.5 21.5 - - + -
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Residues in contact with LYS 296 (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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292E LYS 3.0 7.3 + - - +
293E ASN* 2.6 46.0 + - - +
295E VAL* 1.3 82.8 - - + +
297E TYR* 1.3 62.0 + - - +
299E LYS* 3.8 8.0 + - - +
300E LYS* 3.2 23.4 + - - +
313E SER* 6.3 0.4 - - - -
348E ARG* 6.1 1.8 - - - +
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Residues in contact with TYR 297 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293E ASN 3.3 14.0 + - - +
294E ILE* 2.9 11.2 + - - +
295E VAL 2.7 5.7 + - - -
296E LYS* 1.3 73.5 - - - +
298E PHE* 1.3 68.9 + + - -
300E LYS* 3.1 12.3 + - + -
301E ALA* 2.7 55.5 + - + +
303E LEU* 4.0 16.5 - - + +
339E ILE* 6.4 0.2 - - + -
340E LEU* 4.5 13.9 - - + -
343E ALA* 4.3 11.8 - - + +
345E GLU* 3.6 41.8 + - + +
348E ARG* 4.0 27.8 - - - +
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Residues in contact with PHE 298 (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* 3.2 15.3 + - + -
295E VAL 2.9 4.7 + - - +
297E TYR* 1.3 85.0 - + - +
299E LYS* 1.3 54.5 + - - +
302E ASN* 2.7 29.8 + - - -
303E LEU* 3.0 42.7 + - + +
304E GLN* 3.7 19.5 - - + -
307E LEU* 3.9 24.0 - - + -
311E LEU* 3.2 33.7 - - + -
336E VAL* 3.8 28.9 - - + -
339E ILE* 4.3 15.3 - - + -
340E LEU* 3.9 26.7 - - + -
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Residues in contact with LYS 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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188A LYS* 4.2 18.2 + - - +
295E VAL* 3.1 23.9 + - + +
296E LYS* 3.8 8.7 - - - +
298E PHE* 1.3 78.7 - - - +
300E LYS* 1.3 60.0 + - - +
302E ASN* 3.6 8.7 + - - +
304E GLN* 4.1 24.7 - - - +
311E LEU 3.6 18.2 + - - -
312E LYS* 4.8 1.8 - - - +
313E SER* 3.9 29.8 - - - +
14G T 5.0 7.9 + - - +
15G C 3.8 25.8 + - - +
16G T 6.1 1.9 - - - +
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Residues in contact with LYS 300 (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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19C G 3.2 50.9 + - - +
296E LYS 3.2 17.5 + - - +
297E TYR* 3.1 13.0 + - + +
299E LYS* 1.3 74.3 - - - +
301E ALA* 1.3 66.6 + - - +
302E ASN* 2.9 8.8 + - - +
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Residues in contact with ALA 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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19C G 6.0 2.9 - - - -
20C T 4.7 11.7 + - - +
297E TYR* 2.7 41.5 + - + +
300E LYS* 1.3 78.4 - - + +
302E ASN* 1.3 70.6 - - - +
303E LEU* 3.3 28.7 + - + +
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Residues in contact with ASN 302 (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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183A THR* 5.9 0.6 - - - +
187A ILE 3.9 5.5 - - - +
188A LYS* 3.2 45.7 + - + +
190A ASN* 5.2 7.9 + - - +
216A PHE* 4.9 3.2 - - - -
298E PHE 2.7 11.3 + - - -
299E LYS* 4.0 7.6 - - - +
300E LYS 2.9 7.5 - - - +
301E ALA* 1.3 81.8 - - - +
303E LEU* 1.3 69.8 + - - +
305E HIS* 3.0 26.0 + - - -
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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