Contacts of the helix formed by residues 287 - 308 (chain E) in PDB entry 1K9A
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 287 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284E SER* 4.6 8.1 + - - -
285E VAL 3.9 1.6 - - - -
286E LEU* 1.3 75.8 - - - +
288E GLY* 1.3 68.5 + - - +
289E ASP* 2.7 5.3 + - - +
290E CYS* 2.6 19.8 + - - +
291E LEU* 3.5 3.5 + - - -
450E LEU* 6.0 0.2 - - - -
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Residues in contact with GLY 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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287E GLY* 1.3 66.9 - - - -
289E ASP* 1.3 55.1 + - - +
291E LEU* 3.0 13.3 + - - +
292E LEU* 2.6 36.2 + - - +
380E TYR* 5.1 4.5 - - - -
449E HIS* 3.3 30.7 - - - -
450E LEU* 5.0 3.7 - - - +
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Residues in contact with ASP 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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287E GLY 2.7 6.1 + - - +
288E GLY* 1.3 70.5 - - - +
290E CYS* 1.3 60.2 + - - +
292E LEU* 3.5 0.3 + - - +
293E LYS* 2.7 47.8 + - - +
444E ARG* 5.7 0.2 - - - +
449E HIS* 3.4 20.6 + - - -
450E LEU* 3.5 22.8 - - - +
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Residues in contact with CYS 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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277E TYR* 4.8 7.0 - - - -
286E LEU* 3.8 35.7 - - + -
287E GLY 2.6 15.8 + - - +
289E ASP* 1.3 74.7 - - - +
291E LEU* 1.3 55.4 + - - +
293E LYS* 2.7 32.5 + - - +
294E PHE* 3.1 35.4 + - - -
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Residues in contact with LEU 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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278E LEU* 4.0 22.4 - - + -
286E LEU* 3.9 20.9 - - + +
287E GLY* 3.5 1.9 + - - +
288E GLY 3.0 12.9 + - - +
290E CYS* 1.3 79.1 - - + +
292E LEU* 1.3 63.4 + - - +
294E PHE* 3.1 17.8 + - + +
295E SER* 3.1 14.9 + - - -
379E ILE* 3.9 22.0 - - + +
380E TYR* 3.7 45.5 - - + +
382E PHE* 4.2 25.4 - - + -
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Residues in contact with LEU 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 GLY 2.6 21.1 + - - +
289E ASP 3.8 3.6 - - - +
291E LEU* 1.3 71.8 - - - +
293E LYS* 1.3 58.9 + - + +
295E SER* 3.6 6.8 - - - -
296E LEU* 3.1 39.9 + - + +
380E TYR* 3.3 17.6 + - - +
415E VAL* 4.8 4.0 - - + -
440E LEU* 4.1 32.5 - - + +
443E ILE* 4.5 11.4 - - + -
444E ARG* 3.5 44.2 - - + +
449E HIS* 3.7 25.8 - - + +
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Residues in contact with LYS 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 ASP* 2.7 45.8 + - - +
290E CYS* 2.7 14.8 + - - +
292E LEU* 1.3 83.3 - - + +
294E PHE* 1.3 66.4 + - + +
296E LEU* 3.5 10.4 + - + +
297E ASP* 3.0 34.6 + - - +
444E ARG* 2.9 47.3 - - - +
449E HIS* 4.6 0.4 + - - -
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Residues in contact with PHE 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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274E LEU* 3.4 26.2 - - + -
277E TYR* 3.3 44.9 - + - -
278E LEU* 4.3 13.2 - - + -
290E CYS* 3.1 29.1 + - - -
291E LEU* 3.1 11.9 + - + +
293E LYS* 1.3 80.2 - - + +
295E SER* 1.3 65.4 + - - +
297E ASP* 3.3 13.3 + - - +
298E VAL* 3.1 29.8 + - - +
322E VAL* 4.3 12.1 - - + -
326E ASN* 4.0 24.7 - - + -
328E ALA* 4.3 9.9 - - + -
379E ILE* 4.1 13.9 - - + -
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Residues in contact with SER 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 LEU 3.1 11.7 + - - -
292E LEU* 3.6 14.8 - - - -
294E PHE* 1.3 79.3 - - - +
296E LEU* 1.3 62.3 + - - +
298E VAL* 3.5 2.3 + - - +
299E CYS* 3.0 24.0 + - - +
372E PHE* 3.9 7.9 - - - -
376E LEU* 3.1 31.7 - - - +
379E ILE* 3.8 12.0 - - - +
380E TYR* 3.5 10.0 - - - -
440E LEU* 4.2 14.1 - - - -
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Residues in contact with LEU 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 LEU* 3.1 32.6 + - + +
293E LYS* 3.7 9.4 - - + +
295E SER* 1.3 74.6 - - - +
297E ASP* 1.3 56.2 + - - +
299E CYS* 3.1 4.6 + - - +
300E GLU* 2.7 47.4 + - + +
437E ARG* 4.0 19.5 - - + +
440E LEU* 3.6 31.6 - - + +
441E GLU* 4.1 13.0 - - + +
444E ARG* 3.3 35.2 - - - +
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Residues in contact with ASP 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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247E ASN* 3.6 26.8 + - - +
293E LYS* 3.0 24.3 + - - +
294E PHE* 3.3 15.7 + - - +
296E LEU* 1.3 79.0 - - - +
298E VAL* 1.3 62.3 + - - +
300E GLU* 3.1 11.3 + - - +
301E ALA 3.0 17.0 + - - -
326E ASN 4.5 2.3 - - - +
327E VAL* 4.0 8.6 - - - +
328E ALA* 3.2 38.1 + - + +
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Residues in contact with VAL 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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247E ASN* 5.4 0.2 - - - -
274E LEU* 4.8 4.3 - - + -
294E PHE 3.1 18.5 + - - +
295E SER 3.9 3.4 - - - +
297E ASP* 1.3 75.6 - - - +
299E CYS* 1.3 62.7 + - - +
301E ALA* 3.1 10.4 + - - +
302E MET* 3.0 20.5 + - + +
315E LEU* 4.1 8.5 - - + -
320E VAL* 4.3 23.8 - - + -
328E ALA* 4.4 7.2 - - + -
330E VAL* 3.9 18.8 - - + -
372E PHE* 4.2 15.3 - - + -
375E LEU* 3.8 35.0 - - + -
379E ILE* 4.9 0.2 - - + -
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Residues in contact with CYS 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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295E SER 3.0 18.9 + - - +
296E LEU* 3.3 9.0 - - - +
298E VAL* 1.3 75.5 - - - +
300E GLU* 1.3 60.4 + - - +
302E MET* 3.0 5.8 + - - +
303E GLU* 2.8 30.5 + - - +
372E PHE* 4.0 18.1 - - + -
433E PHE* 3.6 30.0 - - - -
436E LEU* 3.7 13.5 - - - -
437E ARG* 3.6 24.5 - - + -
440E LEU* 4.3 4.0 - - + -
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Residues in contact with GLU 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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245E HIS* 3.6 12.6 + - + +
247E ASN* 4.0 18.3 + - - +
296E LEU* 2.7 29.4 + - + +
297E ASP* 3.1 11.7 + - - +
299E CYS* 1.3 71.9 - - - +
301E ALA* 1.3 61.9 + - - +
303E GLU* 3.7 11.8 - - - +
304E TYR* 3.1 22.0 + - - +
437E ARG* 4.0 25.4 - - + +
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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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245E HIS* 4.4 4.3 - - - -
247E ASN* 3.2 36.5 - - + +
248E LEU* 3.8 9.1 - - + +
297E ASP 3.0 5.9 + - - +
298E VAL* 3.1 11.2 - - - +
299E CYS 3.0 0.2 - - - -
300E GLU* 1.3 78.9 - - - +
302E MET* 1.3 58.4 + - - +
304E TYR* 3.3 5.7 + - - +
305E LEU* 3.0 30.1 + - - +
330E VAL* 3.6 17.0 - - + -
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Residues in contact with MET 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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298E VAL* 3.0 18.4 + - + +
299E CYS 3.0 3.6 + - - +
301E ALA* 1.3 77.6 - - + +
303E GLU* 1.3 61.3 + - - +
305E LEU* 3.2 33.6 + - + +
306E GLU* 2.9 28.9 + - - +
312E HIS* 4.6 4.3 - - + -
315E LEU* 3.8 29.4 - - + -
330E VAL* 3.8 26.9 - - + -
368E ASP* 4.5 13.9 - - - +
372E PHE* 4.6 0.7 - - + -
433E PHE* 3.3 48.1 - - + -
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Residues in contact with GLU 303 (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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299E CYS 2.8 14.4 + - - +
300E GLU* 3.7 9.4 - - - +
302E MET* 1.3 76.5 - - - +
304E TYR* 1.3 53.2 + - - +
306E GLU* 3.2 5.3 + - + +
307E GLY* 2.7 32.9 + - - -
433E PHE* 3.7 14.1 - - + +
434E LEU* 3.3 34.5 - - + +
437E ARG* 2.7 50.4 + - - +
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Residues in contact with TYR 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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242E GLN 3.8 9.2 + - - -
243E LEU* 3.7 8.1 - - + -
244E ARG* 2.8 42.9 + - - +
245E HIS* 3.5 33.2 - + + -
248E LEU* 3.6 32.1 - - + -
300E GLU 3.1 8.0 + - - +
301E ALA 3.3 7.6 - - - +
303E GLU* 1.3 73.6 - - - +
305E LEU* 1.3 76.1 + - + +
307E GLY* 3.0 2.7 + - - -
308E ASN* 3.0 57.8 + - + +
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Residues in contact with LEU 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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243E LEU* 3.9 24.9 - - + -
248E LEU* 3.9 30.5 - - + -
301E ALA 3.0 10.1 + - - +
302E MET* 3.2 35.9 - - + +
304E TYR* 1.3 80.0 - - + +
306E GLU* 1.3 61.8 + - - +
308E ASN* 3.1 8.7 + - - -
309E ASN 3.1 0.2 + - - -
310E PHE* 2.8 47.9 + - + +
312E HIS* 4.2 26.9 - - + +
333E PHE* 4.7 2.5 - - + -
336E THR* 4.9 2.7 - - + -
368E ASP* 5.7 0.7 - - - +
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Residues in contact with GLU 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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302E MET 2.9 17.1 + - - +
303E GLU* 3.4 6.5 - - + +
305E LEU* 1.3 75.8 - - - +
307E GLY* 1.3 64.8 + - - +
308E ASN 3.1 1.0 + - - -
309E ASN* 3.1 15.6 + - - +
310E PHE 4.2 6.0 + - - +
365E THR* 3.5 35.1 - - + +
366E LYS* 5.7 1.4 + - - -
432E THR* 3.6 18.5 + - - -
433E PHE* 3.1 34.4 + - - +
434E LEU 4.3 2.1 + - - -
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Residues in contact with GLY 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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303E GLU 2.7 18.3 + - - -
304E TYR* 3.0 6.4 + - - -
306E GLU* 1.3 74.2 - - - +
308E ASN* 1.3 63.5 + - - +
309E ASN* 3.5 4.8 + - - -
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Residues in contact with ASN 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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242E GLN 5.9 0.9 - - - -
304E TYR* 3.0 62.1 + - + +
305E LEU 3.1 0.2 + - - -
306E GLU 3.1 0.2 - - - -
307E GLY* 1.3 81.5 - - - +
309E ASN* 1.3 78.5 + - - +
310E PHE* 3.4 29.9 - - + -
338E GLU* 4.1 3.8 - - - +
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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