Contacts of the helix formed by residues 289 - 311 (chain C) in PDB entry 4X4R
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 VAL 289 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG* 3.4 40.8 - - + +
94C TYR 3.6 22.4 - - - +
95C ALA* 4.9 5.6 - - + -
288C ILE* 1.3 75.7 - - - +
290C ASP* 1.3 71.2 - - + +
291C ASP* 3.5 23.6 - - + +
292C ASN* 2.9 29.8 + - - +
293C LEU* 3.1 9.5 + - - +
36D C 4.9 6.7 - - - +
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Residues in contact with ASP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 5.1 0.3 - - - +
166C LYS* 4.1 22.5 + - + +
285C LYS* 5.0 10.0 - - - -
288C ILE 4.6 3.8 - - - +
289C VAL* 1.3 76.5 - - + +
291C ASP* 1.3 63.1 + - - +
292C ASN 3.1 0.2 - - - -
293C LEU* 3.7 5.8 - - - +
294C TYR* 3.1 63.6 + - + +
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Residues in contact with ASP 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA* 4.6 3.8 - - + -
164C GLU* 3.7 17.0 - - - +
165C TYR* 3.8 7.3 + - - -
166C LYS 5.4 0.3 + - - -
289C VAL* 3.0 21.1 + - + +
290C ASP* 1.3 80.4 + - - +
292C ASN* 1.3 59.1 + - - +
295C PRO* 3.3 20.7 - - - +
1D G 4.8 1.4 + - - -
35D A 2.6 54.3 + - + +
36D C 3.1 30.9 + - - +
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Residues in contact with ASN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG* 5.8 0.4 - - - +
94C TYR 5.0 0.2 + - - -
95C ALA* 3.9 17.8 + - - +
288C ILE* 4.0 17.1 - - + +
289C VAL* 2.9 31.6 + - - +
291C ASP* 1.3 84.7 - - - +
293C LEU* 1.3 63.5 + - - +
294C TYR 3.6 0.7 - - - -
295C PRO* 3.6 4.8 - - - +
296C GLN* 3.2 15.1 + - - +
403C ASN* 5.3 0.7 - - - +
1D G 3.1 48.5 + - - +
35D A 3.8 12.8 - - - +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LYS* 4.1 25.6 - - + -
286C PRO* 3.6 31.2 - - + +
288C ILE* 3.5 22.0 - - + +
289C VAL 3.1 11.4 + - - +
290C ASP* 3.3 9.6 + - - +
292C ASN* 1.3 78.4 - - - +
294C TYR* 1.3 67.6 + - + +
296C GLN* 2.9 21.8 + - - +
297C LEU* 2.9 22.5 + - + +
322C ALA* 4.0 27.1 - - + -
327C CYS* 4.3 3.4 - - - -
404C VAL* 4.0 12.1 - - + -
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Residues in contact with TYR 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR 4.2 16.4 - - - +
166C LYS* 3.4 47.3 + - + -
290C ASP* 3.1 51.7 + - + +
293C LEU* 1.3 88.0 - - + +
295C PRO* 1.3 72.8 - - + +
297C LEU* 3.2 12.4 + - + +
298C GLU* 2.9 30.4 + - - +
320C PHE* 3.7 29.2 - + + -
321C LYS* 5.8 0.9 - - - -
322C ALA* 3.8 26.8 + - + +
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Residues in contact with PRO 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 3.6 30.3 - - + -
290C ASP 3.9 0.2 - - - +
291C ASP 3.3 30.5 - - - +
292C ASN* 3.6 4.7 - - - +
293C LEU 3.6 2.9 - - - -
294C TYR* 1.3 94.9 - - + +
296C GLN* 1.3 55.9 + - - +
298C GLU* 3.6 16.2 - - - +
299C ARG* 3.2 23.6 + - - +
1D G 5.0 1.1 - - - +
2D G 3.3 41.4 + - - +
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Residues in contact with GLN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ILE* 4.1 4.3 - - - +
292C ASN* 3.2 15.9 + - - +
293C LEU 2.9 10.7 + - - +
295C PRO* 1.3 74.9 - - - +
297C LEU* 1.3 59.5 + - - +
298C GLU 3.2 0.2 - - - -
299C ARG* 3.3 6.5 + - - +
300C ALA* 2.9 32.1 + - - +
400C LEU 4.0 2.1 - - - +
401C GLY* 4.3 4.7 - - - -
402C LYS 3.7 2.4 + - - -
403C ASN* 2.8 50.6 + - - +
404C VAL* 2.8 30.2 + - + +
1D G 3.1 28.0 + - - +
2D G 3.7 20.4 - - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 4.0 13.2 - - + -
293C LEU* 2.9 30.8 + - + +
294C TYR* 3.7 14.1 - - + +
296C GLN* 1.3 73.6 - - - +
298C GLU* 1.3 65.4 + - - +
300C ALA* 4.6 1.1 - - - +
301C SER* 3.0 28.6 + - - -
320C PHE* 3.7 38.1 - - + -
321C LYS 4.8 3.4 - - - +
322C ALA* 4.3 19.5 - - + -
327C CYS* 4.3 11.9 - - + -
329C LEU* 3.9 20.9 - - + +
404C VAL* 4.0 19.3 - - + -
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 3.9 10.9 - - - +
168C ARG* 2.8 49.6 + - - -
294C TYR* 2.9 20.6 + - - +
295C PRO* 3.6 12.6 - - - +
297C LEU* 1.3 78.1 - - - +
299C ARG* 1.3 56.3 + - - +
301C SER* 3.9 1.8 - - - -
302C ARG* 3.0 36.0 + - - +
320C PHE* 3.7 25.8 - - + -
2D G 5.2 1.4 + - - -
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C PRO 3.2 12.0 + - - +
296C GLN* 3.3 8.7 + - - +
298C GLU* 1.3 76.2 - - - +
300C ALA* 1.3 60.6 + - - +
302C ARG* 3.0 20.5 + - - +
303C LYS* 2.8 51.5 + - + +
399C THR* 2.6 48.2 + - - +
401C GLY* 3.7 19.1 - - - +
2D G 4.1 10.3 + - - +
3D C 2.8 46.7 + - - +
23D G 5.3 2.2 + - - -
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C GLN 2.9 19.6 + - - +
297C LEU* 4.2 3.1 - - - +
299C ARG* 1.3 73.4 - - - +
301C SER* 1.3 62.5 + - - +
303C LYS* 3.4 1.4 + - - +
304C ILE* 3.1 29.5 + - - +
329C LEU* 3.9 19.7 - - + -
400C LEU* 3.5 37.9 - - + +
404C VAL* 4.0 9.9 - - + -
408C ILE* 5.1 0.2 - - + -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU 3.0 21.1 + - - -
298C GLU* 3.9 3.4 - - - -
300C ALA* 1.3 75.9 - - - +
302C ARG* 1.3 56.9 + - - +
305C PHE* 3.0 28.3 + - - +
318C SER* 3.3 27.7 + - - -
319C ALA 4.1 9.5 + - - -
320C PHE* 4.1 13.8 - - - -
329C LEU* 4.3 10.0 - - - +
331C PHE* 3.5 18.6 - - - -
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Residues in contact with ARG 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C GLU* 3.0 32.7 + - - +
299C ARG* 3.0 24.0 + - - +
301C SER* 1.3 75.4 - - - +
303C LYS* 1.3 61.2 + - - +
305C PHE* 3.1 8.2 + - + +
306C GLU* 2.8 58.5 + - + +
318C SER* 5.6 1.3 - - - -
3D C 3.2 33.7 + - - -
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Residues in contact with LYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C ARG* 2.8 58.4 + - + +
300C ALA 3.9 3.4 - - - +
302C ARG* 1.3 80.5 - - + +
304C ILE* 1.3 58.4 + - - +
306C GLU* 3.4 23.4 + - - +
307C PHE* 3.0 27.2 + - - +
310C ARG* 4.7 1.0 + - - -
392C TYR* 3.6 17.0 + - - +
399C THR* 4.0 21.5 + - + +
400C LEU* 3.9 10.1 - - + -
22D U 3.9 27.6 + - - +
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Residues in contact with ILE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 4.3 7.6 - - + -
300C ALA 3.1 18.6 + - - +
303C LYS* 1.3 73.0 - - - +
305C PHE* 1.3 61.4 + - - +
307C PHE* 3.3 5.3 + - + +
308C LEU* 2.9 28.3 + - + +
329C LEU* 3.7 25.1 - - + -
331C PHE* 3.4 25.6 - - + -
389C VAL* 3.6 42.4 - - + -
392C TYR* 4.0 24.0 - - + -
393C ALA* 5.2 3.8 - - + -
400C LEU* 4.3 15.0 - - + -
408C ILE* 5.5 0.4 - - + -
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Residues in contact with PHE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 5.3 3.6 - - - -
370A GLU* 5.7 2.9 - - - -
301C SER 3.0 21.0 + - - +
302C ARG* 3.3 10.8 - - + +
304C ILE* 1.3 76.5 - - - +
306C GLU* 1.3 64.3 + - + +
308C LEU* 3.0 20.4 + - - +
309C GLU* 3.1 40.5 + - - +
315C PRO* 3.5 39.3 - - + +
316C LEU 4.1 16.4 - - - -
317C ARG* 4.1 13.2 - - - -
318C SER* 3.9 20.4 - - - +
331C PHE* 4.4 5.6 - + + -
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ARG* 2.8 47.0 + - + +
303C LYS* 3.7 29.7 + - - +
305C PHE* 1.3 71.1 - - + +
307C PHE* 1.3 66.4 + - - +
309C GLU* 3.1 34.2 - - + +
310C ARG* 3.1 25.2 + - - +
21D C 5.4 4.0 + - - -
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Residues in contact with PHE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C LYS 3.0 15.1 + - - +
304C ILE* 3.5 10.8 - - + +
306C GLU* 1.3 74.9 - - - +
308C LEU* 1.3 75.4 + - + +
310C ARG* 3.4 21.1 - - - +
311C GLU* 3.1 50.5 + - + +
313C PHE* 5.1 1.6 - + - -
382C PHE* 4.1 14.6 - + - -
388C GLY* 3.1 44.0 - - - -
389C VAL* 3.6 11.2 - - + -
392C TYR* 3.3 45.8 - + + -
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C PHE* 4.2 0.9 - - + -
304C ILE* 2.9 24.6 + - + +
305C PHE* 3.0 9.2 + - - +
307C PHE* 1.3 81.7 - - + +
309C GLU* 1.3 62.3 + - - +
311C GLU* 3.4 6.5 + - - -
313C PHE* 3.1 44.8 + - + +
315C PRO* 3.6 16.4 - - + -
331C PHE* 3.9 31.9 - - + -
333C CYS* 4.1 26.0 - - - -
385C PRO* 4.2 9.9 - - + +
389C VAL* 3.5 24.2 - - + -
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PHE* 3.1 30.9 + - - +
306C GLU* 3.1 38.7 - - - +
308C LEU* 1.3 76.6 - - - +
310C ARG* 1.3 55.8 + - + +
311C GLU 3.0 0.2 - - - -
312C ASN* 2.8 26.5 + - - -
314C MET* 4.8 1.4 + - - +
315C PRO* 3.6 20.5 - - + +
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Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LYS 4.7 1.8 + - - -
306C GLU* 3.1 23.8 + - - +
307C PHE* 3.4 40.9 - - - +
309C GLU* 1.3 76.7 - - + +
311C GLU* 1.3 67.1 + - - +
312C ASN* 3.3 9.3 + - - +
392C TYR* 3.3 33.5 + - - -
396C HIS* 5.3 0.4 + - - -
503C GOL 5.2 4.0 + - - -
20D C 5.1 4.7 - - - -
21D C 3.6 49.2 + - - -
22D U 5.2 0.6 + - - -
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PHE* 3.1 35.3 + - + +
308C LEU 3.9 0.2 - - - +
309C GLU 3.0 1.0 - - - -
310C ARG* 1.3 87.1 + - - +
312C ASN* 1.3 72.1 + - - +
313C PHE* 3.3 27.5 + - + -
338C ILE* 4.7 2.1 - - - +
380C ARG* 4.6 12.3 + - - +
382C PHE* 3.5 32.0 - - + -
503C GOL 3.3 44.2 + - - -
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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
------------------------------------------------------------
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