Contacts of the helix formed by residues 269 - 288 (chain D) in PDB entry 1P7L
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 LYS 269 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684C PPK 5.7 1.3 - - - +
685C SAM 3.1 38.2 + - + +
38D ARG* 4.4 2.6 - - - +
39D VAL 3.1 26.4 + - - +
40D ALA* 4.1 7.4 - - - -
98D GLN* 3.9 8.9 - - - +
117D GLY* 4.8 9.1 - - - -
118D ASP* 6.5 0.2 - - - -
265D LYS* 3.6 28.9 - - + -
266D ASP* 2.9 51.2 + - - +
267D PRO 2.8 1.7 - - - +
268D SER* 1.3 82.1 + - - +
270D VAL* 1.3 66.2 + - - +
271D ASP* 2.9 7.6 + - + +
272D ARG* 2.9 13.3 + - + +
273D SER* 3.1 9.9 + - - -
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ALA* 4.1 13.7 - - + -
117D GLY 4.1 0.7 - - - +
118D ASP* 3.6 39.7 - - + +
119D GLN 5.3 2.5 - - - +
120D GLY* 6.3 0.2 - - - -
122D MET* 2.9 18.3 - - + +
268D SER 3.5 4.0 + - - +
269D LYS* 1.3 70.9 - - - +
271D ASP* 1.3 64.6 + - - +
272D ARG 3.1 0.2 - - - -
273D SER* 3.3 10.3 + - - +
274D ALA* 2.9 25.6 + - + +
275D ALA 3.6 0.2 + - - -
300D TYR* 3.8 44.0 - - + -
337D PRO* 5.2 5.2 - - + -
340D LEU* 5.0 6.7 - - + -
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Residues in contact with ASP 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C PPK 3.0 30.1 + - - +
118D ASP* 5.1 5.3 - - - +
119D GLN 5.0 3.3 - - - +
120D GLY* 5.4 1.7 - - - -
121D LEU 5.3 1.2 - - - +
122D MET* 3.3 16.5 - - - +
260D GLY* 3.6 22.3 + - - +
261D ALA 3.6 15.5 - - - +
262D PHE* 3.1 20.9 - - - -
265D LYS* 3.1 11.9 + - + +
269D LYS* 2.9 4.0 + - + +
270D VAL* 1.3 79.8 - - - +
272D ARG* 1.3 59.1 + - - +
275D ALA* 3.1 10.9 - - - +
687D MG 3.2 17.7 - - - -
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Residues in contact with ARG 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP* 2.6 41.0 + - - -
27D LEU* 4.3 0.8 - - - +
261D ALA 4.8 0.2 - - - +
262D PHE* 2.8 45.6 + - + +
263D SER* 3.6 1.0 - - - +
264D GLY 3.8 0.6 - - - +
265D LYS* 3.3 25.6 + - + +
266D ASP 5.1 4.3 - - - +
267D PRO* 5.3 2.5 - - + -
269D LYS* 2.9 9.5 + - + +
271D ASP* 1.3 80.6 - - + +
273D SER* 1.3 59.5 + - - +
274D ALA 3.6 0.4 - - - -
275D ALA* 3.5 0.9 - - - +
276D TYR* 2.7 66.0 + - + -
346D LEU* 6.3 0.4 - - + -
351D TYR* 3.4 27.4 - - - +
354D THR* 3.1 25.7 - - - +
359D HIS* 3.6 5.3 - - - -
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Residues in contact with SER 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D PRO* 2.7 30.3 + - - -
269D LYS 3.1 7.7 + - - -
270D VAL* 3.3 8.1 - - - +
272D ARG* 1.3 76.4 - - - +
274D ALA* 1.3 61.1 + - - +
275D ALA 3.1 1.3 - - - -
276D TYR* 3.5 3.1 + - - +
277D ALA* 2.9 28.8 + - - +
340D LEU* 3.9 20.5 - - - +
341D ILE* 5.1 0.4 - - - -
344D LEU* 4.4 3.6 - - - +
346D LEU* 3.7 26.5 - - - -
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Residues in contact with ALA 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D MET* 3.5 10.3 - - + -
270D VAL* 2.9 24.8 + - + +
273D SER* 1.3 73.7 + - - +
275D ALA* 1.3 61.0 + - - +
277D ALA* 3.8 1.8 - - - +
278D ALA* 3.0 28.1 + - - +
298D VAL* 4.1 6.3 - - + +
300D TYR* 3.3 44.0 - - + +
335D LEU* 6.2 0.4 - - - +
340D LEU* 4.2 8.0 - - + +
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D MET* 4.1 16.1 - - + +
123D PHE 4.9 5.6 - - - +
124D GLY* 4.8 1.2 - - - -
262D PHE* 3.4 25.6 - - + -
270D VAL 3.6 2.0 + - - -
271D ASP 3.1 24.2 - - - +
272D ARG 3.5 2.2 - - - +
274D ALA* 1.3 77.9 - - - +
276D TYR* 1.3 68.2 + - - +
278D ALA* 2.9 15.7 + - - +
279D ARG* 3.0 12.5 + - - +
360D PHE* 4.5 4.3 - - + -
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Residues in contact with TYR 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D PHE* 4.1 14.1 - + - -
272D ARG* 2.7 62.3 + - + +
273D SER* 3.7 6.3 - - - +
274D ALA 3.4 0.2 - - - -
275D ALA* 1.3 80.6 - - + +
277D ALA* 1.3 62.3 + - - +
279D ARG* 2.9 16.1 + - - +
280D TYR* 3.0 12.1 + - - +
344D LEU* 4.3 6.1 - - + -
346D LEU* 4.4 10.3 - - + -
351D TYR* 3.7 8.8 - + - -
354D THR* 3.9 3.8 - - - +
359D HIS* 3.0 33.4 + - + -
360D PHE* 3.8 17.0 - + - -
367D TRP* 3.5 60.5 - + + +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D SER 2.9 18.1 + - - +
274D ALA 3.9 3.4 - - - +
276D TYR* 1.3 75.9 - - - +
278D ALA* 1.3 59.0 + - - +
280D TYR* 3.1 10.6 - - - +
281D VAL* 3.0 25.1 - - - +
335D LEU* 4.4 8.5 - - + -
340D LEU* 3.8 21.3 - - + -
343D MET* 3.2 31.3 - - + +
344D LEU* 3.9 3.7 - - + +
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D MET 5.0 0.4 - - - +
123D PHE* 4.2 2.9 - - - -
124D GLY* 3.4 26.1 - - - +
274D ALA 3.0 15.2 + - - +
275D ALA* 2.9 13.0 + - - +
277D ALA* 1.3 73.8 - - - +
279D ARG* 1.3 64.7 + - - +
280D TYR 3.1 1.6 - - - -
281D VAL* 4.3 3.0 - - - +
282D ALA* 3.2 24.8 + - - +
296D ILE* 4.1 21.3 - - + +
298D VAL* 4.9 8.3 - - + -
335D LEU* 6.4 0.2 - - - -
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Residues in contact with ARG 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLY* 3.9 0.8 - - - -
125D TYR 3.0 27.4 + - - +
126D ALA* 3.6 2.8 - - - +
132D VAL 3.6 11.9 + - - -
133D LEU 2.9 26.7 + - - -
134D MET* 3.7 17.4 - - - +
251D TYR* 3.3 20.4 + - - +
275D ALA 3.0 4.4 + - - -
276D TYR 2.9 7.0 + - - +
278D ALA* 1.3 76.9 - - - +
280D TYR* 1.3 55.8 + - - +
282D ALA* 3.8 0.2 - - - +
283D LYS* 2.8 55.3 + - - +
360D PHE* 3.3 33.7 - - + -
367D TRP* 3.9 16.4 - - + +
368D GLU* 2.7 53.0 + - - +
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Residues in contact with TYR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D TYR 3.0 11.4 + - - +
277D ALA* 3.1 13.0 - - - +
278D ALA 3.1 0.2 - - - -
279D ARG* 1.3 77.8 - - - +
281D VAL* 1.3 57.3 + - - +
283D LYS* 4.0 0.9 - - - +
284D ASN* 2.9 51.9 + - - -
333D PHE* 3.7 30.5 - + - -
343D MET* 3.4 36.8 + - + +
344D LEU* 4.0 13.5 - - + -
366D PRO 4.0 9.9 - - - -
367D TRP* 3.6 26.0 - - + +
369D LYS* 3.5 11.2 - - + -
371D ASP* 3.1 15.4 + - - -
372D LYS* 3.1 29.4 + - + +
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ALA* 3.0 19.0 + - + +
278D ALA* 4.3 4.0 - - - +
280D TYR* 1.3 74.2 - - + +
282D ALA* 1.3 59.4 + - - +
284D ASN 3.2 0.7 + - - -
285D ILE* 2.7 51.8 + - + +
296D ILE* 3.6 31.6 - - + -
329D VAL* 4.7 8.3 - - + -
333D PHE* 3.6 50.0 - - + -
335D LEU* 5.0 9.9 - - + -
343D MET* 5.5 0.2 - - + -
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLY 4.1 2.2 - - - +
125D TYR 3.7 30.1 - - - +
126D ALA* 3.2 10.0 - - - +
278D ALA 3.2 16.7 + - - +
279D ARG 3.8 1.1 - - - +
281D VAL* 1.3 84.6 - - - +
283D LYS* 1.3 65.4 + - - +
285D ILE* 3.2 8.1 + - - +
286D VAL* 3.2 9.7 + - - +
294D CYS* 3.7 26.8 - - - +
296D ILE* 4.5 4.7 - - + -
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Residues in contact with LYS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA* 3.3 9.5 - - - +
132D VAL 3.1 19.1 - - - -
133D LEU* 3.5 25.6 - - + +
279D ARG* 2.8 40.1 + - - +
280D TYR* 4.0 3.4 - - - +
282D ALA* 1.3 71.9 - - - +
284D ASN* 1.3 59.9 + - - +
286D VAL* 3.1 5.4 + - - +
287D ALA* 2.9 27.7 + - - +
363D GLU* 2.8 23.6 + - - -
367D TRP 4.8 0.4 - - - +
368D GLU* 2.5 66.9 + - - +
369D LYS* 5.7 0.4 - - - +
370D THR* 3.9 14.8 + - + +
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Residues in contact with ASN 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D TYR* 2.9 43.6 + - - +
281D VAL* 3.2 7.2 + - - +
283D LYS* 1.3 77.9 - - - +
285D ILE* 1.3 55.5 + - - +
287D ALA* 4.3 0.2 - - - -
288D ALA* 3.0 28.8 + - - +
333D PHE* 4.5 2.0 - - + -
369D LYS 3.1 24.4 + - - -
370D THR* 3.4 16.9 - - - +
371D ASP 4.4 0.2 - - - +
372D LYS* 3.2 15.6 + - - -
373D ALA* 2.9 32.4 + - - +
376D LEU* 3.8 13.0 - - + +
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Residues in contact with ILE 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D VAL* 2.7 45.5 + - + +
282D ALA 3.5 4.5 - - - +
283D LYS 3.1 0.2 - - - -
284D ASN* 1.3 71.5 - - - +
286D VAL* 1.3 65.2 + - - +
288D ALA* 3.2 7.1 + - - +
289D GLY 3.1 4.0 + - - -
290D LEU* 3.0 46.8 + - + -
291D ALA* 4.2 12.3 - - + -
294D CYS* 3.7 26.9 - - - -
296D ILE* 4.6 3.6 - - + -
312D VAL* 5.4 2.0 - - + -
325D LEU* 4.2 19.3 - - + -
328D LEU* 6.4 0.7 - - + -
329D VAL* 4.3 17.3 - - + -
333D PHE* 5.5 0.7 - - + -
376D LEU* 4.3 13.7 - - + -
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Residues in contact with VAL 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA* 3.9 14.8 - - + -
127D THR 4.5 0.2 - - - -
128D ASN* 4.2 11.9 - - + +
133D LEU* 4.0 24.5 - - + -
282D ALA 3.2 10.2 + - - +
283D LYS 3.1 7.2 + - - +
285D ILE* 1.3 76.2 - - - +
287D ALA* 1.3 57.9 - - - +
289D GLY* 2.7 24.6 + - - -
291D ALA* 3.2 26.7 - - + +
292D ASP* 3.7 23.6 - - - +
293D ARG* 3.8 11.0 - - - +
294D CYS* 4.3 4.3 - - - +
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Residues in contact with ALA 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D LEU* 5.1 10.7 - - + +
283D LYS 2.9 15.9 + - - +
284D ASN 3.9 0.4 - - - +
286D VAL* 1.3 73.5 - - - +
288D ALA* 1.3 59.4 + - - +
289D GLY* 2.8 10.5 + - - -
370D THR* 3.7 26.9 - - + +
373D ALA* 3.8 14.5 - - + +
374D GLN* 5.3 3.5 - - - +
377D ARG* 5.8 0.3 - - - -
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D ASN 3.0 21.4 + - - +
285D ILE 3.3 6.3 - - - +
286D VAL 3.1 0.2 - - - -
287D ALA* 1.3 75.7 - - - +
289D GLY* 1.3 59.6 + - - +
290D LEU* 3.2 22.6 + - + +
373D ALA* 3.3 30.9 - - - +
374D GLN* 5.8 0.7 - - - -
376D LEU* 3.9 2.9 - - + -
377D ARG* 2.9 34.4 + - - +
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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