Contacts of the helix formed by residues 269 - 293 (chain B) in PDB entry 3SAJ
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 2.9 52.7 + - - +
20B GLU* 4.1 14.5 + - - -
188B SER* 6.1 2.5 - - - -
189B GLU* 5.8 3.8 + - - -
219B ASP* 4.1 19.5 - - + +
220B ILE* 4.0 30.3 - - + -
240B TYR* 4.2 0.4 - - - -
267B ARG 3.6 3.8 + - - +
268B PRO* 1.3 74.7 - - - +
270B TYR* 1.3 67.9 + - + +
271B THR* 3.3 11.9 + - - +
272B SER* 3.0 13.4 + - - -
273B ALA* 3.0 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 3.2 30.8 + - - -
187B GLU* 3.4 8.7 + - - -
188B SER* 3.7 21.1 - - - -
214B ASN* 4.0 15.6 + - - -
215B LEU* 3.6 40.8 + - + +
216B GLY* 3.7 14.1 - - - -
219B ASP* 3.5 23.2 + - - +
236B GLN* 6.2 1.3 - - - +
237B LEU* 5.1 5.8 - - + -
238B VAL* 4.8 12.1 - - + -
240B TYR* 4.3 2.1 + - - +
268B PRO 4.0 0.2 + - - -
269B LYS* 1.3 75.5 - - + +
271B THR* 1.3 69.3 + - + +
273B ALA* 3.1 10.4 + - - +
274B LEU* 2.7 60.6 + - + +
332B THR* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 2.6 29.9 + - - +
70B PHE* 5.6 4.9 - - + -
93B PRO* 4.4 8.6 - - + +
108B ARG* 3.8 25.4 - - - +
187B GLU* 4.9 3.4 - - - +
269B LYS* 4.2 9.9 + - - +
270B TYR* 1.3 98.3 - - + +
272B SER* 1.3 56.4 + - - +
274B LEU* 3.3 9.5 + - - +
275B THR* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 2.8 37.7 + - - +
20B GLU* 3.7 19.4 + - - -
23B ALA* 3.2 25.9 - - - +
252B TRP* 5.1 2.0 - - - -
268B PRO* 4.4 8.5 - - - -
269B LYS 3.0 11.2 + - - -
271B THR* 1.3 75.1 + - - +
273B ALA* 1.3 61.3 + - - +
275B THR* 3.2 1.3 + - - -
276B TYR* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 3.8 19.7 - - + -
240B TYR* 5.6 2.5 - - + +
268B PRO* 5.0 6.0 - - + +
269B LYS 3.0 11.0 + - - +
270B TYR* 3.1 9.4 + - - +
272B SER* 1.3 75.5 - - - +
274B LEU* 1.3 62.1 - - - +
276B TYR* 3.4 2.8 + - - +
277B ASP* 3.0 27.7 + - - -
331B LEU* 4.0 23.2 - - + +
332B THR* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 3.6 21.3 - - + +
107B LEU* 3.3 41.4 - - + +
108B ARG* 3.7 27.6 - - + -
109B PRO* 4.9 0.9 - - + -
237B LEU* 4.2 7.6 - - + -
270B TYR* 2.7 42.6 + - + +
271B THR* 3.4 10.3 - - - +
273B ALA* 1.3 76.9 - - - +
275B THR* 1.3 54.8 + - - +
277B ASP* 3.4 4.6 + - + +
278B GLY 3.0 22.9 + - - -
332B THR* 3.9 14.4 - - + +
343B ARG* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 5.3 0.9 - - + -
20B GLU* 3.4 37.4 - - + +
24B PHE* 3.8 19.5 - - + +
68B PHE* 3.8 27.1 - - + -
70B PHE* 3.9 3.4 - - + -
93B PRO* 3.8 14.6 - - - +
271B THR 2.9 14.5 + - - -
272B SER* 3.2 10.3 + - - -
274B LEU* 1.3 72.4 - - - +
276B TYR* 1.3 63.3 + - - +
278B GLY* 3.3 1.7 + - - -
279B VAL* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 4.1 10.5 - - + +
26B PHE* 3.3 29.2 - + - -
27B ALA* 3.6 23.7 - - + +
30B GLN* 2.4 32.7 + - - -
248B ILE* 3.5 34.4 - - + +
251B GLN* 4.6 0.7 + - - -
252B TRP* 5.2 4.9 - + + -
272B SER 2.9 18.7 + - - +
273B ALA 3.6 5.2 - - - +
275B THR* 1.3 75.0 - - - +
277B ASP* 1.3 62.2 + - - +
279B VAL* 3.4 10.0 + - - +
280B LYS* 3.0 61.7 + - + +
331B LEU* 3.4 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.8 2.9 - - + -
273B ALA 3.0 15.9 + - - +
274B LEU* 3.8 5.6 - - + +
275B THR 3.3 0.2 - - - -
276B TYR* 1.3 78.9 - - - +
278B GLY* 1.3 57.1 + - - +
280B LYS* 2.4 41.0 + - - +
281B VAL* 2.9 31.0 + - + +
328B PHE* 3.8 1.3 - - + -
330B GLY* 3.8 5.3 - - - -
331B LEU* 3.1 11.4 + - - +
332B THR* 2.5 46.2 + - - +
335B VAL* 3.9 14.2 - - + +
343B ARG* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.1 8.7 - - - -
91B ILE* 4.3 3.0 - - - +
107B LEU* 3.4 34.5 - - - +
274B LEU 3.0 10.3 + - - -
275B THR 3.3 3.7 + - - -
277B ASP* 1.3 73.2 - - - +
279B VAL* 1.3 63.8 + - - +
281B VAL* 3.4 3.3 + - - +
282B MET* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.5 40.6 - - + +
27B ALA* 3.7 29.2 - - + +
28B LEU* 3.9 24.2 - - + -
31B LEU* 4.0 10.1 - - + -
37B LEU* 4.0 2.8 - - + +
68B PHE* 5.0 0.4 - - + -
275B THR 3.3 14.5 + - - +
276B TYR 3.6 7.6 - - - +
277B ASP 3.3 0.4 - - - -
278B GLY* 1.3 75.6 - - - +
280B LYS* 1.3 60.6 + - + +
282B MET* 3.3 11.4 + - + +
283B ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 5.1 2.2 - - + +
31B LEU* 5.0 12.3 - - + -
248B ILE* 4.6 3.0 - - - +
276B TYR* 3.0 50.8 + - + +
277B ASP* 2.4 35.3 + - - +
279B VAL* 1.3 76.7 - - + +
281B VAL* 1.3 59.3 + - - +
283B ALA* 3.8 6.0 - - - +
284B GLU* 2.8 36.9 + - + +
328B PHE* 3.6 26.9 - - + -
329B GLU 4.9 1.6 - - - -
330B GLY* 3.5 15.7 - - - -
331B LEU 3.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 4.9 4.5 - - + -
105B LEU* 3.5 29.8 - - + -
107B LEU* 3.8 20.6 - - + -
277B ASP 2.9 19.3 + - - +
278B GLY* 3.4 9.9 - - - +
279B VAL 3.3 0.2 - - - -
280B LYS* 1.3 74.2 - - - +
282B MET* 1.3 64.9 + - - +
284B GLU* 3.8 1.2 - - - +
285B ALA* 3.0 23.6 + - - +
323B LEU* 4.1 19.1 - - + +
326B VAL* 4.0 4.9 - - + +
328B PHE* 3.9 10.1 - - + -
335B VAL* 3.9 24.7 - - + -
337B PHE* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.7 39.0 - - + -
24B PHE* 4.4 9.6 - - + -
28B LEU* 5.9 1.3 - - + -
37B LEU* 4.0 16.8 - - + -
66B ALA* 4.8 2.7 - - + -
68B PHE* 3.8 23.8 - - + -
91B ILE* 3.9 33.0 - - + -
278B GLY 3.1 17.0 + - - +
279B VAL* 3.5 15.7 - - + +
280B LYS 3.3 0.2 - - - -
281B VAL* 1.3 80.3 - - - +
283B ALA* 1.3 62.2 + - - +
285B ALA* 3.5 1.6 + - - +
286B PHE* 3.1 32.7 + - + -
323B LEU* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.0 33.9 - - + -
37B LEU* 4.0 9.8 - - + +
279B VAL 3.0 16.1 + - - +
280B LYS* 3.2 4.9 + - - +
282B MET* 1.3 75.4 - - - +
284B GLU* 1.3 66.8 + - - +
286B PHE* 3.0 15.0 + - - +
287B GLN* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LYS* 2.8 25.5 + - + +
281B VAL 3.8 0.2 - - - +
283B ALA* 1.3 73.6 - - - +
285B ALA* 1.3 55.1 + - - +
287B GLN* 3.4 15.9 + - - +
288B SER* 2.9 28.9 + - - -
291B ARG* 4.7 13.0 + - - -
326B VAL* 3.6 22.7 - - + -
327B ARG 5.5 1.4 - - - +
328B PHE* 3.9 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL 3.0 8.5 + - - +
282B MET 3.5 2.5 - - - +
284B GLU* 1.3 75.2 - - - +
286B PHE* 1.3 66.4 + - + +
288B SER* 3.2 1.8 + - - -
289B LEU* 3.0 21.2 + - + +
319B ILE* 4.8 0.9 - - + +
322B ALA* 3.4 24.5 - - + +
323B LEU* 3.0 53.4 - - + +
326B VAL* 3.9 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET* 3.5 13.9 - - - +
7B ILE* 3.7 45.1 - - + -
9B ILE* 4.4 11.7 - - + -
35B PRO* 3.9 20.3 - - + +
37B LEU* 4.2 7.2 - - + -
65B TYR* 3.9 20.9 - + + -
66B ALA* 4.9 4.5 - - + -
282B MET* 3.1 28.4 + - + -
283B ALA* 3.0 9.2 + - - +
285B ALA* 1.3 80.8 - - + +
287B GLN* 1.3 57.5 + - - +
289B LEU* 3.4 13.7 + - + -
290B ARG* 3.0 27.4 + - - +
296B ILE* 5.3 1.6 - - + -
319B ILE* 3.8 35.9 - - + -
323B LEU* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 4.3 22.2 + - + +
34B PRO 3.2 18.3 + - - +
35B PRO* 3.7 12.3 + - - +
283B ALA* 3.0 29.7 + - + +
284B GLU* 3.6 19.5 - - - +
285B ALA 3.3 0.2 - - - -
286B PHE* 1.3 75.0 - - - +
288B SER* 1.3 57.6 + - - +
290B ARG* 2.8 37.1 + - - +
291B ARG* 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU 2.9 18.3 + - - -
285B ALA* 3.2 9.4 + - - -
287B GLN* 1.3 74.9 - - - +
289B LEU* 1.3 63.4 + - - +
291B ARG* 3.3 25.9 + - - +
292B GLN* 3.0 40.3 + - - +
322B ALA* 4.6 13.5 - - - +
325B GLN* 6.0 2.1 - - - +
326B VAL* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET* 3.0 18.2 - - + -
285B ALA 3.0 14.2 + - - +
286B PHE* 3.6 17.5 - - + +
287B GLN 3.3 0.2 - - - -
288B SER* 1.3 76.1 - - - +
290B ARG* 1.3 60.6 + - - +
292B GLN* 3.4 7.7 + - - +
293B ARG 3.1 16.6 + - - -
294B ILE* 3.3 41.0 + - + +
296B ILE* 3.8 12.3 - - + -
318B ASP* 3.6 24.7 - - + +
319B ILE* 3.8 40.2 - - + -
322B ALA* 3.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET* 3.4 26.2 - - + +
33B GLU* 4.8 9.9 + - - -
34B PRO* 3.3 32.0 + - - +
35B PRO* 4.1 16.2 - - - -
286B PHE 3.0 12.6 + - - +
287B GLN* 2.8 40.8 + - - +
288B SER 3.2 0.2 - - - -
289B LEU* 1.3 78.4 - - - +
291B ARG* 1.3 62.5 + - - +
293B ARG* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 4.7 10.9 + - - -
287B GLN* 2.9 34.4 + - - +
288B SER* 3.3 35.3 + - - +
290B ARG* 1.3 76.0 - - - +
292B GLN* 1.3 62.3 + - + +
293B ARG* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER* 3.0 28.5 + - - +
289B LEU* 3.9 10.0 - - - +
291B ARG* 1.3 78.7 - - + +
293B ARG* 1.3 70.2 + - - +
294B ILE* 3.2 29.7 + - + +
322B ALA* 5.8 1.2 - - - +
325B GLN* 5.5 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA 5.2 4.9 + - - +
289B LEU 3.1 5.0 + - - -
290B ARG* 3.2 16.7 + - - +
291B ARG 4.5 4.3 - - - +
292B GLN* 1.3 81.8 - - - +
294B ILE* 1.3 62.5 + - - +
295B ASP* 3.4 7.6 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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