Contacts of the helix formed by residues 279 - 301 (chain B) in PDB entry 3KG2
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 279 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.4 20.9 + - - +
25B GLU* 5.0 1.6 - - - +
229B ASP* 3.2 17.0 - - + +
278B ILE* 1.3 77.0 - - - +
280B TYR* 1.3 67.5 + - + +
281B THR* 3.8 16.8 - - + +
282B SER* 2.9 5.7 + - - +
283B ALA* 2.9 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PRO 5.4 2.0 - - - -
114B ARG* 5.4 3.8 - - + -
141B ARG* 4.9 13.2 - - - -
197B GLU* 6.1 1.2 - - - -
198B ARG* 6.0 7.0 - - + -
224B ASN* 4.7 12.7 - - + +
225B LEU* 3.7 41.5 - - + +
226B GLY* 3.6 17.9 - - - -
229B ASP* 2.9 23.4 + - + +
246B GLN* 5.9 0.4 - - - +
247B ILE* 3.5 24.4 - - + +
248B VAL* 4.2 12.8 - - + -
278B ILE 3.5 1.2 + - - -
279B LYS* 1.3 72.3 - - + +
281B THR* 1.3 80.5 + - + +
283B ALA* 3.7 1.1 - - - +
284B LEU* 3.0 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 2.8 30.9 + - - +
76B PHE* 4.9 8.6 - - + -
99B PRO* 3.9 10.5 - - + +
100B SER* 6.5 0.4 - - - -
279B LYS* 3.8 10.3 - - + +
280B TYR* 1.3 110.5 - - + +
282B SER* 1.3 59.0 + - - +
284B LEU* 3.5 7.8 + - - +
285B THR* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.3 38.8 + - - +
25B GLU* 3.3 23.4 + - - +
28B ALA* 3.4 8.3 - - - +
278B ILE* 3.6 19.1 - - - -
279B LYS* 2.9 8.7 + - - +
281B THR* 1.3 78.7 + - - +
283B ALA* 1.3 64.5 + - - +
285B THR* 3.1 17.9 + - - -
286B TYR* 3.1 10.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
248B VAL* 3.6 30.3 - - + -
278B ILE* 3.5 18.1 - - + +
279B LYS 2.9 11.5 + - - +
280B TYR 3.7 2.9 - - - +
281B THR 3.4 0.2 - - - -
282B SER* 1.3 76.6 - - - +
284B LEU* 1.3 59.0 + - + +
286B TYR* 3.4 4.1 + - - +
287B ASP* 3.1 32.7 + - - +
341B LEU* 4.1 19.9 - - + +
342B SER* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PRO* 3.7 27.6 - - + +
113B MET* 3.3 30.4 - - + +
114B ARG* 3.6 32.5 - - + +
115B PRO* 4.8 4.7 - - + -
225B LEU* 5.3 0.9 - - + -
247B ILE* 5.4 4.3 - - + -
280B TYR* 3.0 34.3 + - + +
281B THR* 3.8 1.1 - - - +
282B SER 3.2 0.2 - - - -
283B ALA* 1.3 73.9 - - + +
285B THR* 1.3 56.6 + - - +
287B ASP* 3.2 5.7 + - + +
288B ALA* 2.8 34.5 + - - +
342B SER* 3.6 31.0 - - - +
353B ARG* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.4 0.9 - - + -
25B GLU* 3.3 27.7 + - - +
29B PHE* 3.6 21.3 - - + +
74B PHE* 3.4 29.6 - - + -
76B PHE* 3.7 8.8 - - - -
99B PRO* 3.7 11.3 - - - +
281B THR 3.0 16.8 + - - -
282B SER* 3.1 12.7 + - - -
284B LEU* 1.3 77.0 - - - +
286B TYR* 1.3 61.7 + - - +
288B ALA* 3.1 16.5 + - - +
289B VAL* 3.3 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 3.9 18.6 + - + +
31B VAL* 4.2 7.0 - - + -
32B GLY* 3.7 26.7 - - - -
35B GLN* 3.3 25.3 + - + +
36B PHE* 3.5 31.1 - + - -
254B LEU* 5.8 4.2 - - + +
258B PHE* 3.4 38.0 - + + -
282B SER 3.1 9.4 + - - +
283B ALA* 3.6 7.4 - - - +
285B THR* 1.3 78.2 - - - +
287B ASP* 1.3 78.4 + - - +
288B ALA 3.3 0.5 + - - -
289B VAL* 3.3 15.7 + - - +
290B GLN* 3.5 9.6 + - - -
340B GLY* 6.0 0.2 - - - -
341B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 4.3 4.3 - - - -
283B ALA 3.1 17.7 + - - +
284B LEU* 3.7 7.4 - - + +
286B TYR* 1.3 88.2 - - - +
288B ALA* 1.3 65.5 + - - +
290B GLN* 3.4 10.1 + - - +
291B VAL* 3.1 27.3 + - - +
340B GLY* 3.5 11.1 - - - -
341B LEU* 3.0 21.2 + - - +
342B SER* 3.0 37.6 + - - +
345B ILE* 3.8 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 3.4 33.4 - - + -
97B ILE* 3.9 5.8 - - + +
113B MET* 3.7 19.7 - - + -
284B LEU 2.8 13.9 + - - +
285B THR 3.1 11.0 + - - +
287B ASP* 1.3 75.1 - - - +
289B VAL* 1.3 65.0 + - + +
291B VAL* 3.1 4.8 + - - +
292B MET* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.8 42.2 - - + +
32B GLY* 3.4 32.3 - - - +
33B MET* 3.8 15.5 - - - +
36B PHE* 4.1 4.7 - - + -
43B LEU* 4.9 5.3 - - + +
285B THR 3.3 13.9 + - - +
286B TYR* 3.6 7.6 - - - +
287B ASP 3.3 0.2 - - - -
288B ALA* 1.3 77.1 - - + +
290B GLN* 1.3 58.0 + - - +
292B MET* 3.3 10.4 + - - +
293B THR* 3.0 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 3.5 49.4 - - + -
286B TYR* 3.5 5.4 + - - +
287B ASP* 3.4 15.1 + - - +
288B ALA 3.2 0.6 - - - -
289B VAL* 1.3 79.2 - - - +
291B VAL* 1.3 57.7 + - - +
293B THR* 3.4 2.6 + - - -
294B GLU* 3.0 28.5 + - + +
338B VAL* 3.3 36.5 - - + +
339B GLU 3.3 25.4 + - - +
340B GLY* 4.0 9.7 - - - -
345B ILE* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 5.8 2.0 - - + -
111B ILE* 5.0 3.6 - - + -
113B MET* 4.3 10.1 - - + -
287B ASP 3.1 17.8 + - - +
288B ALA* 3.1 8.8 + - - +
290B GLN* 1.3 77.4 - - - +
292B MET* 1.3 57.8 + - + +
294B GLU 3.9 0.2 - - - -
295B ALA* 3.0 27.4 + - - +
333B LEU* 4.1 18.2 - - + +
336B VAL* 3.5 29.8 - - + +
338B VAL* 4.9 3.4 - - + -
345B ILE* 4.2 29.4 - - + -
347B PHE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.7 42.8 - - + -
29B PHE* 5.4 4.3 - - - -
43B LEU* 4.5 11.9 - - + +
72B ALA* 4.1 19.7 - - + -
74B PHE* 4.1 26.5 - - + +
97B ILE* 4.3 18.6 - - + -
288B ALA 3.0 21.0 + - - +
289B VAL* 3.7 8.5 - - - +
291B VAL* 1.3 74.7 - - + +
293B THR* 1.3 63.9 + - - +
295B ALA* 3.7 1.0 - - - +
296B PHE* 3.1 24.6 + - - +
333B LEU* 3.8 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 3.7 38.7 + - + +
38B THR* 5.4 3.4 - - + -
41B PHE* 3.5 25.7 - - + -
43B LEU* 4.2 14.9 - - - +
289B VAL* 3.0 19.0 + - - +
290B GLN 3.7 5.4 - - - -
292B MET* 1.3 75.6 - - - +
294B GLU* 1.3 61.9 + - - +
295B ALA 3.2 0.2 + - - -
296B PHE 3.3 1.4 + - - -
297B ARG* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN* 3.0 16.8 + - + +
293B THR* 1.3 78.4 - - - +
295B ALA* 1.3 56.7 + - - +
297B ARG* 3.7 8.1 - - - +
298B ASN* 3.1 58.6 + - - +
336B VAL* 3.8 26.9 - - + -
337B GLN 5.0 0.7 - - - +
338B VAL* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL 3.0 18.9 + - - +
292B MET 3.7 2.2 - - - +
293B THR 3.1 0.2 - - - -
294B GLU* 1.3 74.0 - - - +
296B PHE* 1.3 64.7 + - - +
297B ARG 3.1 2.0 + - - -
298B ASN* 3.3 11.0 + - - +
299B LEU* 3.4 9.6 + - - +
329B ILE* 6.4 0.2 - - + -
332B ALA* 3.7 19.4 - - + +
333B LEU* 3.4 37.7 - - + +
336B VAL* 3.6 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.6 33.1 - - + +
41B PHE* 4.1 13.1 - - + -
43B LEU* 5.6 1.6 - - + -
292B MET 3.1 16.0 + - - +
293B THR 4.0 2.2 - - - +
295B ALA* 1.3 79.3 - - - +
297B ARG* 1.3 59.2 + - - +
299B LEU* 3.6 14.2 + - + +
300B ARG* 3.5 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.7 20.8 - - + -
293B THR* 3.0 19.7 + - + +
294B GLU* 3.7 13.2 - - - +
295B ALA 3.1 0.2 - - - -
296B PHE* 1.3 76.2 - - - +
298B ASN* 1.3 63.9 + - - +
299B LEU 3.1 4.7 - - - -
300B ARG* 3.3 5.3 + - - +
301B LYS* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 3.1 48.1 + - - +
295B ALA* 3.3 5.8 + - - +
297B ARG* 1.3 78.4 - - - +
299B LEU* 1.3 63.4 + - + +
301B LYS* 4.2 7.2 - - - +
302B GLN* 3.0 25.6 + - - +
332B ALA* 5.1 5.6 + - + +
335B GLN* 5.2 5.5 + - - +
336B VAL* 4.8 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 3.4 6.4 + - - +
296B PHE* 3.8 13.9 - - - +
297B ARG 3.1 1.0 - - - -
298B ASN* 1.3 84.9 - - + +
300B ARG* 1.3 61.6 + - - +
301B LYS 3.4 0.2 - - - -
302B GLN* 3.5 2.1 + - + -
303B ARG 3.4 2.4 + - - -
304B ILE* 3.1 61.7 + - + +
306B ILE* 3.9 28.9 - - + -
328B GLU* 4.3 7.0 - - - +
329B ILE* 4.2 17.0 - - + +
332B ALA* 3.3 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 5.8 3.6 - - - +
40B GLU* 6.5 0.7 - - + -
41B PHE* 5.4 9.2 - - + -
296B PHE 3.5 9.8 + - - +
297B ARG* 3.3 10.4 + - - +
299B LEU* 1.3 79.0 - - - +
301B LYS* 1.3 60.7 + - - +
302B GLN 3.1 1.1 - - - -
303B ARG* 3.2 12.8 + - - -
304B ILE 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG 3.2 13.6 + - - +
298B ASN* 4.7 6.1 - - - +
300B ARG* 1.3 78.6 - - - +
302B GLN* 1.3 57.7 + - - +
303B ARG* 3.3 2.4 + - - +
----------------------------------------------------------
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