Contacts of the helix formed by residues 291 - 311 (chain R) in PDB entry 5LN3
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 HIS 291 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R VAL* 2.8 50.5 + - + -
190R ALA* 4.1 5.9 + - - -
192R ARG* 3.9 26.4 - - + +
194R PHE* 4.9 1.5 - + - -
282R MET* 4.6 0.2 - - - -
287R LEU 3.2 26.2 + - - -
288R PHE* 3.4 25.2 + + - +
289R ALA 2.7 5.7 + - - -
290R PRO* 1.4 76.5 - - + +
292R TYR* 1.3 69.6 + - - +
294R TYR* 3.4 19.8 + - - +
295R TYR* 3.6 32.6 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R LEU* 5.9 1.6 - - - +
282R MET* 3.3 25.7 - - + +
283R LYS* 4.8 17.3 - - + -
289R ALA* 2.8 43.8 + - + +
290R PRO* 3.4 24.0 - - + +
291R HIS* 1.3 75.8 - - - +
293R ARG* 1.4 64.6 + - + +
294R TYR* 5.9 0.9 - - + -
295R TYR* 3.2 10.4 + - - +
296R VAL* 3.5 2.4 + - - +
50Y ASP* 4.0 22.9 - - + -
51Y ASP* 4.2 22.8 - - + +
54Y ASN* 3.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292R TYR* 1.4 77.2 - - + +
294R TYR* 1.4 95.5 + - + +
296R VAL* 4.5 0.7 - - - -
297R ARG* 3.0 57.9 + - - +
336R ARG* 6.1 0.6 - - - +
345S ARG* 5.0 9.7 - - - +
50Y ASP* 3.1 65.4 + - + +
52Y PHE* 6.3 0.2 - - - -
53Y SER* 4.1 10.7 + - - -
54Y ASN* 3.3 15.0 - - - +
57Y ARG* 4.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192R ARG* 3.3 45.1 - - - +
194R PHE* 6.0 1.1 - - + -
291R HIS 3.8 6.7 - - - +
292R TYR* 3.2 2.3 - - + -
293R ARG* 1.4 112.2 + - + +
295R TYR* 1.3 62.3 + - - +
297R ARG* 4.7 10.1 - - + -
298R GLU* 3.1 36.5 + - + +
345S ARG* 3.7 22.8 + - - -
50Y ASP* 4.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R VAL* 6.1 1.6 - - + -
192R ARG* 5.0 1.0 - - - +
194R PHE* 4.2 18.2 - + - -
225R TYR* 2.9 68.3 + + - -
226R VAL* 4.5 2.6 - - + -
229R ILE* 3.5 37.4 - - + +
278R VAL* 5.5 1.8 - - + -
282R MET* 3.6 22.0 - - + -
288R PHE* 6.0 5.4 - + + -
291R HIS* 3.6 28.1 + + + +
292R TYR 3.2 11.7 + - - +
294R TYR* 1.3 77.1 - - - +
296R VAL* 1.4 63.6 + - + +
299R MET* 3.3 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275R LEU* 3.5 30.3 - - + -
278R VAL* 3.6 26.7 - - + -
282R MET* 3.7 10.1 - - + -
292R TYR 3.6 8.7 - - - +
293R ARG 3.4 1.9 + - - +
295R TYR* 1.4 73.9 - - + +
297R ARG* 1.4 62.2 + - - +
299R MET* 3.1 11.2 + - + +
300R ARG* 3.0 32.8 + - + +
54Y ASN* 3.0 24.2 - - + +
57Y ARG* 3.5 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293R ARG* 3.0 33.3 + - - +
294R TYR* 4.2 10.8 - - + +
296R VAL* 1.4 78.6 - - - +
298R GLU* 1.4 62.5 + - - +
300R ARG* 3.4 3.0 + - - +
301R ILE* 3.1 33.8 + - + +
333R GLU* 3.0 27.5 + - - -
336R ARG* 3.8 27.5 - - - +
337R PHE* 3.9 23.1 - - + -
53Y SER* 3.6 30.9 + - - -
57Y ARG* 3.8 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194R PHE* 5.6 7.0 - - + -
229R ILE* 3.9 18.6 - - + -
294R TYR* 3.1 30.1 + - + +
297R ARG* 1.4 61.6 - - + +
299R MET* 1.3 56.1 + - - +
301R ILE* 3.6 21.2 - - - +
302R HIS* 2.8 54.2 + - + +
342R ARG* 4.9 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 299 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R TYR* 4.6 5.6 - - + +
228R MET* 3.9 23.3 - - + -
229R ILE* 3.8 19.3 - - + +
259R TYR* 3.7 31.6 - - + -
263R LEU* 6.1 0.5 - - - +
271R PHE* 4.6 10.8 - - + -
278R VAL* 5.1 8.5 - - - -
295R TYR* 3.3 55.6 + - + +
296R VAL* 3.1 11.1 + - - +
298R GLU* 1.3 74.4 - - - +
300R ARG* 1.3 68.1 + - + +
302R HIS* 3.1 18.0 + - - +
303R ALA* 3.3 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259R TYR* 4.5 3.0 + - - -
268R TYR* 3.6 31.3 + - - +
271R PHE* 3.1 58.2 + - - -
272R PHE* 3.8 24.5 - - - +
274R SER* 3.6 5.5 + - - -
275R LEU* 3.3 38.9 - - - +
278R VAL* 5.2 2.4 - - - +
296R VAL* 3.0 29.2 + - + +
297R ARG* 3.4 6.7 + - - +
299R MET* 1.3 75.7 - - - +
301R ILE* 1.4 62.0 + - - +
303R ALA* 3.6 5.5 + - - +
304R TYR* 3.2 21.4 + - - +
337R PHE* 5.5 6.5 - - + -
57Y ARG* 4.6 15.3 - - - +
61Y GLU* 4.2 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297R ARG* 3.1 25.2 + - + +
298R GLU* 3.6 28.7 - - - +
300R ARG* 1.4 74.8 - - - +
302R HIS* 1.4 70.7 + - + +
304R TYR* 3.1 9.1 + - - +
305R SER* 2.9 38.9 + - - +
337R PHE* 3.6 46.0 - - + -
342R ARG* 4.6 27.8 - - + -
343R LEU* 5.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 302 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228R MET 4.9 2.9 + - - +
229R ILE* 3.4 30.4 + - + -
232R GLU* 4.0 23.7 + - + +
263R LEU* 5.5 7.9 - - + -
298R GLU* 2.8 44.5 + - + +
299R MET* 3.1 11.8 + - - +
301R ILE* 1.4 89.9 - - + +
303R ALA* 1.3 62.1 + - - +
305R SER* 3.6 7.9 + - - -
306R GLN* 3.4 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263R LEU* 5.4 8.0 - - + +
266R CYS 4.3 5.9 - - - +
267R ARG 4.5 9.1 - - - +
268R TYR* 4.0 19.0 - - + +
271R PHE* 4.2 17.0 - - + -
299R MET 3.3 8.5 + - - +
300R ARG 3.6 9.2 - - - +
302R HIS* 1.3 80.9 - - - +
304R TYR* 1.4 61.8 + - - +
305R SER 3.5 0.3 + - - -
306R GLN* 3.6 25.9 + - - +
307R LEU* 3.7 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268R TYR* 4.0 28.3 - + + -
300R ARG 3.2 11.1 + - - +
301R ILE 3.1 10.3 + - - +
303R ALA* 1.4 77.4 - - - +
305R SER* 1.4 57.7 + - - +
306R GLN 3.3 0.2 - - - -
307R LEU* 3.3 10.9 + - + +
308R LEU* 3.1 56.9 + - + +
316R LEU* 4.9 1.4 - - - +
319R MET* 4.4 20.6 - - + +
330R ILE* 3.8 32.1 - - + +
334R LEU* 3.4 50.3 - - + +
337R PHE* 4.3 17.7 - + - -
343R LEU* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301R ILE* 2.9 29.3 + - - +
302R HIS* 3.6 8.8 - - - -
304R TYR* 1.4 73.0 - - - +
306R GLN* 1.4 53.8 + - - +
308R LEU* 3.3 5.2 - - - +
309R GLU* 2.9 48.9 + - - +
342R ARG 5.5 0.3 + - - -
343R LEU* 3.5 29.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370Q LEU* 5.3 3.9 - - + +
232R GLU* 3.7 23.4 + - - +
233R ARG* 4.5 14.6 - - - +
262R SER 5.1 0.2 - - - +
263R LEU* 3.6 30.7 + - - +
266R CYS* 3.6 42.2 - - + +
302R HIS 3.4 11.9 - - - +
303R ALA* 3.7 21.8 - - - +
305R SER* 1.4 78.6 - - - +
307R LEU* 1.3 63.8 + - - +
309R GLU* 3.4 10.3 + - - +
310R SER* 3.3 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266R CYS* 3.7 15.8 + - - +
267R ARG* 4.1 2.5 - - - -
268R TYR* 3.4 33.4 - - + +
269R SER* 4.8 0.9 - - - +
303R ALA 3.7 4.6 + - - +
304R TYR* 3.3 14.5 + - + +
306R GLN* 1.3 80.5 - - - +
308R LEU* 1.4 62.3 - - - +
310R SER* 3.3 19.6 - - - -
311R TYR* 4.0 9.0 + - + -
314R LEU* 4.0 14.0 - - + +
319R MET* 4.1 21.1 - - + -
323R PHE* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304R TYR* 3.1 50.1 + - + +
305R SER* 3.3 7.9 - - - +
307R LEU* 1.4 72.6 - - - +
309R GLU* 1.3 61.3 + - + +
311R TYR 2.9 26.2 + - - +
314R LEU* 3.8 23.6 - - + -
319R MET* 4.4 4.7 - - + -
334R LEU* 4.4 3.6 - - + -
343R LEU* 3.3 44.9 - - + -
345R CYS* 3.7 26.5 - - - -
354R VAL* 5.5 4.7 - - + -
356R THR* 4.6 10.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369Q ILE* 4.2 12.2 - - - +
372Q LYS* 4.8 15.6 + - - +
377Q ILE* 4.7 9.2 - - - +
305R SER* 2.9 32.5 + - - +
306R GLN* 3.4 9.1 + - - +
307R LEU 3.3 0.4 - - - -
308R LEU* 1.3 78.8 - - + +
310R SER* 1.3 58.2 + - - +
311R TYR* 3.6 1.9 + - - -
312R ARG* 5.0 0.5 + - - -
356R THR* 6.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Q SER* 5.9 2.6 - - - -
369Q ILE* 4.3 24.1 - - - +
370Q LEU* 4.9 15.0 - - - +
377Q ILE* 5.5 0.9 - - - +
378Q LEU* 4.3 18.0 + - - +
306R GLN 3.3 11.2 + - - -
307R LEU* 3.3 17.3 - - - -
309R GLU* 1.3 76.1 - - - +
311R TYR* 1.3 83.3 + - - +
312R ARG 4.1 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Q SER* 4.9 8.2 + - - -
378Q LEU* 4.4 17.7 - - + +
380Q GLN* 3.2 48.0 + - + -
307R LEU* 4.0 10.3 + - + -
308R LEU 2.9 18.9 + - - +
309R GLU 4.7 0.7 - - - -
310R SER* 1.3 95.8 - - - +
312R ARG* 1.3 66.1 + - - +
313R SER 3.6 17.2 + - - +
314R LEU* 3.8 35.5 - - + +
356R THR* 4.4 0.7 + - - -
----------------------------------------------------------
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