Contacts of the helix formed by residues 291 - 307 (chain R) in PDB entry 5L4K
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R VAL 4.9 0.2 - - - -
190R ALA 3.0 23.7 + - - -
192R ARG* 3.2 55.9 + - + +
194R PHE* 4.0 18.3 - + - -
289R ALA* 2.3 43.3 + - + +
290R PRO 1.3 67.4 - - - +
292R TYR* 1.3 58.7 + - - +
293R ARG* 3.1 4.5 - - - +
294R TYR* 2.9 29.6 + - + +
295R TYR* 3.4 11.6 + - - +
34Y GLU* 5.0 6.5 - - - +
39Y TRP* 3.5 28.3 - + + -
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Residues in contact with TYR 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R LEU* 3.9 15.9 - - + +
279R GLU* 4.6 2.4 - - + +
283R LYS* 2.9 44.7 - - + +
284R LYS* 3.5 36.3 - - + -
286R TRP 3.3 14.9 + - - -
287R LEU* 4.6 2.3 - - - +
288R PHE* 4.5 1.9 + + + -
289R ALA* 2.8 38.4 + - + -
290R PRO* 3.6 24.9 - - + +
291R HIS* 1.3 70.3 - - - +
293R ARG* 1.3 58.7 + - - +
295R TYR* 4.1 6.2 + - - +
296R VAL* 3.4 24.6 + - - +
50Y ASP* 3.3 23.2 + - - +
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Residues in contact with ARG 293 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291R HIS* 3.1 1.3 - - - +
292R TYR* 1.3 78.3 - - - +
294R TYR* 1.3 59.0 + - - +
295R TYR 3.2 0.4 - - - -
296R VAL* 3.5 0.9 + - - +
297R ARG* 2.9 33.1 + - - +
34Y GLU* 5.2 9.2 + - - +
45Y ASP* 3.3 30.3 + - + +
46Y ASP* 4.8 4.2 + - - +
48Y VAL* 3.1 40.2 + - + -
49Y GLU* 3.6 18.6 + - - +
50Y ASP* 3.0 44.4 + - - +
52Y PHE* 4.1 8.9 - - + -
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Residues in contact with TYR 294 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192R ARG* 3.1 36.5 - - + +
194R PHE* 4.2 23.0 - + - -
229R ILE* 6.0 3.8 - - + -
291R HIS* 2.9 35.1 + - + +
293R ARG* 1.3 78.5 - - - +
295R TYR* 1.3 62.4 + - - +
297R ARG* 4.1 7.1 - - - +
298R GLU* 2.8 70.4 + - + +
342R ARG* 5.4 0.2 - - - -
40Y GLU* 2.5 30.2 + - - -
42Y ASN* 4.0 12.8 - - - -
45Y ASP* 3.4 20.0 + - - +
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Residues in contact with TYR 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194R PHE* 4.2 22.4 - + + -
225R TYR* 2.8 33.3 + - - +
228R MET* 5.1 0.5 - - - -
229R ILE* 3.4 26.2 - - + +
259R TYR* 3.0 37.4 + + - -
275R LEU* 4.4 10.8 - - + -
278R VAL* 5.1 1.1 - - + -
279R GLU* 6.4 0.2 - - - -
283R LYS* 3.7 41.9 + - + -
288R PHE* 4.5 4.0 - + + -
291R HIS* 3.4 9.8 + - - +
292R TYR* 4.5 5.8 - - - +
293R ARG 3.2 0.4 - - - -
294R TYR* 1.3 84.8 - - + +
296R VAL* 1.3 71.2 + - + +
298R GLU* 3.5 4.8 + - - +
299R MET* 2.9 26.4 + - - +
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Residues in contact with VAL 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275R LEU* 4.5 15.7 - - + -
279R GLU* 3.9 32.3 - - + +
283R LYS* 5.9 1.1 - - + -
292R TYR 3.4 17.2 + - - +
293R ARG 3.5 3.9 + - - +
295R TYR* 1.3 80.8 - - + +
297R ARG* 1.3 59.3 + - - +
298R GLU 3.0 1.3 - - - -
299R MET* 2.6 27.5 + - - +
300R ARG* 2.9 43.2 + - + +
52Y PHE* 3.9 23.6 - - + -
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Residues in contact with ARG 297 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293R ARG* 2.9 22.7 + - + +
294R TYR* 4.1 11.4 - - - +
296R VAL* 1.3 73.4 - - - +
298R GLU* 1.3 72.6 + - - +
300R ARG* 3.9 3.1 + - - +
301R ILE* 3.4 37.3 + - - +
336R ARG* 3.8 16.8 - - - +
337R PHE* 3.8 27.9 - - + -
340R ALA* 5.5 2.2 - - - +
342R ARG* 3.6 19.4 - - - +
42Y ASN* 3.2 29.9 - - - +
44Y ASP* 3.6 39.9 + - - +
45Y ASP* 3.4 18.6 + - - +
48Y VAL* 5.7 2.2 - - - -
52Y PHE* 4.3 15.2 - - + -
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Residues in contact with GLU 298 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229R ILE* 4.8 17.7 - - + +
294R TYR* 2.8 71.2 + - + +
295R TYR* 3.6 5.4 - - - +
297R ARG* 1.3 85.9 + - - +
299R MET* 1.3 65.6 + - - +
301R ILE* 3.1 31.7 + - - +
302R HIS* 3.1 13.0 + - - +
342R ARG* 3.8 19.3 + - - -
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Residues in contact with MET 299 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228R MET* 3.4 25.1 - - + +
229R ILE* 3.3 26.9 - - + -
259R TYR* 3.4 24.2 - - - +
263R LEU* 3.9 16.6 - - + -
271R PHE* 3.8 21.8 - - + -
275R LEU* 3.6 25.8 - - + -
295R TYR* 2.9 16.6 + - + +
296R VAL* 2.6 15.0 + - - +
298R GLU* 1.3 72.7 - - - +
300R ARG* 1.3 61.4 + - - +
302R HIS* 3.2 20.1 + - + +
303R ALA* 3.0 23.3 + - - +
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Residues in contact with ARG 300 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272R PHE* 4.7 22.0 - - + -
275R LEU* 4.7 15.4 - - + +
276R ALA* 5.6 6.3 - - - +
279R GLU* 5.2 0.6 + - - -
296R VAL* 2.9 28.6 + - + +
297R ARG* 4.3 3.1 - - - +
299R MET* 1.3 75.2 - - - +
301R ILE* 1.3 62.4 + - - +
303R ALA* 3.4 5.4 + - - +
304R TYR* 3.0 37.7 + - + -
329R PHE* 3.4 31.2 - - - -
333R GLU* 3.2 26.9 + - - +
337R PHE* 4.1 15.9 - - + -
52Y PHE* 3.3 53.6 + - - +
55Y GLN* 4.9 4.0 + - - +
56Y LEU* 5.1 7.9 - - - +
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Residues in contact with ILE 301 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297R ARG* 3.4 24.8 + - - +
298R GLU* 3.1 27.0 + - - +
300R ARG* 1.3 78.9 - - - +
302R HIS* 1.3 66.3 + - - +
303R ALA 3.1 0.3 + - - -
304R TYR* 3.8 0.5 - - - -
305R SER* 2.9 23.9 + - - -
337R PHE* 3.9 32.5 - - + -
342R ARG* 3.7 53.4 - - + +
343R LEU* 3.9 8.3 - - + +
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Residues in contact with HIS 302 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228R MET* 4.1 13.1 + - - -
229R ILE* 4.5 12.5 + - + -
231R LEU 4.1 10.9 + - - -
232R GLU* 3.4 34.3 + - - -
233R ARG* 5.9 4.9 - - + -
263R LEU* 4.2 16.9 - - + +
298R GLU 3.1 9.3 + - - +
299R MET* 3.4 28.8 - - + +
301R ILE* 1.3 79.5 - - - +
303R ALA* 1.3 63.6 + - - +
305R SER* 3.1 22.6 - - - -
306R GLN* 3.1 19.1 + - + +
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Residues in contact with ALA 303 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263R LEU* 4.7 11.4 - - + +
268R TYR* 4.8 5.2 - - + -
271R PHE* 3.9 27.1 - - + -
272R PHE* 4.7 1.8 - - + -
299R MET 3.0 15.6 + - - +
300R ARG* 3.8 5.4 - - - +
302R HIS* 1.3 70.8 - - - +
304R TYR* 1.3 68.4 + - - +
305R SER 2.9 1.3 - - - -
306R GLN* 2.8 20.4 + - - +
307R LEU* 3.1 11.8 + - - +
323R PHE* 4.4 18.6 - - + -
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Residues in contact with TYR 304 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272R PHE* 3.6 15.5 - + - -
300R ARG* 3.0 29.6 + - + +
303R ALA* 1.3 75.6 - - - +
305R SER* 1.3 61.1 + - - +
307R LEU* 3.7 2.5 + - - +
308R LEU* 3.2 29.8 + - + +
319R MET* 4.1 6.7 - - + -
323R PHE* 3.4 44.4 - + - -
329R PHE* 3.7 12.3 - - - -
330R ILE* 4.0 17.1 - - + +
333R GLU* 3.2 39.8 + - + +
334R LEU* 3.3 35.4 - - + -
337R PHE* 4.3 9.9 - + - -
343R LEU* 3.9 12.1 - - + -
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Residues in contact with SER 305 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301R ILE* 2.9 15.9 + - - -
302R HIS* 3.1 17.0 - - - -
303R ALA 2.9 0.4 - - - -
304R TYR* 1.3 74.6 - - - +
306R GLN* 1.3 66.5 + - - +
308R LEU 3.2 2.9 + - - -
309R GLU* 3.0 26.6 + - - +
342R ARG 5.1 3.3 + - - -
343R LEU* 4.0 25.1 + - - +
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Residues in contact with GLN 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370Q LEU* 3.9 31.0 - - + +
233R ARG* 3.6 35.6 + - + +
263R LEU* 3.6 37.1 + - - +
266R CYS* 4.1 8.5 - - - -
268R TYR* 2.7 31.2 + - + +
302R HIS* 3.1 20.4 + - + +
303R ALA* 2.8 15.9 + - - +
305R SER* 1.3 72.4 - - - +
307R LEU* 1.3 53.3 + - - +
308R LEU 2.7 13.5 + - - -
309R GLU* 3.2 13.8 + - - +
310R SER* 4.2 6.2 + - - -
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Residues in contact with LEU 307 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268R TYR* 3.6 35.4 - - + +
303R ALA 3.1 9.9 + - - +
304R TYR 3.7 2.7 - - - +
305R SER 3.4 0.2 - - - -
306R GLN* 1.3 75.2 - - - +
308R LEU* 1.3 66.6 + - - +
310R SER* 6.3 0.4 - - - -
311R TYR* 4.2 25.8 - - + +
314R LEU* 3.8 18.6 - - + +
318R TYR* 4.6 11.4 - - + +
319R MET* 4.3 14.4 - - + +
322R ALA* 4.1 19.5 - - + -
323R PHE* 3.6 30.3 - - + -
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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