Contacts of the helix formed by residues 291 - 309 (chain R) in PDB entry 5GJQ
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
----------------------------------------------------------
189R VAL 3.6 8.9 + - - -
190R ALA 3.5 8.3 - - - -
191R ILE* 2.8 41.9 + - - -
192R ARG* 3.0 52.7 - - + +
194R PHE* 4.4 12.9 - + + -
287R LEU 3.9 3.6 + - - -
288R PHE* 2.5 36.1 + - + +
290R PRO* 1.3 77.1 - - + +
292R TYR* 1.3 56.1 + - - +
293R ARG 2.9 6.3 - - - -
294R TYR* 2.8 23.3 + + + +
295R TYR* 2.9 14.1 + - + +
39Y TRP* 4.5 7.1 - - + +
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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
----------------------------------------------------------
279R GLU* 3.7 19.5 - - + +
282R MET* 4.1 13.7 - - + -
283R LYS* 3.2 43.1 - - + +
288R PHE* 4.4 4.4 + - + +
289R ALA 4.0 6.4 + - - +
290R PRO* 3.2 27.6 - - + -
291R HIS* 1.3 77.4 - - - +
293R ARG* 1.3 92.6 + - + +
295R TYR* 4.2 6.3 - - - -
296R VAL* 3.5 26.9 + - - +
48Y VAL* 4.3 13.2 - - + +
49Y GLU 6.3 0.2 - - - -
51Y ASP* 4.5 1.2 - - - +
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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
----------------------------------------------------------
290R PRO 3.9 5.2 - - - +
291R HIS 2.9 0.6 - - - -
292R TYR* 1.3 98.6 - - + +
294R TYR* 1.3 64.4 + - - +
296R VAL* 4.4 1.4 - - - +
297R ARG* 3.3 27.0 + - - +
47Y ASN 4.2 6.5 - - - +
48Y VAL* 3.5 36.1 - - + -
49Y GLU 5.3 0.2 - - - +
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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* 2.9 60.9 + - + +
194R PHE* 4.4 24.5 - + - -
229R ILE* 5.7 2.5 - - + -
290R PRO 4.4 0.4 + - - -
291R HIS* 2.8 13.6 + + + +
293R ARG* 1.3 78.5 - - - +
295R TYR* 1.3 70.8 + - - +
297R ARG* 3.0 36.3 + - - +
298R GLU* 3.3 31.5 + - + +
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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* 3.9 22.7 - + + -
225R TYR* 2.5 49.7 + + + -
226R VAL* 4.7 2.5 - - + -
229R ILE* 1.2 79.2 - - + +
259R TYR* 3.6 13.8 + + - -
275R LEU* 4.7 8.7 - - + -
278R VAL* 5.4 8.1 - - + -
279R GLU* 6.3 2.0 - - - -
288R PHE* 5.3 11.9 - + + -
291R HIS* 2.9 14.3 + - + +
292R TYR* 4.4 7.6 - - - +
294R TYR* 1.3 83.2 - - - +
296R VAL* 1.3 63.7 + - + +
298R GLU* 3.2 4.3 + - - +
299R MET* 2.9 41.1 + - + +
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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
----------------------------------------------------------
272R PHE* 5.2 1.8 - - + -
275R LEU* 4.1 26.5 - - + -
279R GLU* 3.4 42.2 - - + -
292R TYR 3.5 10.3 + - - +
293R ARG* 4.8 1.3 - - - +
295R TYR* 1.3 80.7 - - + +
297R ARG* 1.3 69.0 + - - +
299R MET* 3.0 7.8 + - - +
300R ARG* 2.8 41.3 + - + +
51Y ASP* 3.5 26.2 - - + +
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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
----------------------------------------------------------
192R ARG* 5.3 2.2 - - - +
293R ARG 3.3 20.4 + - - +
294R TYR* 3.0 50.1 + - - +
296R VAL* 1.3 82.3 - - - +
298R GLU* 1.3 66.2 + - - +
300R ARG* 3.0 26.5 + - - +
301R ILE* 3.3 23.6 + - + +
337R PHE* 4.8 10.2 - - + -
43Y TRP 5.6 3.6 + - - -
44Y ASP 5.9 0.8 + - - -
45Y ASP 5.8 1.6 + - - -
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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* 4.4 24.4 - - + +
294R TYR* 3.3 23.6 + - + +
295R TYR* 3.2 10.4 + - - +
296R VAL 3.2 0.2 - - - -
297R ARG* 1.3 82.4 + - - +
299R MET* 1.3 67.9 + - - +
301R ILE* 2.9 32.8 + - - +
302R HIS* 3.1 43.9 + - + +
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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* 3.5 39.0 - - + +
229R ILE* 4.0 31.9 - - + -
259R TYR* 5.0 1.6 - - + -
263R LEU* 4.4 6.5 - - + -
271R PHE* 3.8 12.8 - - + -
275R LEU* 3.5 37.9 - - + +
295R TYR* 2.9 38.0 + - + +
296R VAL 3.0 1.1 + - - +
298R GLU* 1.3 76.8 - - + +
300R ARG* 1.3 61.0 + - - +
302R HIS* 4.2 14.1 - - + +
303R ALA* 3.9 16.0 + - - +
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Residues in contact with ARG 300 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272R PHE* 4.6 10.9 - - + -
275R LEU* 4.6 6.1 - - + -
296R VAL* 2.8 34.8 + - + +
297R ARG* 3.1 15.8 - - - +
298R GLU 3.0 0.2 + - - -
299R MET* 1.3 76.4 - - - +
301R ILE* 1.3 60.3 + - - +
303R ALA* 3.5 3.5 + - - +
304R TYR* 2.3 50.5 + - + +
329R PHE* 4.0 9.3 - - - -
333R GLU* 2.4 34.5 + - - +
336R ARG* 4.9 4.4 - - - +
337R PHE* 2.7 49.1 - - + -
50Y ASP* 3.8 13.6 + - - -
54Y ASN* 3.6 26.7 - - - +
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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 32.1 - - + +
298R GLU* 2.9 28.9 + - - +
300R ARG* 1.3 72.5 - - - +
302R HIS* 1.3 60.0 + - - +
304R TYR* 2.9 9.8 + - - +
305R SER* 2.6 40.3 + - - -
337R PHE* 3.7 34.5 - - + -
342R ARG* 3.9 36.1 - - + +
343R LEU* 4.8 9.6 - - + -
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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 4.6 9.2 - - - -
229R ILE 3.6 21.5 + - - -
230R ALA* 5.6 0.4 - - - -
231R LEU 4.9 9.4 + - - -
263R LEU* 5.5 8.7 - - + -
298R GLU* 3.1 33.4 + - - +
299R MET* 4.5 20.0 - - + +
300R ARG 3.4 0.2 - - - -
301R ILE* 1.3 81.6 - - - +
303R ALA* 1.3 52.6 + - - +
305R SER* 3.0 8.8 + - - -
306R GLN* 2.5 38.8 + - - +
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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* 4.5 18.0 - - + +
268R TYR* 4.1 8.0 + - + -
271R PHE* 5.5 8.7 - - + -
299R MET* 3.9 10.4 + - - +
300R ARG 3.5 7.9 + - - +
301R ILE 3.2 0.6 - - - -
302R HIS* 1.3 75.2 - - - +
304R TYR* 1.3 59.6 + - + +
306R GLN* 2.9 8.6 + - - +
307R LEU* 2.6 40.2 + - - +
323R PHE* 4.5 14.4 - - + -
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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* 5.6 6.4 - + - -
300R ARG* 2.3 48.1 + - + +
301R ILE* 2.9 6.7 + - - +
303R ALA* 1.3 76.3 - - + +
305R SER* 1.3 63.3 + - - +
307R LEU* 2.8 34.9 - - + +
308R LEU* 3.2 11.6 + - + +
319R MET* 4.5 6.3 - - + -
323R PHE* 4.2 23.5 - + - -
329R PHE* 5.3 4.3 - - - -
330R ILE* 5.1 4.9 - - + -
333R GLU* 3.1 39.2 - - + +
334R LEU* 2.9 37.2 - - + -
337R PHE* 3.7 8.7 - + - -
343R LEU* 4.2 9.9 - - + -
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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* 2.6 20.3 + - - -
302R HIS* 3.1 17.0 - - - -
304R TYR* 1.3 70.8 - - - +
306R GLN* 1.3 63.3 + - - +
307R LEU 2.9 1.4 + - - -
308R LEU* 2.9 14.2 + - - +
309R GLU* 3.1 14.7 + - - +
342R ARG 5.7 1.6 - - - -
343R LEU* 3.9 20.7 - - - +
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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
----------------------------------------------------------
370Q LEU* 3.4 43.1 - - + +
233R ARG* 3.8 17.4 + - - +
263R LEU* 3.5 43.7 + - - +
266R CYS* 3.9 5.3 - - - -
268R TYR* 3.0 17.6 + - - +
302R HIS* 2.5 19.5 + - - +
303R ALA* 3.5 7.9 - - - +
305R SER* 1.3 73.0 - - - +
307R LEU* 1.3 59.7 + - - +
308R LEU 3.6 0.3 + - - -
309R GLU* 3.8 18.2 + - - +
310R SER* 4.9 3.8 + - - -
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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* 3.1 29.4 - - + -
303R ALA 2.6 9.4 + - - +
304R TYR* 2.8 33.2 - - - +
306R GLN* 1.3 73.9 - - - +
308R LEU* 1.3 87.0 + - + +
310R SER* 4.4 1.2 + - - -
311R TYR* 3.3 24.4 - - - -
314R LEU* 3.8 5.4 - - + -
319R MET* 2.8 45.8 - - + -
323R PHE* 3.4 19.1 - - + -
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Residues in contact with LEU 308 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304R TYR* 3.2 14.8 - - + +
305R SER* 2.9 6.1 + - - +
307R LEU* 1.3 104.1 - - + +
309R GLU* 1.3 54.7 + - - +
310R SER 2.6 5.5 + - - -
311R TYR* 2.5 41.9 + - - +
314R LEU* 3.7 17.0 - - + -
319R MET* 3.9 15.3 - - + -
334R LEU* 5.6 1.3 - - + -
343R LEU* 4.2 17.9 - - + -
344R HIS 5.5 0.2 - - - -
345R CYS* 3.6 33.9 - - + +
354R VAL* 4.3 7.9 - - + -
356R THR* 3.8 19.2 - - + +
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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* 3.2 26.8 - - + +
370Q LEU* 3.7 25.4 - - + +
372Q LYS* 2.9 36.2 + - - +
376Q GLY 4.4 1.4 - - - +
377Q ILE* 4.0 11.8 - - - +
305R SER 3.1 14.6 + - - +
306R GLN* 3.8 10.9 + - - +
307R LEU 3.6 1.2 - - - -
308R LEU* 1.3 75.9 - - - +
310R SER* 1.3 58.4 + - - +
311R TYR 3.3 2.3 + - - +
356R THR* 6.0 0.2 - - - -
358R ARG* 6.1 1.2 - - - -
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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