Contacts of the helix formed by residues 269 - 283 (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 SER 269 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267R ARG 5.0 1.1 - - - -
268R TYR* 1.3 73.3 - - - +
270R VAL* 1.3 60.6 + - - -
272R PHE* 3.9 12.7 - - - +
273R GLN* 3.3 15.6 - - - +
322R ALA 2.8 26.8 + - - -
323R PHE* 3.7 27.4 - - - +
324R GLY* 5.2 1.1 - - - -
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Residues in contact with VAL 270 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262R SER* 3.3 8.3 - - - +
267R ARG* 2.7 49.4 - - + +
268R TYR 2.3 11.1 + - - -
269R SER* 1.3 68.9 - - - +
271R PHE* 1.3 64.4 + - - +
272R PHE 3.1 1.8 - - - -
273R GLN* 2.8 26.6 + - + +
274R SER* 3.3 11.3 + - - +
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Residues in contact with PHE 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228R MET* 2.3 33.0 - - + -
259R TYR* 3.3 23.8 - + + +
262R SER* 2.8 18.9 + - - +
263R LEU* 2.2 68.2 - - + -
268R TYR* 2.2 37.1 + + - +
270R VAL* 1.3 66.4 - - - +
272R PHE* 1.3 62.1 + - - +
274R SER* 3.4 3.7 + - - -
275R LEU* 2.9 32.2 + - + +
299R MET* 3.8 16.2 - - + -
303R ALA* 5.5 6.5 - - + -
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Residues in contact with PHE 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268R TYR 3.7 2.4 + - - -
269R SER* 3.9 13.9 - - - +
270R VAL 2.9 1.4 + - - -
271R PHE* 1.3 79.1 - - - +
273R GLN* 1.3 65.9 + - + +
275R LEU* 2.8 34.4 + - + +
276R ALA* 2.9 15.4 + - + +
296R VAL* 5.2 0.4 - - + -
300R ARG* 4.6 16.6 - - + -
304R TYR* 5.6 6.3 - + - -
323R PHE* 5.5 9.4 - - + +
325R VAL* 5.6 5.8 - - + -
329R PHE* 5.5 2.7 - + - -
51Y ASP* 3.4 17.0 - - + -
54Y ASN* 3.4 33.0 - - + -
55Y GLN* 3.4 32.8 - - + -
58Y ALA* 4.1 16.4 - - + -
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Residues in contact with GLN 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269R SER 3.3 17.3 - - - +
270R VAL* 2.8 20.2 + - + +
272R PHE* 1.3 78.1 - - + +
274R SER* 1.3 62.2 + - - +
276R ALA* 3.2 5.6 + - - +
277R VAL* 2.9 29.5 + - + +
55Y GLN* 5.3 5.8 - - + -
58Y ALA* 6.5 0.7 - - + -
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Residues in contact with SER 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255R ALA* 4.2 9.2 - - - -
258R GLN* 3.5 29.6 + - - +
259R TYR* 3.5 29.0 + - - -
270R VAL* 3.3 7.6 + - - +
271R PHE 3.9 3.1 - - - -
272R PHE 3.3 0.6 - - - -
273R GLN* 1.3 79.0 - - - +
275R LEU* 1.3 62.6 + - - +
277R VAL* 3.3 11.0 + - - +
278R VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259R TYR* 4.5 16.1 - - + +
271R PHE* 2.9 24.2 + - + +
272R PHE* 2.8 27.9 + - + +
274R SER* 1.3 78.0 - - - +
276R ALA* 1.3 63.1 + - - +
278R VAL* 3.3 4.1 + - + +
279R GLU* 2.9 22.7 + - - +
295R TYR* 4.7 8.5 - - + -
296R VAL* 4.1 31.9 - - + +
299R MET* 3.5 50.5 - - + +
300R ARG* 4.4 3.1 - - + +
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Residues in contact with ALA 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272R PHE* 2.9 14.6 + - + +
273R GLN 3.6 6.5 - - - +
275R LEU* 1.3 73.3 - - - +
277R VAL* 1.3 70.3 + - - +
279R GLU* 3.1 9.1 + - - +
280R GLN* 2.9 25.0 + - - +
296R VAL* 5.8 0.2 - - - -
51Y ASP* 4.3 9.4 - - + +
52Y PHE* 4.1 22.0 - - + +
55Y GLN* 4.0 25.8 - - + -
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Residues in contact with VAL 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255R ALA* 5.2 10.1 - - + -
273R GLN* 2.9 25.9 + - + +
274R SER* 3.4 11.0 - - - +
276R ALA* 1.3 74.6 - - - +
278R VAL* 1.3 60.7 + - + +
280R GLN* 2.6 39.6 + - + +
281R GLU* 3.2 6.4 + - + +
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Residues in contact with VAL 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R TYR* 2.3 61.0 - - + +
255R ALA* 4.4 11.2 - - + -
256R VAL* 4.0 23.3 - - - +
259R TYR* 5.3 7.0 - - + -
274R SER* 2.9 23.8 + - - +
275R LEU* 3.9 5.4 - - + +
277R VAL* 1.3 73.6 - - + +
279R GLU* 1.3 55.5 + - - +
281R GLU* 2.7 28.7 + - + +
282R MET* 2.9 12.7 + - + +
295R TYR* 5.4 9.0 - - + -
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Residues in contact with GLU 279 (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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275R LEU 2.9 10.1 + - - +
276R ALA* 3.2 10.5 - - - +
278R VAL* 1.3 77.1 - - - +
280R GLN* 1.3 62.4 + - - +
282R MET* 2.9 23.6 + - - +
283R LYS* 3.4 13.0 + - - +
292R TYR* 3.7 24.7 - - + +
295R TYR* 6.3 1.8 - - - -
296R VAL* 3.4 26.5 - - + -
51Y ASP* 2.5 30.7 - - - +
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Residues in contact with GLN 280 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276R ALA 2.9 16.0 + - - +
277R VAL* 2.6 20.8 + - + +
279R GLU* 1.3 72.1 - - - +
281R GLU* 1.3 54.8 + - - -
282R MET 3.6 0.2 - - - -
283R LYS* 4.7 9.4 - - - +
284R LYS* 4.7 9.2 + - - +
51Y ASP* 4.7 7.7 + - - -
52Y PHE* 3.1 44.6 - - + +
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Residues in contact with GLU 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R TYR* 4.9 4.7 - - + +
277R VAL* 3.2 4.8 + - + +
278R VAL* 2.7 30.8 + - + +
280R GLN* 1.3 73.5 - - - +
282R MET* 1.3 59.5 + - - +
284R LYS* 3.8 15.6 - - - +
285R ASP* 3.9 12.5 + - - +
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Residues in contact with MET 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R TYR* 5.7 4.7 - - + -
278R VAL* 2.9 11.8 + - + +
279R GLU* 2.9 11.2 + - - +
281R GLU* 1.3 75.3 - - - +
283R LYS* 1.3 54.4 + - - +
284R LYS 2.7 5.7 + - - -
285R ASP* 2.6 42.3 + - - +
288R PHE* 4.4 28.2 - - + +
289R ALA 4.7 0.5 + - - -
292R TYR* 4.1 15.9 - - + -
295R TYR* 6.3 2.7 - - + -
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Residues in contact with LYS 283 (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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24R PHE* 4.0 9.7 - - - -
28R LEU* 5.5 3.6 - - - +
29R PRO* 5.8 4.1 - - + +
279R GLU 3.4 7.1 + - - +
280R GLN* 5.1 9.4 - - - +
282R MET* 1.3 77.3 - - - +
284R LYS* 1.3 59.6 + - - +
285R ASP 3.7 5.9 - - - +
289R ALA 4.1 13.1 - - - +
292R TYR* 3.2 37.5 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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