Contacts of the helix formed by residues 272 - 286 (chain A) in PDB entry 4J1O
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 GLY 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA* 3.7 12.0 - - - +
105A ASP* 3.6 11.4 - - - -
106A ILE* 5.1 0.9 - - - -
267A LEU* 3.1 22.3 + - - +
270A ILE* 3.8 1.7 - - - +
271A GLY* 1.3 79.8 - - - +
273A LEU* 1.3 60.9 + - - -
274A GLN 3.4 2.5 - - - -
275A GLN 3.5 2.2 + - - -
276A MET* 2.9 27.7 + - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP* 2.7 17.1 + - - +
106A ILE* 4.2 15.9 - - + -
109A TYR* 3.7 40.2 - - + -
120A VAL* 3.9 15.0 - - + -
124A LEU* 4.0 13.9 - - + +
267A LEU* 3.8 23.1 - - + -
272A GLY* 1.3 70.9 - - - -
274A GLN* 1.3 63.3 + - - +
276A MET* 3.7 1.5 - - - +
277A ALA* 2.9 26.0 + - - +
304A ALA* 3.7 29.2 - - + +
308A ILE* 3.9 18.7 - - + +
352A LEU* 5.1 1.3 - - + -
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 4.3 6.7 - - + +
84A LEU* 3.9 36.0 - - + +
87A ARG* 3.1 15.9 + - - -
105A ASP* 3.3 17.1 + - - +
109A TYR* 3.5 21.3 - - + +
273A LEU* 1.3 77.6 - - - +
275A GLN* 1.3 87.8 + - + +
277A ALA* 3.6 5.3 + - - +
278A ALA* 3.6 14.6 + - - +
124B LEU 5.5 0.2 + - - -
125B GLY* 5.7 1.7 - - - -
280B ARG* 3.7 10.5 - - - +
281B ASP* 3.3 34.3 + - - +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.4 42.4 + - - +
248A LEU* 3.6 38.9 + - - +
270A ILE* 3.5 33.0 - - + +
271A GLY* 4.7 4.5 - - - -
272A GLY 3.5 6.5 + - - +
274A GLN* 1.3 96.9 + - - +
276A MET* 1.3 60.3 + - - +
278A ALA* 3.2 6.5 + - - +
279A PHE* 3.0 27.5 + - - +
281B ASP* 5.0 7.3 + - - +
285B ALA* 5.8 0.5 - - - +
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A MET* 3.6 49.1 - - + +
267A LEU* 3.6 26.0 - - + +
270A ILE* 3.8 13.6 - - - +
272A GLY 2.9 18.8 + - - +
273A LEU* 3.3 6.0 + - - +
275A GLN* 1.3 77.4 - - - +
277A ALA* 1.3 57.4 + - - +
279A PHE* 3.3 15.8 + - + +
280A ARG* 2.9 28.3 + - + +
291A SER 4.0 0.9 - - - +
292A CYS* 3.8 31.2 - - + -
308A ILE* 3.7 21.3 - - + -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.3 17.0 - - + +
273A LEU 2.9 17.0 + - - +
274A GLN* 3.9 5.8 - - - +
276A MET* 1.3 77.0 - - - +
278A ALA* 1.3 62.5 + - - +
280A ARG* 3.3 25.7 + - - +
281A ASP* 3.0 29.7 + - - +
308A ILE* 4.0 9.8 - - + +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.0 15.7 - - + -
274A GLN 3.6 5.3 + - - +
275A GLN* 3.2 10.6 + - - +
277A ALA* 1.3 75.8 - - - +
279A PHE* 1.3 64.8 + - - +
281A ASP* 3.2 9.2 + - - +
282A ILE* 3.0 27.7 + - + +
278B ALA* 5.1 7.2 - - - +
281B ASP* 3.6 38.1 + - + +
282B ILE* 6.2 0.2 - - + -
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.7 8.8 - - + +
251A VAL* 3.7 26.9 - - + -
263A PHE* 3.7 22.2 - + + -
265A MET* 3.6 46.7 - - + -
270A ILE* 3.5 22.9 - - + -
275A GLN 3.0 6.0 + - - +
276A MET* 3.3 19.9 + - + +
278A ALA* 1.3 76.5 - - - +
280A ARG* 1.3 66.3 + - + +
282A ILE* 3.2 6.9 + - - +
283A CYS* 3.0 44.2 + - - -
290A HIS* 3.5 29.6 - + + -
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU 2.8 30.7 + - - -
276A MET 2.9 12.8 + - - +
277A ALA* 3.3 22.7 + - - +
279A PHE* 1.3 77.2 - - + +
281A ASP* 1.3 91.4 + - - +
283A CYS* 3.3 3.1 + - - +
284A GLU* 2.9 33.1 + - + +
290A HIS* 4.1 20.4 + - + +
308A ILE* 3.7 16.9 - - + +
311A THR* 2.9 42.6 + - - -
312A VAL* 4.2 19.7 - - + +
84B LEU* 3.5 17.6 - - - +
88B ARG* 4.8 0.9 - - - +
274B GLN* 3.7 5.9 - - - +
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA* 3.0 16.3 + - - +
278A ALA* 3.2 7.6 + - - +
280A ARG* 1.3 101.2 + - - +
282A ILE* 1.3 63.6 + - - +
284A GLU* 3.4 8.1 + - - +
285A ALA 3.1 17.7 + - - -
84B LEU* 4.1 5.4 - - - +
87B ARG* 5.4 1.1 + - - +
248B LEU* 3.6 15.0 - - + +
274B GLN* 3.3 26.8 + - - +
275B GLN* 4.9 5.7 + - - +
278B ALA* 3.6 30.0 + - + +
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.8 24.9 - - + -
251A VAL* 4.0 22.2 - - + +
252A ILE* 3.9 24.0 - - + -
255A ALA* 4.1 18.4 - - + -
278A ALA* 3.0 20.3 + - + +
279A PHE* 3.2 6.5 + - - +
281A ASP* 1.3 74.6 - - - +
283A CYS* 1.3 66.3 + - - +
285A ALA* 3.3 12.6 + - - +
286A ARG* 3.4 11.1 + - - +
248B LEU* 4.6 1.8 - - + -
252B ILE* 3.9 23.2 - - + +
278B ALA* 6.1 0.7 - - + -
282B ILE* 4.0 28.7 - - + -
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Residues in contact with CYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A VAL* 5.2 2.2 - - - -
263A PHE* 3.6 22.4 - - - -
279A PHE* 3.0 49.2 + - - +
280A ARG 3.7 4.3 - - - +
282A ILE* 1.3 78.3 - - - +
284A GLU* 1.3 61.0 - - - +
286A ARG 3.2 1.7 + - - -
287A ALA* 3.0 4.5 + - - -
288A LEU* 2.9 51.1 + - - +
290A HIS* 3.6 18.4 - - + -
316A LEU* 4.4 1.1 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ARG* 2.9 21.6 + - + +
281A ASP* 3.9 9.3 - - - +
283A CYS* 1.3 77.3 - - - +
285A ALA* 1.3 62.9 + - - +
286A ARG 3.2 0.7 + - - -
287A ALA* 3.4 9.4 + - - +
290A HIS* 5.7 0.2 - - - -
313A GLN* 3.7 29.1 + - - +
315A ARG* 5.4 2.8 + - - -
316A LEU* 3.6 14.1 - - + +
84B LEU* 4.2 5.0 - - - +
87B ARG* 4.2 21.0 + - - +
88B ARG* 2.7 51.6 + - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ASP 3.1 13.3 + - - +
282A ILE 3.6 9.6 - - - +
283A CYS 3.3 0.2 - - - -
284A GLU* 1.3 77.2 - - - +
286A ARG* 1.3 64.1 + - - +
287A ALA 4.0 0.2 + - - -
248B LEU* 4.2 9.9 - - + -
249B SER* 4.1 25.5 + - - +
252B ILE* 3.9 18.6 - - + -
275B GLN* 5.7 0.7 - - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA* 3.2 29.4 + - + -
256A GLY* 4.4 4.6 + - - -
282A ILE 3.4 9.3 + - - +
283A CYS 3.2 2.4 + - - -
284A GLU 3.1 0.4 - - - -
285A ALA* 1.3 79.4 - - - +
287A ALA* 1.3 71.2 + - - +
288A LEU* 3.2 31.7 + - + +
249B SER* 2.8 47.9 + - - +
252B ILE* 4.0 17.0 - - + +
253B ARG* 3.4 27.1 - - - +
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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