Contacts of the helix formed by residues 272 - 284 (chain A) in PDB entry 5JLH
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
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Residue Dist Surf HB Arom Phob DC
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260A LEU 3.3 13.9 - - - -
261A PHE* 4.3 6.9 + - - -
263A PRO* 3.7 17.2 - - - +
271A CYS* 1.3 77.9 - - - +
273A ILE* 1.3 65.7 + - - -
274A HIS 3.3 2.7 - - - -
275A GLU* 3.0 18.2 + - - +
276A THR* 3.0 18.6 + - - +
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Residues in contact with ILE 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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152A MET* 3.6 31.4 - - + +
159A THR* 4.7 4.0 - - + +
177A LEU* 3.7 18.4 - - + -
179A LEU* 4.3 4.7 - - + -
260A LEU* 3.1 39.9 + - + +
261A PHE* 3.7 24.5 - - + -
272A GLY* 1.3 71.2 - - - -
274A HIS* 1.3 60.3 + - - +
276A THR* 2.3 26.7 + - - -
277A THR* 2.9 18.4 + - - -
298A LEU* 6.4 0.7 - - + -
303A THR* 6.4 1.8 - - + -
308A ILE* 5.1 4.9 - - + -
312A MET* 3.5 26.7 - - + -
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Residues in contact with HIS 274 (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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261A PHE* 3.5 29.8 - + + -
262A GLN* 5.5 2.2 - - - -
273A ILE* 1.3 80.3 + - - +
275A GLU* 1.3 102.7 + - - +
277A THR* 3.1 7.2 + - - -
278A PHE* 3.1 24.3 + - - +
311A ARG* 5.6 0.2 - - - -
312A MET* 3.8 19.1 - - - -
315A GLU* 2.9 52.4 + - + +
316A ILE* 4.1 15.9 - - + +
319A LEU* 4.0 16.6 - - + +
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Residues in contact with GLU 275 (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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261A PHE 4.9 2.1 - - - +
262A GLN* 5.9 0.5 + - - -
271A CYS* 3.7 22.2 - - + -
272A GLY* 3.1 20.1 - - - +
274A HIS* 1.3 116.4 + - + +
276A THR* 1.3 57.3 + - - +
278A PHE* 3.5 9.8 + - + +
279A ASN* 2.9 25.1 + - - +
319A LEU* 4.3 13.0 - - + +
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Residues in contact with THR 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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152A MET* 4.9 1.9 - - - +
159A THR* 5.7 0.2 - - - +
161A THR* 4.5 11.1 + - - -
175A LEU* 3.5 24.5 - - + +
177A LEU* 3.8 26.5 - - + +
271A CYS* 3.6 20.4 - - + +
272A GLY 3.0 12.7 + - - +
273A ILE* 2.3 31.7 + - - +
275A GLU* 1.3 73.4 - - - +
277A THR* 1.3 60.7 + - - +
279A ASN* 3.2 5.3 + - - +
280A SER* 2.9 31.6 + - - -
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Residues in contact with THR 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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150A ILE* 4.0 17.9 - - + -
152A MET* 4.3 13.8 - - + +
161A THR* 4.7 5.5 - - - +
273A ILE 2.9 13.5 + - - -
274A HIS 3.1 9.4 + - - -
276A THR* 1.3 77.3 + - - +
278A PHE* 1.3 55.8 + - + +
280A SER* 2.9 10.3 + - - -
281A ILE* 2.9 46.9 + - + +
296A THR* 4.9 6.9 - - + +
312A MET* 3.9 12.6 - - - +
316A ILE* 3.9 20.6 - - + -
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Residues in contact with PHE 278 (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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274A HIS 3.1 13.0 + - - +
275A GLU* 3.5 12.1 - - + +
277A THR* 1.3 71.0 - - - +
279A ASN* 1.3 65.8 + - - +
281A ILE* 4.4 6.5 - - + +
282A MET* 2.8 50.8 + - + +
293A TYR* 3.9 18.6 - + - -
316A ILE* 3.9 22.9 - - + -
319A LEU* 3.3 40.2 - - + -
320A ALA* 3.3 38.6 - - + -
321A PRO* 5.3 1.6 - - + -
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Residues in contact with ASN 279 (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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175A LEU* 3.5 25.9 - - + +
275A GLU 2.9 16.0 + - - +
276A THR* 3.2 10.6 + - - +
278A PHE* 1.3 74.7 - - - +
280A SER* 1.3 63.6 + - - +
282A MET* 4.1 5.1 - - - +
283A LYS* 3.3 46.2 + - - +
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Residues in contact with SER 280 (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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150A ILE* 3.5 20.0 - - - -
161A THR* 3.3 16.2 - - - +
163A PRO* 4.6 4.0 - - - -
173A ALA* 3.4 24.2 + - - +
175A LEU* 3.4 10.6 - - - +
276A THR 2.9 15.7 + - - -
277A THR 2.9 8.0 + - - -
279A ASN* 1.3 75.4 - - - +
281A ILE* 1.3 65.4 + - - +
283A LYS* 3.1 16.1 + - - +
284A CYS* 3.3 15.8 - - - -
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Residues in contact with ILE 281 (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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150A ILE* 3.7 21.1 - - + -
277A THR* 2.9 36.3 + - + +
278A PHE* 4.0 5.4 - - + +
280A SER* 1.3 75.0 - - - +
282A MET* 1.3 58.3 + - + +
284A CYS* 3.0 24.0 + - - +
289A ARG* 2.9 45.0 + - + -
292A LEU* 4.2 25.6 - - + +
293A TYR* 3.7 42.8 - - + +
296A THR* 5.1 1.1 - - - +
316A ILE* 5.9 1.8 - - + -
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Residues in contact with MET 282 (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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278A PHE* 2.8 39.8 + - + +
279A ASN* 4.1 6.5 - - - +
280A SER 3.2 0.2 - - - -
281A ILE* 1.3 77.7 - - + +
283A LYS* 1.3 58.7 + - + +
289A ARG* 2.7 52.0 + - - +
293A TYR* 3.2 27.1 - - - +
243C ASP* 4.6 4.7 - - - +
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Residues in contact with LYS 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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172A HIS* 3.3 48.1 + - + +
173A ALA* 3.9 16.8 - - - +
174A ILE 5.7 0.9 - - - +
175A LEU* 5.5 8.7 - - + -
279A ASN* 3.3 39.3 + - - +
280A SER* 3.1 10.4 + - - +
282A MET* 1.3 77.5 - - + +
284A CYS* 1.3 60.2 + - - +
285A ASP* 4.9 1.4 - - - +
186E ASP* 5.2 11.3 + - - +
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Residues in contact with CYS 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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163A PRO* 3.9 7.0 - - - -
170A LEU* 3.5 30.7 - - + -
172A HIS* 4.6 2.7 - - - -
173A ALA* 3.9 7.9 - - - -
280A SER 3.3 17.5 - - - -
281A ILE* 3.0 13.0 + - - +
283A LYS* 1.3 80.6 - - - +
285A ASP* 1.3 68.4 + - - +
288A ILE* 4.1 8.1 - - + -
289A ARG* 2.8 28.7 + - + -
292A LEU* 3.8 20.6 - - + -
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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