Contacts of the helix formed by residues 273 - 283 (chain J) in PDB entry 3LUE
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 273 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178J LEU* 4.9 0.2 - - - -
261J LEU 3.1 15.3 - - - -
262J PHE 3.4 17.9 + - - -
264J PRO* 3.7 9.3 - - - +
272J CYS* 1.3 77.2 - - - +
274J ILE* 1.3 61.5 + - - -
275J HIS* 2.8 15.9 + - - -
276J GLU* 2.9 16.6 + - - +
277J THR* 3.3 10.6 + - - -
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Residues in contact with ILE 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J MET* 3.5 30.9 - - + +
155J SER* 5.7 0.2 - - - +
160J THR* 3.4 25.1 - - + +
162J THR* 5.6 0.4 - - + -
178J LEU* 3.3 30.1 - - + -
180J LEU 5.4 0.2 - - - +
261J LEU* 2.9 32.7 + - + +
262J PHE* 3.6 32.3 - - + -
273J GLY* 1.3 70.6 - - - -
275J HIS* 1.3 59.4 + - - +
276J GLU 3.4 0.2 - - - -
277J THR* 4.0 7.4 - - + -
278J THR* 3.1 27.9 + - - -
309J ILE* 5.5 2.7 - - + -
313J MET* 4.0 15.3 - - + +
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Residues in contact with HIS 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262J PHE* 3.1 54.1 + + + -
263J GLN* 5.9 0.2 - - + -
273J GLY* 2.8 6.2 + - - -
274J ILE* 1.3 76.3 - - - +
276J GLU* 1.3 87.9 + - + +
278J THR* 4.1 1.0 + - - -
279J PHE* 3.6 18.9 + - - +
312J ARG* 5.6 0.2 - - - -
313J MET* 4.1 11.9 - - - -
316J GLU* 3.7 42.3 + - + -
317J ILE* 4.1 9.6 - - + +
320J LEU* 3.9 16.6 - - + +
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Residues in contact with GLU 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J CYS* 3.9 30.7 - - + +
273J GLY 2.9 8.2 + - - +
275J HIS* 1.3 105.7 + - + +
277J THR* 1.3 59.3 + - - +
279J PHE* 3.4 5.8 + - - +
280J ASN* 2.9 40.7 + - - +
320J LEU* 3.5 25.9 - - + +
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Residues in contact with THR 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J THR* 6.2 0.7 - - + -
161J HIS* 6.0 0.4 - - - -
162J THR* 3.4 25.8 - - + +
176J LEU* 3.7 22.0 - - + +
177J ARG 5.3 1.1 - - - +
178J LEU* 3.8 29.5 - - + +
272J CYS* 3.9 12.1 - - - +
273J GLY 3.3 12.8 + - - -
274J ILE* 4.1 6.5 - - + -
276J GLU* 1.3 73.7 - - - +
278J THR* 1.4 65.9 + - - +
280J ASN* 2.9 18.4 + - - +
281J SER* 3.1 14.7 + - - -
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Residues in contact with THR 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J ILE* 4.0 14.3 - - + +
153J MET* 3.5 12.1 - - + +
162J THR* 3.4 23.5 - - - +
274J ILE 3.1 17.1 + - - -
275J HIS 4.1 5.4 - - - -
277J THR* 1.4 74.1 - - - +
279J PHE* 1.3 62.1 + - - +
281J SER* 3.1 10.7 + - - -
282J ILE* 3.2 25.8 + - + +
297J THR* 3.9 19.3 - - + +
313J MET* 3.9 2.5 - - + +
317J ILE* 3.6 26.5 - - + -
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Residues in contact with PHE 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J HIS 3.6 12.6 + - - +
276J GLU* 3.4 10.7 + - - +
277J THR 3.2 0.6 - - - -
278J THR* 1.3 79.2 - - - +
280J ASN* 1.3 76.4 + - - +
282J ILE* 3.8 8.5 - - - +
283J MET* 3.0 52.2 + - + +
294J TYR* 3.7 27.4 - + + -
317J ILE* 5.4 6.5 - - + +
320J LEU* 3.4 57.7 - - + -
321J ALA* 4.4 2.2 - - - -
322J PRO* 5.1 2.5 - - + -
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Residues in contact with ASN 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LEU* 3.7 17.5 - - + +
272J CYS* 4.7 13.5 - - - -
276J GLU* 2.9 33.3 + - - +
277J THR* 2.9 3.5 + - - +
279J PHE* 1.3 91.1 - - - +
281J SER* 1.3 62.9 + - - +
283J MET* 3.8 10.1 + - - +
284J LYS* 3.6 21.6 + - + +
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Residues in contact with SER 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J ILE* 3.7 22.9 - - - -
162J THR* 3.0 23.5 + - - -
164J PRO* 3.8 5.8 - - - -
174J ALA* 2.7 27.0 + - - +
176J LEU* 3.1 10.0 - - - +
277J THR 3.1 4.3 + - - -
278J THR 3.7 2.0 - - - -
280J ASN* 1.3 72.9 - - - +
282J ILE* 1.3 65.8 + - - +
284J LYS* 2.8 20.3 + - - +
285J CYS* 3.4 11.6 - - - -
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Residues in contact with ILE 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J ILE* 4.3 13.4 - - + +
278J THR* 3.2 26.6 + - + +
279J PHE* 3.8 5.2 - - - +
281J SER* 1.3 77.2 - - - +
283J MET* 1.3 67.7 + - + +
284J LYS 3.2 0.9 + - - -
285J CYS* 3.3 16.0 + - - +
290J ARG* 3.3 25.9 + - + +
293J LEU* 4.0 23.1 - - + +
294J TYR* 3.4 68.6 - - + +
297J THR* 5.1 1.3 - - - +
317J ILE* 5.8 1.1 - - + -
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Residues in contact with MET 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H SER* 6.1 3.4 - - - -
201H THR* 4.2 8.6 + - - +
244H ASP* 4.5 15.9 - - - +
268I GLY 5.1 2.8 - - - +
279J PHE* 3.0 46.5 + - + +
280J ASN* 4.0 8.5 - - - +
281J SER 3.1 1.8 + - - -
282J ILE* 1.3 80.9 - - + +
284J LYS* 1.3 55.5 - - + +
285J CYS 3.4 0.2 - - - -
290J ARG* 2.8 44.6 + - - +
294J TYR* 4.6 5.2 - - - -
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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
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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