Contacts of the helix formed by residues 273 - 283 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178I LEU* 4.4 0.4 - - - -
261I LEU 3.1 14.6 - - - -
262I PHE 3.4 18.6 + - - -
264I PRO* 3.7 8.7 - - - +
272I CYS* 1.3 77.9 - - - +
274I ILE* 1.3 60.5 + - - -
275I HIS* 2.8 16.1 + - - -
276I GLU* 2.9 16.6 + - - +
277I THR* 3.3 10.8 + - - -
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Residues in contact with ILE 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I MET* 3.5 30.9 - - + +
155I SER* 5.7 0.4 - - - +
160I THR* 3.4 24.7 - - + +
162I THR* 4.9 0.8 - - + +
178I LEU* 3.3 30.7 - - + -
261I LEU* 2.9 32.1 + - + +
262I PHE* 3.6 31.6 - - + -
273I GLY* 1.3 70.8 - - - -
275I HIS* 1.3 60.9 + - - +
276I GLU 3.4 0.2 - - - -
277I THR* 4.0 6.6 - - + -
278I THR* 3.1 27.9 + - - -
309I ILE* 5.5 3.1 - - + -
313I MET* 4.0 15.0 - - + +
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Residues in contact with HIS 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I PHE* 3.1 54.6 + + + -
263I GLN* 5.9 0.2 - - + -
273I GLY* 2.8 7.2 + - - -
274I ILE* 1.3 75.6 - - - +
276I GLU* 1.3 89.2 + - + +
278I THR* 4.1 0.9 + - - -
279I PHE* 3.6 18.7 + - - +
312I ARG* 5.6 0.4 - - - -
313I MET* 4.1 12.6 - - - -
316I GLU* 3.7 44.4 - - + -
317I ILE* 4.1 9.2 - - + +
320I LEU* 3.9 16.3 - - + +
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Residues in contact with GLU 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I CYS* 3.9 29.5 - - + +
273I GLY 3.5 8.4 + - - +
275I HIS* 1.3 106.9 + - + +
277I THR* 1.3 59.9 + - - +
279I PHE* 3.4 6.5 + - - +
280I ASN* 2.9 41.0 + - - +
320I LEU* 3.5 25.5 - - + +
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Residues in contact with THR 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I THR* 6.2 0.4 - - + -
161I HIS* 6.0 0.4 - - - -
162I THR* 3.4 25.1 - - + +
176I LEU* 3.7 22.4 - - + +
177I ARG 5.3 1.3 - - - +
178I LEU* 3.8 29.1 - - + +
272I CYS* 3.9 11.6 - - - +
273I GLY 3.3 12.4 + - - -
274I ILE* 4.1 6.7 - - + -
275I HIS 3.5 0.2 - - - -
276I GLU* 1.3 73.0 - - - +
278I THR* 1.4 66.8 + - - +
280I ASN* 2.9 18.4 + - - +
281I SER* 3.1 14.2 + - - -
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Residues in contact with THR 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I ILE* 4.0 14.4 - - + +
153I MET* 3.5 12.0 - - + +
162I THR* 3.4 23.9 - - - +
274I ILE 3.1 17.2 + - - -
275I HIS 4.1 4.9 - - - -
276I GLU 3.5 0.2 - - - -
277I THR* 1.4 72.7 - - - +
279I PHE* 1.3 62.8 + - - +
281I SER* 3.1 10.2 + - - -
282I ILE* 3.2 26.4 + - + +
297I THR* 3.9 19.3 - - + +
313I MET* 3.9 2.6 - - + +
317I ILE* 3.6 27.1 - - + -
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Residues in contact with PHE 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275I HIS 3.6 13.4 + - - +
276I GLU* 3.4 10.0 + - - +
277I THR 3.2 1.0 - - - -
278I THR* 1.3 79.4 - - - +
280I ASN* 1.3 75.7 + - - +
282I ILE* 3.8 9.2 - - - +
283I MET* 3.0 54.2 + - + +
294I TYR* 3.7 27.1 - + + -
317I ILE* 5.4 6.7 - - + +
320I LEU* 3.4 58.8 - - + -
321I ALA* 4.4 1.1 - - - -
322I PRO* 5.1 2.2 - - + -
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Residues in contact with ASN 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I LEU* 3.7 17.5 - - + +
272I CYS* 4.7 14.0 - - - +
276I GLU* 2.9 32.6 + - - +
277I THR* 2.9 3.5 + - - +
279I PHE* 1.3 92.6 - - - +
281I SER* 1.3 64.9 + - - +
283I MET* 3.8 9.8 + - - +
284I LYS* 3.6 21.6 + - - +
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Residues in contact with SER 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I ILE* 3.7 22.9 - - - -
162I THR* 3.0 23.8 + - - -
164I PRO* 3.8 4.9 - - - -
174I ALA* 2.7 28.8 + - - +
176I LEU* 3.1 10.4 - - - +
277I THR 3.1 5.3 + - - -
278I THR 3.7 2.5 - - - -
280I ASN* 1.3 73.2 - - - +
282I ILE* 1.3 65.6 + - - +
284I LYS* 2.8 19.7 + - - +
285I CYS* 3.4 12.9 - - - -
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Residues in contact with ILE 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I ILE* 4.3 13.6 - - + +
278I THR* 3.2 26.9 + - + +
279I PHE* 3.8 4.9 - - - +
281I SER* 1.3 77.4 - - - +
283I MET* 1.3 67.2 + - + +
284I LYS 3.2 1.2 + - - -
285I CYS* 3.3 15.8 + - - +
290I ARG* 3.3 25.5 + - + +
293I LEU* 4.0 22.2 - - + +
294I TYR* 3.4 69.1 - - + +
297I THR* 5.1 1.6 - - - +
317I ILE* 5.8 1.1 - - + -
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Residues in contact with MET 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G SER* 6.1 3.8 - - - -
201G THR* 4.2 8.7 + - - +
244G ASP* 4.5 15.7 - - - +
268H GLY 5.1 2.4 - - - +
279I PHE* 3.0 47.0 + - + +
280I ASN* 4.0 8.3 - - - +
281I SER 3.1 1.8 + - - -
282I ILE* 1.3 80.3 - - + +
284I LYS* 1.3 57.2 + - + +
285I CYS 3.4 0.4 - - - -
290I ARG* 2.8 45.2 + - - +
294I 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