Contacts of the helix formed by residues 289 - 296 (chain D) 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 ILE 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B GLU 4.9 0.4 - - - +
60B SER* 1.2 85.2 - - - +
61B LYS* 2.9 46.0 - - + +
64B ILE* 4.1 0.2 - - + -
166D TYR* 3.8 4.7 - - + -
171D LEU* 3.7 25.4 - - + -
285D CYS* 4.4 6.1 - - + -
286D ASP* 2.8 29.0 + - + +
288D ASP* 1.4 68.7 - - - +
290D ARG* 1.3 55.1 + - - +
291D LYS 3.2 2.9 - - - -
292D ASP* 2.6 37.2 + - + +
293D LEU* 3.0 17.9 + - + +
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Residues in contact with ARG 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR* 2.6 39.0 + - - -
202B THR* 1.5 55.7 + - + +
205B GLU* 3.4 14.7 + - - +
244B ASP* 5.6 6.7 - - + -
268C GLY 5.8 0.6 + - - -
270C GLU* 4.8 2.0 + - - -
282D ILE* 3.3 31.0 + - + +
283D MET* 2.8 42.8 + - - +
284D LYS 4.6 0.2 - - - -
285D CYS* 2.8 14.3 + - + -
286D ASP 3.5 0.8 + - - -
287D VAL 3.9 4.0 + - - +
288D ASP 3.7 0.8 - - - -
289D ILE* 1.3 74.0 - - - +
291D LYS* 1.3 66.3 + - - +
293D LEU* 2.9 12.4 + - - +
294D TYR* 2.9 35.3 + - + -
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Residues in contact with LYS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ALA* 3.0 19.6 - - + +
205B GLU* 4.0 4.8 + - - +
208B ILE* 5.0 3.8 - - - -
243B PRO* 3.4 47.2 - - + +
287D VAL 2.5 31.9 + - - -
288D ASP* 3.5 19.4 - - - +
290D ARG* 1.3 82.2 - - - +
292D ASP* 1.3 70.9 + - - +
294D TYR* 3.9 8.7 + - - +
295D ALA* 3.5 19.9 + - - +
325D MET* 4.8 4.0 - - - -
326D LYS 5.2 1.2 - - - +
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Residues in contact with ASP 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 4.7 14.7 - - - +
60B SER* 4.6 1.2 - - - -
149D THR* 4.4 24.0 - - + +
150D GLY* 5.0 1.1 - - - -
288D ASP 4.1 5.4 - - - +
289D ILE* 2.6 32.4 + - + +
291D LYS* 1.3 80.7 - - - +
293D LEU* 1.3 62.1 + - - +
295D ALA* 3.3 2.3 + - - -
296D ASN* 2.8 38.4 + - - +
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Residues in contact with LEU 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LYS* 5.2 0.2 - - - +
149D THR* 5.1 4.3 - - + -
150D GLY* 3.0 38.8 - - - +
151D ILE* 3.4 9.6 - - + +
164D PRO* 3.8 11.7 - - + -
165D ILE 4.1 7.4 - - - +
171D LEU* 5.9 0.2 - - + -
282D ILE* 4.0 24.5 - - + -
285D CYS* 3.6 37.7 - - + -
289D ILE* 3.0 19.7 + - + +
290D ARG* 2.9 12.0 + - - +
292D ASP* 1.3 77.0 - - - +
294D TYR* 1.4 60.1 + - - +
296D ASN 3.3 12.1 + - - +
297D THR* 3.2 15.2 + - - -
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Residues in contact with TYR 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASP* 3.7 15.8 + - - -
279D PHE* 3.7 26.6 - + - -
282D ILE* 3.4 42.6 - - + +
283D MET* 4.6 1.6 - - - -
290D ARG* 2.9 39.2 + - + +
291D LYS* 4.3 4.5 - - - +
293D LEU* 1.4 73.3 - - - +
295D ALA* 1.3 56.6 + - - +
296D ASN 3.2 1.0 + - - -
297D THR* 3.8 6.7 + - - -
317D ILE* 4.0 15.5 - - + -
321D ALA* 3.7 20.6 - - + -
322D PRO* 3.9 2.6 - - + +
325D MET* 4.1 24.0 - - + -
326D LYS 3.9 13.7 - - - +
327D ILE* 3.4 23.7 - - + +
328D LYS 3.1 22.9 + - - +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LYS 3.5 11.9 + - - +
292D ASP* 3.3 5.4 + - - +
294D TYR* 1.3 78.1 - - - +
296D ASN* 1.3 77.7 + - - +
326D LYS* 4.0 24.7 + - + +
328D LYS* 3.1 36.5 - - + +
330D ILE* 3.7 1.7 - - - +
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Residues in contact with ASN 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B MET* 3.5 20.4 - - + +
147D ARG* 2.8 34.4 + - - +
149D THR* 3.9 8.6 + - - -
150D GLY* 3.4 0.5 - - - -
151D ILE 2.9 25.5 + - - +
292D ASP* 2.8 32.1 + - - +
293D LEU 3.3 5.5 - - - +
294D TYR 3.2 0.2 - - - -
295D ALA* 1.3 92.4 - - - +
297D THR* 1.3 61.5 + - - +
298D VAL* 3.7 1.3 + - - -
330D ILE* 3.7 7.9 - - - -
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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