Contacts of the helix formed by residues 289 - 296 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU 4.9 0.7 - - - +
60A SER* 1.2 84.3 - - - +
61A LYS* 2.9 45.3 - - + +
64A ILE* 4.1 0.2 - - + -
166C TYR* 3.8 4.7 - - + -
171C LEU* 3.7 26.0 - - + -
285C CYS* 4.4 6.3 - - + -
286C ASP* 2.8 29.2 + - + +
288C ASP* 1.4 67.9 - - - +
290C ARG* 1.3 55.8 + - - +
291C LYS 3.2 2.5 - - - -
292C ASP* 2.6 37.9 + - + +
293C LEU* 3.0 17.1 + - + +
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Residues in contact with ARG 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR* 2.6 39.4 + - - -
202A THR* 1.5 55.7 + - + +
205A GLU* 3.4 14.9 + - - +
244A ASP* 5.6 6.5 - - + -
268B GLY 5.8 0.8 + - - -
270B GLU* 4.8 1.8 + - - -
282C ILE* 3.3 31.5 + - + +
283C MET* 2.8 42.9 + - - +
284C LYS 4.6 0.4 - - - -
285C CYS* 2.8 13.5 + - + -
286C ASP 3.5 1.4 + - - +
287C VAL 4.0 3.8 - - - +
288C ASP 3.7 0.6 - - - -
289C ILE* 1.3 75.8 - - - +
291C LYS* 1.3 64.7 + - - +
293C LEU* 2.9 12.3 + - - +
294C TYR* 2.9 34.4 + - + -
325C MET* 6.2 0.4 - - - -
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Residues in contact with LYS 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 3.0 20.2 - - + +
205A GLU* 4.0 5.2 + - - +
208A ILE* 5.0 4.5 - - - -
243A PRO* 3.4 44.6 - - + +
287C VAL 2.5 31.7 + - - -
288C ASP* 3.5 19.4 - - - +
289C ILE 3.0 0.2 + - - -
290C ARG* 1.3 81.1 - - - +
292C ASP* 1.3 70.6 + - - +
294C TYR* 3.9 8.1 + - - +
295C ALA* 3.5 19.8 + - - +
325C MET* 4.8 4.7 - - - -
326C LYS 5.2 1.0 - - - +
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Residues in contact with ASP 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 4.7 14.2 - - - +
60A SER* 4.6 1.7 + - - -
149C THR* 4.4 25.3 - - + +
150C GLY* 5.0 1.3 - - - -
288C ASP 4.1 5.0 - - - +
289C ILE* 2.6 32.1 + - - +
291C LYS* 1.3 80.1 - - - +
293C LEU* 1.3 62.4 + - - +
295C ALA* 3.3 2.7 + - - +
296C ASN* 2.8 38.9 + - - +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 5.2 0.2 - - - +
149C THR* 5.0 4.3 - - + -
150C GLY* 3.0 38.8 - - - +
151C ILE* 3.4 10.0 - - + +
164C PRO* 3.8 11.7 - - + -
165C ILE 4.1 7.2 - - - +
171C LEU* 5.9 0.2 - - + -
282C ILE* 4.0 24.7 - - + -
285C CYS* 3.6 37.9 - - + -
289C ILE* 3.6 20.2 - - + +
290C ARG* 2.9 12.8 + - - +
292C ASP* 1.3 76.4 - - - +
294C TYR* 1.4 59.8 + - - +
296C ASN 3.3 12.1 + - - +
297C THR* 3.2 15.2 + - - -
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Residues in contact with TYR 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ASP* 3.7 15.7 + - - -
279C PHE* 3.7 26.7 - + - -
282C ILE* 3.4 43.0 - - + +
283C MET* 4.6 1.2 - - - -
290C ARG* 2.9 39.2 + - + +
291C LYS* 4.3 3.8 - - - +
293C LEU* 1.4 72.0 - - - +
295C ALA* 1.3 57.8 + - - +
296C ASN 3.2 1.2 + - - -
297C THR* 3.8 7.5 + - - -
317C ILE* 4.0 16.2 - - + -
321C ALA* 3.7 22.2 - - + -
322C PRO* 3.9 2.7 - - + +
325C MET* 4.1 22.9 - - + -
326C LYS 3.9 12.3 - - - +
327C ILE* 3.4 23.5 - - + +
328C LYS 3.1 22.7 + - - +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ARG* 5.6 0.2 + - - -
291C LYS 3.5 11.2 + - - +
292C ASP* 3.3 6.0 + - - +
294C TYR* 1.3 78.1 - - - +
296C ASN* 1.3 77.2 + - - +
326C LYS* 4.0 24.8 + - + +
328C LYS* 3.1 36.0 - - + +
330C ILE* 3.7 2.3 - - - +
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Residues in contact with ASN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET* 3.5 21.3 - - + +
147C ARG* 2.8 34.3 + - - +
149C THR* 3.9 8.9 + - - -
150C GLY* 3.4 0.2 - - - -
151C ILE 2.9 26.0 + - - +
292C ASP* 2.8 31.5 + - - +
293C LEU 3.3 5.3 - - - +
294C TYR 3.2 0.2 - - - -
295C ALA* 1.3 93.1 - - - +
297C THR* 1.3 60.6 + - - +
298C VAL* 3.7 1.6 - - - -
330C ILE* 3.7 7.6 - - - -
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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