Contacts of the helix formed by residues 286 - 300 (chain C) in PDB entry 1L0N
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 ASN 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281C LEU* 5.6 0.5 - - - +
284C ILE* 2.9 15.4 + - + +
285C PRO* 1.3 76.7 + - - +
287C LYS* 1.3 67.4 + - - +
288C LEU* 2.9 31.7 + - - +
289C GLY* 3.2 13.7 + - - +
290C GLY* 3.0 22.9 + - - -
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Residues in contact with LYS 287 (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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148C ASN 4.6 2.0 + - - -
149C LEU* 5.2 1.8 + - - +
151C SER* 2.8 46.6 + - - -
152C ALA* 3.6 21.5 - - + +
281C LEU* 5.3 1.9 - - - +
286C ASN* 1.3 77.1 + - - +
288C LEU* 1.3 65.6 + - - +
290C GLY* 3.4 4.7 + - - -
291C VAL* 3.4 9.0 + - - +
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Residues in contact with LEU 288 (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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152C ALA* 3.3 34.1 - - + +
153C ILE* 4.7 2.5 - - + +
154C PRO* 4.3 18.6 - - + -
286C ASN* 2.9 12.5 + - - +
287C LYS* 1.3 75.5 - - - +
289C GLY* 1.3 64.5 + - - +
290C GLY 3.2 0.3 + - - -
291C VAL* 3.2 10.8 - - + +
292C LEU* 2.9 44.9 + - + +
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Residues in contact with GLY 289 (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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284C ILE* 4.0 11.8 - - - +
286C ASN* 3.2 16.5 + - - -
288C LEU* 1.3 80.5 - - - +
290C GLY* 1.3 53.2 + - - +
292C LEU* 3.5 10.3 - - - +
293C ALA* 2.8 37.4 + - - +
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Residues in contact with GLY 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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281C LEU* 3.5 37.3 - - - +
284C ILE* 4.2 9.0 - - - +
286C ASN 3.0 19.7 + - - -
287C LYS 3.9 0.4 - - - -
289C GLY* 1.3 77.7 - - - +
291C VAL* 1.3 56.1 + - - +
293C ALA* 3.7 0.9 - - - +
294C LEU* 2.8 27.5 + - - +
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Residues in contact with VAL 291 (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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149C LEU* 3.8 37.9 - - + +
150C LEU* 5.1 6.3 - - + +
152C ALA* 3.8 25.4 - - + -
153C ILE* 5.5 7.0 - - + +
281C LEU* 3.9 3.4 - - - +
287C LYS 3.4 5.0 + - - +
288C LEU* 3.2 17.7 + - + +
290C GLY* 1.3 73.7 - - - +
292C LEU* 1.3 66.5 + - + +
294C LEU* 3.7 18.8 - - + -
295C ALA* 3.1 22.5 + - + +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 2.9 40.6 + - + +
289C GLY* 3.5 9.9 - - - +
291C VAL* 1.3 82.6 - - + +
293C ALA* 1.3 56.8 + - - +
295C ALA* 3.4 5.8 + - + +
296C PHE* 2.9 28.2 + - - +
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Residues in contact with ALA 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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280C ILE* 3.8 15.9 - - + +
284C ILE* 3.7 22.9 - - + -
289C GLY 2.8 16.6 + - - +
290C GLY 4.0 2.2 - - - +
292C LEU* 1.3 76.3 - - - +
294C LEU* 1.3 63.4 + - - +
296C PHE* 3.8 8.3 - - - -
297C SER* 3.1 23.9 + - - -
359C PHE* 3.9 10.7 - - + -
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Residues in contact with LEU 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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149C LEU* 3.8 27.1 - - + -
274C PHE* 6.2 2.2 - - + -
277C ALA* 3.8 38.0 - - + +
278C TYR* 4.7 0.9 - - - +
280C ILE* 4.8 4.0 - - - +
281C LEU* 4.2 20.2 - - + -
290C GLY 2.8 18.8 + - - +
291C VAL* 3.6 17.9 - - + +
292C LEU 3.2 0.2 - - - -
293C ALA* 1.3 76.9 - - - +
295C ALA* 1.3 65.1 + - + +
297C SER* 2.8 25.8 + - - -
298C ILE* 4.0 2.8 + - - +
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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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291C VAL* 3.1 14.3 + - + +
292C LEU* 3.6 6.3 - - + +
294C LEU* 1.3 85.3 - - + +
296C PHE* 1.3 62.7 + - - +
298C ILE* 2.9 17.3 + - - +
299C LEU* 3.1 27.8 + - + +
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Residues in contact with PHE 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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292C LEU 2.9 18.1 + - - +
293C ALA* 3.9 9.2 - - - +
294C LEU 3.4 0.2 - - - -
295C ALA* 1.3 76.1 - - - +
297C SER* 1.3 60.4 + - - +
298C ILE 3.1 1.2 + - - -
299C LEU* 4.5 9.9 - - + +
300C ILE* 3.1 46.4 + - + +
303C LEU* 4.4 25.6 - - + -
359C PHE* 3.3 32.8 - + + -
363C LEU* 4.6 16.4 - - + -
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Residues in contact with SER 297 (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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276C PHE* 4.1 15.3 - - - -
277C ALA* 4.3 10.0 - - - +
280C ILE* 3.9 28.3 - - - -
293C ALA 3.1 14.1 + - - -
294C LEU 2.8 17.8 + - - -
295C ALA 3.0 0.6 + - - -
296C PHE* 1.3 76.4 - - - +
298C ILE* 1.3 62.7 + - - +
300C ILE* 3.4 4.7 - - - +
301C LEU* 5.6 0.7 - - - +
358C TYR* 2.7 30.1 + - - -
359C PHE* 3.8 9.8 - - - -
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Residues in contact with ILE 298 (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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95C TYR* 5.7 0.7 - - + +
117C VAL* 5.1 4.3 - - + +
120C LEU* 4.4 22.2 - - + -
121C LEU* 3.8 29.8 - - + -
124C MET* 3.5 34.8 - - + -
276C PHE* 3.6 28.3 - - + -
277C ALA* 5.1 5.6 - - + -
294C LEU 5.0 2.0 - - - +
295C ALA* 2.9 9.7 + - - +
297C SER* 1.3 86.9 + - - +
299C LEU* 1.3 59.8 + - + +
300C ILE* 3.0 9.6 + - - -
301C LEU* 3.1 26.8 + - + +
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Residues in contact with LEU 299 (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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117C VAL* 5.0 9.6 - - + -
121C LEU* 4.3 25.6 - - + -
295C ALA* 3.1 29.3 + - + +
296C PHE* 4.6 10.3 - - + +
298C ILE* 1.3 72.1 - - + +
300C ILE* 1.3 55.8 + - - +
301C LEU 3.0 6.3 - - - -
302C ALA* 2.9 32.3 + - + +
303C LEU* 4.0 4.0 + - - +
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Residues in contact with ILE 300 (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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296C PHE* 3.1 25.0 + - + +
297C SER* 3.4 24.9 - - - +
298C ILE 4.1 1.1 - - - +
299C LEU* 1.3 77.6 - - - +
301C LEU* 1.3 66.4 + - + +
302C ALA 3.0 0.4 - - - -
303C LEU* 2.8 28.8 + - + +
304C ILE* 3.2 10.5 + - + +
307C LEU* 5.9 0.2 - - + -
358C TYR* 3.8 11.0 - - + +
359C PHE* 3.9 24.5 - - + -
362C ILE* 3.7 38.4 - - + -
363C LEU* 3.8 24.0 - - + -
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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