Contacts of the helix formed by residues 290 - 300 (chain C) in PDB entry 4LQL
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 290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289C PRO* 1.3 77.4 - - - +
291C LEU* 1.3 59.5 + - - +
292C ALA* 4.0 4.0 - - - +
293C VAL* 2.7 30.8 + - - +
294C GLN* 2.8 22.1 + - - +
350C LEU* 4.2 11.9 - - - -
351C GLU* 4.2 7.2 - - - -
377C ALA 3.4 7.3 + - - -
378C ARG* 4.5 0.4 - - - -
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Residues in contact with LEU 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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233C LEU* 5.1 13.9 - - + -
253C VAL* 3.6 30.7 - - + -
256C GLN* 5.3 4.3 - - + -
290C GLY* 1.3 63.0 - - - +
292C ALA* 1.3 53.8 + - - +
294C GLN* 2.9 15.2 + - - +
295C LEU* 2.8 56.2 + - + +
362C ARG* 4.4 9.4 - - + -
363C VAL 5.0 1.1 - - - +
377C ALA* 2.3 46.7 + - + +
378C ARG* 3.8 4.8 - - - +
379C LEU* 3.6 32.5 - - + -
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Residues in contact with ALA 292 (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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256C GLN* 3.9 16.9 - - + +
257C LEU* 5.7 0.9 - - - +
259C GLU* 4.1 7.6 - - + -
260C TYR* 3.4 42.7 - - + +
289C PRO* 4.9 4.7 - - + -
290C GLY 4.3 8.1 - - - +
291C LEU* 1.3 79.6 - - - +
293C VAL* 1.3 56.1 + - - +
295C LEU* 4.1 3.5 - - - +
296C LEU* 3.2 29.8 + - - +
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C PHE* 3.4 31.2 - - + -
289C PRO* 3.4 17.9 - - + -
290C GLY 2.7 35.6 + - - +
292C ALA* 1.3 69.8 - - - +
294C GLN* 1.3 53.5 + - - +
295C LEU 3.1 2.0 - - - -
296C LEU* 2.8 5.7 + - - +
297C MET* 2.5 39.7 + - + +
303C PHE* 3.4 32.3 - - + -
351C GLU* 3.5 20.6 - - + +
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Residues in contact with GLN 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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290C GLY 2.8 17.9 + - - +
291C LEU* 3.6 5.9 - - - +
293C VAL* 1.3 71.9 - - - +
295C LEU* 1.3 58.9 - - - +
297C MET* 3.4 11.8 + - + -
298C ILE 3.4 7.6 + - - -
350C LEU 2.5 28.4 + - - -
351C GLU* 3.9 2.0 - - - -
352C VAL* 2.9 37.8 + - - +
354C PRO* 3.0 35.7 - - + +
378C ARG* 3.5 2.6 - - - -
379C LEU* 2.6 59.3 + - + +
381C PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C LEU* 5.7 6.3 - - + -
260C TYR* 4.9 10.5 - - + -
291C LEU* 2.8 39.4 + - + +
292C ALA* 4.1 7.0 - - - +
294C GLN* 1.3 75.7 - - - +
296C LEU* 1.3 64.5 + - - +
298C ILE* 3.0 22.4 + - - +
299C ASP* 3.5 12.1 + - - -
354C PRO* 5.2 0.2 - - - -
379C LEU* 4.5 6.5 - - + -
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Residues in contact with LEU 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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260C TYR* 4.7 9.8 - - + +
263C ILE* 3.7 26.9 - - + -
264C LYS* 3.9 28.7 - - + +
267C LEU* 4.2 3.4 - - + -
275C PHE* 3.5 36.1 - - + -
292C ALA 3.2 19.0 + - - +
293C VAL* 2.8 12.9 + - - +
295C LEU* 1.3 77.9 - - - +
297C MET* 1.3 54.4 + - + +
298C ILE 3.0 4.7 + - - -
299C ASP* 3.6 2.6 + - - -
301C TYR* 3.4 62.0 + - + +
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Residues in contact with MET 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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293C VAL 2.5 21.3 + - - +
294C GLN* 3.4 37.7 - - + +
295C LEU 3.2 0.4 - - - -
296C LEU* 1.3 70.3 - - - +
298C ILE* 1.3 57.5 + - - +
300C GLY 4.4 0.4 - - - -
301C TYR 3.9 4.3 - - - +
303C PHE* 3.9 37.5 - - + +
315C THR* 5.8 1.3 - - - +
319C LYS* 2.6 35.5 + - - +
329C LEU* 4.8 14.6 - - - -
351C GLU* 3.7 17.7 - - + +
352C VAL 3.6 1.3 - - - -
353C ASP* 3.0 50.6 - - + +
355C THR* 3.3 2.3 + - - -
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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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294C GLN 3.4 9.4 + - - +
295C LEU* 3.0 15.6 + - - +
297C MET* 1.3 80.0 - - - +
299C ASP* 1.3 66.2 + - - +
300C GLY* 3.0 7.0 + - - -
319C LYS* 5.4 0.5 + - - -
354C PRO* 4.2 15.5 - - + -
355C THR* 4.3 9.7 + - - +
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Residues in contact with ASP 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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264C LYS* 5.6 10.1 - - - -
295C LEU 3.5 14.3 + - - -
296C LEU* 3.6 3.1 + - - -
298C ILE* 1.3 76.5 - - - +
300C GLY* 1.3 57.1 + - - +
301C TYR* 3.5 30.2 - - + -
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Residues in contact with GLY 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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273C ASP* 5.9 1.6 - - - +
296C LEU 3.8 0.8 + - - -
298C ILE 3.0 7.7 - - - +
299C ASP* 1.3 79.4 - - - +
301C TYR* 1.3 67.0 + - - +
302C GLY 3.4 2.6 + - - -
316C ARG* 4.9 5.0 - - - +
319C LYS* 4.2 31.4 - - - +
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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