Contacts of the helix formed by residues 290 - 299 (chain A) in PDB entry 1LCY
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 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 5.1 7.4 - - - +
235A THR* 3.3 22.9 - - + +
258A VAL* 3.2 16.1 - - - +
289A GLN* 1.3 83.9 + - - +
291A ALA* 1.3 64.1 + - - +
292A GLU* 2.9 42.7 + - + +
293A ASP* 2.9 37.6 + - - +
294A VAL* 3.8 2.4 + - - +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 5.2 10.3 - - + +
233A MET* 4.0 26.2 - - + +
235A THR* 2.8 20.2 + - - +
258A VAL* 3.6 14.0 - - + +
290A ASN* 1.3 70.9 - - - +
292A GLU* 1.3 65.7 + - + +
294A VAL* 3.1 11.8 + - - +
295A TYR* 3.2 25.1 + - + -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 4.2 23.5 - - + +
158A ASN* 2.7 45.0 + - - +
159A VAL* 5.4 2.1 - - + +
204A ARG* 5.4 4.5 + - - -
290A ASN* 2.9 17.3 + - + +
291A ALA* 1.3 78.1 - - + +
293A ASP* 1.3 61.0 + - - +
295A TYR* 3.4 3.8 + - - +
296A GLU* 3.0 27.1 + - + +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 4.5 2.6 - - - +
287A MET 5.0 3.6 - - - +
288A VAL* 4.2 18.6 - - + -
289A GLN* 2.9 31.3 + - - +
290A ASN* 2.9 32.7 + - - +
291A ALA 3.2 0.4 - - - -
292A GLU* 1.3 78.2 - - - +
294A VAL* 1.3 63.7 + - - +
296A GLU* 3.5 7.5 + - - +
297A ALA* 3.4 17.8 + - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 4.4 7.9 - - + -
233A MET* 3.4 42.2 - - + -
258A VAL* 4.2 8.1 - - + -
280A ILE* 4.0 18.2 - - + -
283A ILE* 3.6 25.6 - - + -
288A VAL* 4.8 2.7 - - + -
290A ASN 3.9 10.8 - - - +
291A ALA 3.1 3.7 + - - +
293A ASP* 1.3 76.6 - - - +
295A TYR* 1.3 57.9 + - - +
297A ALA* 3.0 7.3 + - - +
298A VAL* 2.9 40.1 + - + +
304A LEU* 5.1 2.2 - - + -
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO* 3.4 48.3 + - + +
93A VAL* 4.2 28.9 - - + -
227A ARG 5.5 4.7 - - - -
229A ILE* 4.4 17.3 - - + +
231A VAL* 3.8 21.8 + - - +
233A MET* 3.3 29.7 + - + +
291A ALA* 3.2 26.6 + - + -
292A GLU* 4.1 5.2 - - - +
294A VAL* 1.3 77.2 - - - +
296A GLU* 1.3 60.9 + - - +
297A ALA 3.1 0.2 - - - -
298A VAL* 3.6 15.2 - - + +
299A ARG* 3.0 44.4 + - + +
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.0 19.1 + - + +
293A ASP* 3.7 7.9 - - - +
294A VAL 3.2 0.4 - - - -
295A TYR* 1.3 77.4 - - - +
297A ALA* 1.3 57.2 + - - +
299A ARG* 3.5 15.5 + - - +
300A THR* 2.7 43.4 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ILE* 4.0 15.3 - - + -
293A ASP 3.4 8.6 + - - +
294A VAL 3.0 10.0 + - - +
296A GLU* 1.3 78.4 - - - +
298A VAL* 1.3 58.3 - - - +
299A ARG 3.1 1.8 - - - -
300A THR* 4.3 1.3 - - - -
301A GLN* 2.8 62.6 + - - +
304A LEU* 3.3 14.1 - - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ARG* 2.9 60.6 + - + +
229A ILE* 3.8 42.4 - - + -
294A VAL* 2.9 23.8 + - + +
295A TYR* 3.3 15.5 + - + +
297A ALA* 1.3 77.2 - - - +
299A ARG* 1.3 58.0 + - + +
300A THR 3.4 0.6 + - - -
301A GLN 3.8 0.5 - - - +
304A LEU* 3.6 20.9 - - + -
321A PRO* 3.9 8.5 - - + +
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO* 6.2 2.2 - - - +
93A VAL* 4.9 14.8 - - - +
226A ARG 6.0 2.5 - - - +
227A ARG* 4.0 28.5 - - + +
295A TYR* 3.0 29.9 + - - +
296A GLU* 3.5 14.4 + - - +
298A VAL* 1.3 81.2 - - + +
300A THR* 1.3 67.7 + - - +
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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