Contacts of the helix formed by residues 290 - 302 (chain A) in PDB entry 1E0W
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 LYS 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLY 5.2 1.3 + - - -
242A ALA* 3.6 10.4 - - + +
270A ASP* 2.7 28.2 + - - +
279A THR* 3.1 18.9 + - - -
281A LEU 3.0 27.6 + - - +
282A LEU* 3.1 15.8 + - - +
283A PHE 3.6 19.5 - - - +
284A ASN* 3.4 30.7 - - - +
289A LYS* 1.3 74.7 - - - +
291A ALA* 1.3 67.3 + - - +
292A ALA* 3.2 6.5 - - + +
293A TYR* 3.0 17.1 + - - +
294A THR* 3.6 6.4 + - - -
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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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244A ALA* 4.2 13.9 - - + +
290A LYS* 1.3 73.4 - - - +
292A ALA* 1.3 61.6 + - - +
294A THR* 3.2 10.9 + - - +
295A ALA* 3.2 19.4 + - - +
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Residues in contact with ALA 292 (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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242A ALA* 3.6 28.5 + - + +
244A ALA* 4.1 15.6 - - - +
247A TYR* 3.7 25.9 - - + +
281A LEU 5.1 0.2 - - - +
282A LEU* 3.8 9.9 - - + -
290A LYS* 3.2 6.0 - - + +
291A ALA* 1.3 75.9 - - - +
293A TYR* 1.3 64.8 + - - +
295A ALA* 3.3 1.6 + - - +
296A VAL* 3.1 27.2 + - - +
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Residues in contact with TYR 293 (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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3A SER 3.5 16.5 + - - -
4A THR* 3.9 4.0 - - - -
5A LEU* 3.6 27.8 + - + +
37A GLU* 2.7 33.2 + - - -
282A LEU* 3.7 26.3 + - + +
283A PHE* 3.7 30.1 - + - -
289A LYS* 3.7 37.1 - - + -
290A LYS 3.0 13.6 + - - +
292A ALA* 1.3 77.1 - - - +
294A THR* 1.3 64.7 + - - +
296A VAL* 3.3 5.7 + - - +
297A LEU* 3.0 45.6 + - + +
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Residues in contact with THR 294 (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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289A LYS* 5.5 2.9 - - - +
290A LYS 3.6 6.1 + - - -
291A ALA* 3.2 12.4 + - - -
293A TYR* 1.3 85.3 - - - +
295A ALA* 1.3 58.0 + - - +
297A LEU* 3.9 5.0 - - + +
298A ASP* 2.9 47.1 + - - +
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Residues in contact with ALA 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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244A ALA* 3.6 39.9 - - + +
248A ALA* 4.2 14.1 - - + +
291A ALA 3.2 6.5 + - - +
292A ALA 3.7 7.4 - - - +
293A TYR 3.3 0.4 - - - -
294A THR* 1.3 77.8 - - - +
296A VAL* 1.3 60.7 + - - +
298A ASP* 4.0 5.8 - - - +
299A ALA* 3.1 22.9 + - - +
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Residues in contact with VAL 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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5A LEU* 3.9 12.6 - - + -
16A PHE* 3.7 33.4 - - + -
247A TYR* 3.8 34.3 - - + +
248A ALA* 5.2 0.9 - - - +
251A THR* 3.8 20.0 - - - +
282A LEU* 4.3 8.1 - - + -
292A ALA 3.1 18.2 + - - +
293A TYR* 3.7 4.9 - - - +
295A ALA* 1.3 73.2 - - - +
297A LEU* 1.3 65.4 + - - +
299A ALA* 3.2 4.6 + - - +
300A LEU* 2.9 28.0 + - + +
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Residues in contact with LEU 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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2A GLU 3.8 16.2 - - - +
3A SER* 4.1 12.8 - - - +
4A THR* 3.7 31.0 - - - +
5A LEU* 4.2 13.6 - - + +
8A ALA* 3.8 16.8 - - + -
293A TYR* 3.0 35.4 + - + +
294A THR* 3.9 5.4 - - + +
296A VAL* 1.3 75.3 - - - +
298A ASP* 1.3 62.7 + - - +
300A LEU* 3.3 5.5 + - - +
301A ASN* 3.0 36.1 + - - +
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Residues in contact with ASP 298 (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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294A THR* 2.9 36.3 + - - +
295A ALA* 4.0 6.4 - - - +
297A LEU* 1.3 82.0 - - - +
299A ALA* 1.3 60.6 + - - +
301A ASN* 3.3 8.0 + - - +
302A GLY 2.8 32.2 + - - +
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Residues in contact with ALA 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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248A ALA* 4.5 6.3 - - + +
251A THR* 3.9 18.2 - - + -
252A ASN* 3.8 28.2 - - - +
255A LEU* 3.5 15.2 - - - +
295A ALA 3.1 19.0 + - - +
296A VAL 3.2 4.9 + - - +
298A ASP* 1.3 74.2 - - - +
300A LEU* 1.3 62.9 + - - +
302A GLY* 3.2 13.9 + - - -
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Residues in contact with LEU 300 (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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5A LEU* 3.7 31.2 - - + +
8A ALA* 3.8 20.7 - - + +
9A ALA* 4.2 18.6 - - + +
11A GLN* 4.0 10.1 + - - -
12A SER* 4.5 10.0 + - - -
14A ARG* 6.4 0.4 - - + -
16A PHE* 4.0 22.0 - - + -
251A THR* 3.7 20.2 - - + -
255A LEU* 4.3 19.4 - - + +
263A ILE* 5.6 2.2 - - + -
296A VAL* 2.9 25.4 + - + +
297A LEU* 3.3 6.3 + - - +
299A ALA* 1.3 78.0 - - - +
301A ASN* 1.3 60.0 + - - +
302A GLY 3.5 0.5 + - - -
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Residues in contact with ASN 301 (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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1A ALA* 3.6 19.6 - - + +
2A GLU 3.0 42.9 + - - +
8A ALA* 3.7 6.3 - - - +
11A GLN* 3.0 19.4 + - - +
297A LEU* 3.0 31.2 + - - +
298A ASP* 3.9 8.3 + - - +
300A LEU* 1.3 74.2 - - - +
302A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 302 (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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298A ASP* 2.8 20.5 + - - +
299A ALA* 3.2 13.6 + - - -
300A LEU 3.3 1.2 + - - -
301A ASN* 1.3 79.2 - - - +
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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