Contacts of the helix formed by residues 292 - 302 (chain A) in PDB entry 1EKV
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 THR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ASP* 3.6 31.2 - - + +
233A HIS 3.8 3.6 - - - -
234A GLN* 4.6 2.7 - - + -
235A LEU* 4.0 3.1 - - - -
290A THR* 4.0 17.9 - - + -
291A ILE* 1.3 82.2 - - - +
293A MET* 1.3 66.0 + - - +
294A LYS* 3.4 11.6 + - - +
295A GLN* 3.0 36.3 + - - +
296A LEU* 3.0 18.5 + - - +
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Residues in contact with MET 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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186A ALA* 5.2 0.2 - - - -
226A LEU* 4.5 7.4 - - - -
228A LEU* 3.9 25.1 - - + -
232A ASP 3.9 1.2 + - - +
233A HIS* 3.2 23.3 + - + +
235A LEU* 3.7 16.8 - - + +
292A THR* 1.3 73.8 - - - +
294A LYS* 1.3 63.0 - - - +
296A LEU* 3.0 21.6 + - + +
297A LEU* 2.8 35.7 + - + +
323A ILE* 4.7 5.4 - - + -
325A TYR* 3.5 52.7 - - + +
330A LEU* 3.9 20.0 - - + -
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Residues in contact with LYS 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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232A ASP* 5.0 3.0 + - + +
250A GLU* 5.8 2.2 - - - +
292A THR* 3.0 11.8 - - - +
293A MET* 1.3 81.1 - - - +
295A GLN* 1.3 69.2 + - + +
297A LEU* 3.2 10.0 + - - +
298A ARG* 3.2 21.9 + - + +
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Residues in contact with GLN 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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247A TRP* 3.7 29.8 - - + -
249A HIS* 4.8 8.4 + - - -
250A GLU* 3.6 33.0 - - + +
289A ARG* 5.4 3.8 - - - +
290A THR 3.7 16.9 + - - +
291A ILE* 3.8 1.8 - - - +
292A THR* 3.0 37.7 + - - +
294A LYS* 1.3 85.5 - - + +
296A LEU* 1.3 57.0 + - - +
298A ARG* 3.5 5.2 + - - +
299A ALA* 2.9 30.3 + - - +
304A ARG* 4.7 2.6 + - - +
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Residues in contact with LEU 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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235A LEU* 4.8 9.6 - - + -
245A VAL* 5.0 14.4 - - + -
247A TRP* 4.4 10.7 - - + -
291A ILE* 5.2 6.1 - - + -
292A THR 3.0 11.8 + - - +
293A MET* 3.0 36.2 + - + +
295A GLN* 1.3 74.9 - - - +
297A LEU* 1.3 59.4 + - - +
299A ALA* 3.3 2.4 + - - +
300A LEU* 2.9 51.3 + - + +
305A VAL* 4.1 21.1 - - + -
308A VAL* 5.0 10.3 - - + -
323A ILE* 4.2 22.0 - - + -
330A LEU* 5.1 1.1 - - + -
332A ILE* 4.8 3.4 - - + -
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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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293A MET* 2.8 32.4 + - + +
294A LYS* 3.2 8.3 + - - +
296A LEU* 1.3 73.1 - - + +
298A ARG* 1.3 64.3 + - - +
300A LEU* 3.1 11.2 + - + +
301A GLU* 2.9 29.0 + - + +
325A TYR* 4.2 21.3 - - + -
326A LYS* 5.1 7.4 - - - +
328A ARG* 4.2 19.3 - - - +
330A LEU* 3.6 40.6 - - + -
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Residues in contact with ARG 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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250A GLU* 3.6 41.7 + - - +
294A LYS* 3.2 13.0 + - + +
295A GLN* 3.9 4.3 - - - +
297A LEU* 1.3 79.2 - - - +
299A ALA* 1.3 61.0 + - - +
301A GLU* 3.3 9.4 + - - +
302A GLU* 2.8 66.9 + - + +
304A ARG* 3.7 10.7 - - - +
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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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247A TRP* 3.6 28.3 - - + -
295A GLN 2.9 19.0 + - - +
296A LEU 3.7 2.2 - - - +
297A LEU 3.2 0.2 - - - -
298A ARG* 1.3 76.2 - - - +
300A LEU* 1.3 61.4 + - - +
303A GLY 3.2 2.8 + - - -
304A ARG* 2.7 55.9 + - + +
305A VAL* 3.6 13.2 + - + -
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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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296A LEU* 2.9 33.6 + - + +
297A LEU* 3.1 15.2 + - + +
299A ALA* 1.3 78.2 - - - +
301A GLU* 1.3 62.4 + - - +
303A GLY* 2.9 15.2 + - - -
305A VAL* 4.1 16.8 - - + -
330A LEU* 4.3 22.7 - - + -
331A HIS 3.9 10.5 - - - +
332A ILE* 4.0 23.3 - - + -
333A PRO* 3.9 30.2 - - + +
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Residues in contact with GLU 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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297A LEU* 2.9 18.7 + - + +
298A ARG* 3.7 11.0 - - - +
300A LEU* 1.3 73.9 - - + +
302A GLU* 1.3 62.3 + - + +
303A GLY* 2.9 9.4 + - - -
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Residues in contact with GLU 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 ARG* 2.8 61.1 + - + +
301A GLU* 1.3 78.5 - - + +
303A GLY* 1.3 65.2 + - - +
304A ARG* 3.3 28.8 + - - +
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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