Contacts of the helix formed by residues 292 - 303 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B ASP* 3.7 31.6 - - + +
233B HIS 3.9 4.0 - - - -
234B GLN* 4.1 2.7 - - + +
235B LEU* 4.0 3.8 - - - -
290B THR* 4.2 15.3 - - + -
291B ILE* 1.3 80.8 - - - +
293B MET* 1.3 65.4 + - - +
294B LYS* 3.4 10.7 + - - +
295B GLN* 3.0 41.4 + - - +
296B LEU* 3.0 19.6 + - - +
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ALA* 5.2 0.2 - - - -
226B LEU* 4.5 8.3 - - - -
228B LEU* 3.9 21.3 - - + -
232B ASP 4.0 1.2 + - - +
233B HIS* 3.2 27.2 + - + +
235B LEU* 3.7 17.5 - - + +
292B THR* 1.3 72.6 - - - +
294B LYS* 1.3 54.1 + - - +
296B LEU* 2.9 21.3 + - + +
297B LEU* 2.7 42.6 + - + +
323B ILE* 4.7 5.2 - - + -
325B TYR* 3.5 52.9 - - + +
330B LEU* 3.9 20.4 - - + -
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ASP* 4.9 3.0 + - + +
250B GLU* 5.9 1.8 - - - +
292B THR* 3.4 11.1 + - - +
293B MET* 1.3 81.5 - - - +
295B GLN* 1.3 69.2 + - + +
297B LEU* 3.2 9.3 + - - +
298B ARG* 3.0 22.3 + - + +
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TRP* 3.7 30.0 - - + -
249B HIS* 4.7 10.8 - - - -
250B GLU* 3.9 31.3 - - - +
289B ARG* 5.2 4.2 - - - +
290B THR 3.7 15.9 + - - +
291B ILE* 3.8 1.2 - - - +
292B THR* 3.0 38.1 + - + +
294B LYS* 1.3 85.9 - - + +
296B LEU* 1.3 57.8 + - - +
298B ARG* 3.5 3.4 + - - +
299B ALA* 2.9 28.6 + - - +
304B ARG* 4.2 2.8 + - - -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU* 4.8 9.4 - - + -
245B VAL* 5.0 13.5 - - + -
247B TRP* 4.3 13.6 - - + -
291B ILE* 5.2 6.3 - - + -
292B THR 3.0 11.1 + - - +
293B MET* 2.9 35.7 + - + +
295B GLN* 1.3 75.4 - - - +
297B LEU* 1.3 66.6 + - - +
299B ALA* 3.2 1.6 + - - +
300B LEU* 3.0 39.7 + - + +
305B VAL* 4.1 21.3 - - + -
308B VAL* 5.0 9.9 - - + -
323B ILE* 4.2 21.8 - - + -
330B LEU* 5.1 2.0 - - + -
332B ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B MET* 2.7 28.4 + - + +
294B LYS* 3.7 7.4 - - - +
296B LEU* 1.3 74.6 - - - +
298B ARG* 1.3 65.6 + - - +
300B LEU* 3.1 17.9 + - + +
301B GLU* 3.1 14.7 + - - +
325B TYR* 4.4 20.4 - - + -
326B LYS* 5.1 6.5 - - - +
328B ARG* 4.0 28.5 - - - +
330B LEU* 3.7 34.3 - - + -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 3.4 42.5 + - - +
294B LYS* 3.0 14.4 + - + +
295B GLN* 3.8 5.4 - - - +
297B LEU* 1.3 81.6 - - - +
299B ALA* 1.3 59.7 + - - +
301B GLU* 3.5 11.9 - - + +
302B GLU* 2.7 70.4 + - + +
304B ARG* 4.0 6.7 - - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TRP* 3.7 13.0 - - + -
295B GLN 2.9 18.4 + - - +
296B LEU 3.2 2.4 + - - +
298B ARG* 1.3 75.3 - - - +
300B LEU* 1.3 58.1 + - - +
302B GLU 3.3 0.3 + - - -
303B GLY 2.8 24.9 + - - -
304B ARG* 2.8 41.4 + - + +
305B VAL* 3.4 24.9 + - + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 3.0 28.9 + - + +
297B LEU* 3.1 13.4 + - + +
299B ALA* 1.3 76.5 - - - +
301B GLU* 1.3 63.5 + - - +
303B GLY* 3.2 12.4 + - - -
305B VAL* 4.1 17.3 - - + -
330B LEU* 4.2 24.9 - - + -
331B HIS 3.9 18.6 - - - +
332B ILE* 3.9 23.6 - - + -
333B PRO* 3.9 24.5 - - + +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B LEU 3.1 11.4 + - - +
298B ARG* 3.5 18.1 - - - +
300B LEU* 1.3 81.2 - - - +
302B GLU* 1.3 74.1 + - + +
303B GLY* 3.1 1.3 + - - -
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 2.7 65.6 + - + +
299B ALA 4.1 0.7 - - - +
301B GLU* 1.3 87.0 - - + +
303B GLY* 1.3 62.6 + - - +
304B ARG* 2.6 37.9 + - + +
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ALA 2.8 7.8 + - - -
300B LEU 3.2 8.2 + - - -
301B GLU 3.1 6.0 + - - -
302B GLU* 1.3 79.3 - - - +
304B ARG* 1.3 60.0 + - - -
305B VAL 3.3 8.2 + - - +
306B ARG* 5.9 0.7 - - - +
333B PRO* 6.5 1.3 - - - -
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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