Contacts of the helix formed by residues 288 - 304 (chain B) in PDB entry 5ULM
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 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ARG 5.4 2.5 - - - +
285B ASN 6.1 0.4 - - - +
286B LEU 4.4 0.6 + - - +
287B TYR* 1.3 79.5 - - - +
289B GLY* 1.3 69.5 + - - +
291B GLU* 3.3 17.0 + - - +
292B LEU* 3.0 20.7 + - + -
324B ILE* 4.9 1.1 - - - -
619B GLU* 5.6 2.9 - - - +
640B GLU* 4.2 14.7 + - - -
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Residues in contact with GLY 289 (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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288B THR* 1.3 78.8 - - - +
290B LYS* 1.3 62.8 + - - -
291B GLU* 4.8 2.0 - - - -
293B ALA* 3.3 16.3 + - - +
324B ILE* 3.6 26.2 - - - +
640B GLU* 6.0 1.1 - - - -
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLY* 1.3 70.4 - - - -
291B GLU* 1.3 85.6 + - + +
293B ALA* 3.2 9.9 + - + +
294B ALA* 3.0 34.3 + - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B TYR* 3.9 24.2 - - + +
288B THR* 3.5 18.2 + - - +
289B GLY* 3.2 1.3 - - - -
290B LYS* 1.3 104.7 + - + +
292B LEU* 1.3 60.9 + - - +
294B ALA* 3.5 6.5 + - - +
295B GLU* 3.3 19.6 + - - +
640B GLU* 5.6 4.0 - - - +
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Residues in contact with LEU 292 (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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283B ALA* 3.6 33.0 - - + +
284B ARG* 4.2 7.9 - - + +
287B TYR* 3.5 23.2 - - + +
288B THR* 3.0 18.3 + - + -
289B GLY 3.7 7.9 - - - +
290B LYS 3.3 0.2 - - - -
291B GLU* 1.3 74.4 - - - +
293B ALA* 1.3 65.0 + - - +
295B GLU* 3.2 2.2 + - + +
296B LEU* 3.0 48.0 + - + +
320B SER 4.1 14.8 - - - +
323B ASP* 4.1 16.2 - - + +
324B ILE* 3.9 19.7 - - + -
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Residues in contact with ALA 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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289B GLY 3.3 5.9 + - - +
290B LYS* 3.2 14.1 + - + +
292B LEU* 1.3 76.9 - - - +
294B ALA* 1.3 62.2 + - - +
296B LEU* 3.4 6.2 + - - +
297B ALA* 3.0 24.3 + - - +
321B TYR* 5.8 1.7 - - + -
324B ILE* 3.7 25.5 - - + +
326B ASP* 5.9 1.3 - - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LYS* 3.0 27.2 + - - +
291B GLU* 3.6 10.3 - - - +
293B ALA* 1.3 74.4 - - - +
295B GLU* 1.3 62.8 + - - +
297B ALA* 3.3 8.9 + - - +
298B ARG* 3.1 41.1 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASP* 5.1 2.6 - - - +
283B ALA* 3.5 28.7 - - + -
287B TYR* 3.9 30.5 + - + -
291B GLU 3.3 9.6 + - - +
292B LEU 3.2 8.4 + - - +
294B ALA* 1.3 79.1 - - - +
296B LEU* 1.3 56.4 + - - +
298B ARG* 2.8 36.5 + - - +
299B ILE* 3.0 40.2 + - + +
302B ARG* 5.4 1.6 + - - -
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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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280B ILE* 4.9 4.7 - - + -
283B ALA* 4.6 11.2 - - + -
292B LEU* 3.0 39.8 + - + +
293B ALA* 3.8 4.7 - - - +
295B GLU* 1.3 72.6 - - - +
297B ALA* 1.3 55.9 + - - +
299B ILE* 3.3 11.5 + - + +
300B ARG* 2.7 39.4 + - - +
317B LEU* 4.6 9.7 - - + +
320B SER* 3.3 47.1 - - - +
321B TYR* 3.7 35.4 - - + +
324B ILE* 4.6 7.0 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 3.0 17.8 + - - +
294B ALA* 3.3 7.2 + - - +
296B LEU* 1.3 71.7 - - - +
298B ARG* 1.3 64.4 + - - +
300B ARG* 3.4 16.6 + - - +
301B GLN* 3.4 16.8 + - - +
321B TYR* 5.2 1.1 + - - -
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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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294B ALA* 3.1 26.7 + - - +
295B GLU* 2.8 60.3 + - - +
296B LEU 3.2 0.2 - - - -
297B ALA* 1.3 78.4 - - - +
299B ILE* 1.3 61.9 + - + +
300B ARG 3.5 0.3 + - - -
301B GLN* 3.6 34.6 + - - +
302B ARG* 4.0 8.5 + - - +
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Residues in contact with ILE 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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276B ILE* 4.1 12.1 - - + +
279B ASP* 3.5 34.5 - - + +
280B ILE* 3.8 27.1 - - + +
283B ALA* 4.2 3.6 - - + -
295B GLU* 3.0 38.0 + - + +
296B LEU* 3.3 11.9 + - + +
298B ARG* 1.3 76.8 - - - +
300B ARG* 1.3 57.7 + - - +
302B ARG* 3.3 30.3 + - - +
303B VAL* 3.0 35.6 + - + +
317B LEU* 4.9 4.3 - - + -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU 2.7 22.0 + - - +
297B ALA* 3.7 10.8 - - - +
298B ARG 3.3 0.8 - - - -
299B ILE* 1.3 70.3 - - - +
301B GLN* 1.3 57.1 + - - +
303B VAL* 3.0 5.5 + - - +
304B ASP* 2.7 74.2 + - - +
317B LEU* 3.6 26.4 - - + +
321B TYR* 2.8 57.0 + - - +
329B SER* 4.7 5.5 + - - -
332B LYS 5.8 0.2 - - - -
333B LEU* 4.1 36.2 - - - +
336B THR* 5.5 2.2 + - - +
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Residues in contact with GLN 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 ALA 3.4 9.4 + - - +
298B ARG* 3.6 32.7 + - - +
300B ARG* 1.3 77.1 - - - +
302B ARG* 1.3 66.5 + - + +
304B ASP* 3.6 4.1 + - - +
305B ASN* 3.4 26.7 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 3.3 22.6 + - - -
276B ILE* 3.4 27.6 - - + +
279B ASP* 2.8 34.5 + - - +
295B GLU* 5.4 1.8 + - - -
298B ARG 4.6 5.5 + - - +
299B ILE* 3.3 31.8 + - - +
300B ARG 3.2 0.4 - - - -
301B GLN* 1.3 80.4 - - + +
303B VAL* 1.3 59.2 + - - +
305B ASN* 2.9 22.7 + - - +
306B ILE* 3.1 20.4 + - + +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.7 28.7 - - + +
299B ILE* 3.0 25.4 + - + +
300B ARG* 3.6 11.9 - - - +
302B ARG* 1.3 73.2 - - - +
304B ASP* 1.3 68.3 + - - +
305B ASN 3.1 3.7 + - - -
306B ILE* 3.4 23.8 + - + +
309B LEU* 4.0 33.5 - - + +
313B ILE* 4.0 9.2 - - + -
317B LEU* 3.8 26.9 - - + -
333B LEU* 5.5 1.3 - - + -
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Residues in contact with ASP 304 (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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300B ARG* 2.7 61.1 + - - +
301B GLN* 4.0 5.3 - - - +
303B VAL* 1.3 77.0 - - - +
305B ASN* 1.3 66.1 + - - +
306B ILE 3.7 0.4 - - - -
309B LEU* 5.5 2.1 - - - +
333B LEU* 5.6 1.2 - - - +
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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