Contacts of the helix formed by residues 286 - 300 (chain B) in PDB entry 3IXK
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 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LEU 3.7 0.4 + - - -
285B PRO* 1.3 70.1 - - - +
287B LYS* 1.3 72.6 + - + +
289B PHE* 3.3 2.8 + - - +
290B GLU* 3.0 53.6 + - - +
374B GLN* 2.8 35.0 - - + +
375B SER 3.5 9.8 + - - +
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 3.7 22.4 - - + +
267B GLU* 3.7 31.3 + - - +
285B PRO* 2.8 4.8 + - + +
286B LYS* 1.3 87.8 - - + +
288B VAL* 1.3 64.8 + - + +
290B GLU* 3.3 11.7 + - - +
291B ALA* 3.3 19.8 + - - +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 5.3 4.0 - - + -
261B LEU* 4.4 10.4 - - + +
263B MET* 3.9 16.8 - - + -
267B GLU* 3.4 35.0 - - + +
268B TYR* 3.7 32.5 - - + +
284B LEU* 4.3 23.3 - - + -
285B PRO* 2.9 13.0 + - + +
287B LYS* 1.3 74.8 - - + +
289B PHE* 1.3 60.0 + - - +
291B ALA* 3.2 2.3 + - - +
292B ALA* 2.8 32.6 + - + +
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Residues in contact with PHE 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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284B LEU* 3.9 19.6 - - + +
285B PRO 2.9 12.2 + - - +
286B LYS* 3.6 9.0 - - - +
288B VAL* 1.3 78.1 - - - +
290B GLU* 1.3 76.5 + - + +
292B ALA* 3.2 0.7 + - + +
293B VAL* 2.9 53.9 + - + +
310B TRP* 3.7 19.5 - - + -
311B LEU* 4.9 13.0 - - + -
370B PHE* 4.3 1.6 - + - -
372B ILE* 3.5 19.5 - - + -
373B SER* 3.4 40.2 - - - -
374B GLN* 4.0 26.5 - - + -
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LYS* 3.0 57.0 + - + +
287B LYS* 4.0 12.2 - - - +
288B VAL 3.2 0.2 - - - -
289B PHE* 1.3 91.8 - - + +
291B ALA* 1.3 58.6 + - - +
293B VAL* 3.7 5.6 - - - +
294B LYS* 2.9 31.1 + - - +
374B GLN* 4.9 1.9 - - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.4 16.6 - - + +
263B MET* 4.1 20.0 - - + -
287B LYS 3.3 11.0 + - - +
288B VAL 3.2 6.7 + - - +
289B PHE 3.2 0.4 - - - -
290B GLU* 1.3 80.5 - - - +
292B ALA* 1.3 56.9 + - - +
294B LYS* 3.3 10.7 - - - +
295B SER* 3.0 27.7 + - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 6.3 0.4 - - + -
256B ILE* 3.9 22.4 - - + +
261B LEU* 4.6 6.9 - - + +
284B LEU* 4.2 18.4 - - + -
288B VAL* 2.8 17.3 + - + +
289B PHE 3.7 3.1 - - - +
291B ALA* 1.3 75.7 - - - +
293B VAL* 1.3 60.7 + - + +
295B SER* 3.2 2.1 + - - -
296B ILE* 2.8 43.9 + - + +
331B ILE* 5.8 2.5 - - + -
372B ILE* 5.7 3.1 - - + -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 2.9 54.7 + - + +
290B GLU* 3.7 6.1 - - - +
292B ALA* 1.3 72.7 - - + +
294B LYS* 1.3 58.8 - - - +
296B ILE* 3.9 6.4 - - - +
297B LYS* 2.7 63.8 + - - +
310B TRP* 4.7 15.3 - - + +
370B PHE* 4.3 17.5 - - + -
372B ILE* 5.9 0.4 - - + -
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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
----------------------------------------------------------
290B GLU 2.9 18.6 + - - +
291B ALA* 3.3 10.8 - - - +
293B VAL* 1.3 79.9 - - - +
295B SER* 1.3 61.9 + - - +
297B LYS* 3.5 7.9 - - - +
298B ALA* 3.1 23.4 + - - +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 3.4 32.5 + - - +
259B GLN* 6.2 0.3 - - - +
261B LEU* 4.7 7.1 - - - +
291B ALA 3.0 15.4 + - - -
292B ALA 3.2 3.5 + - - -
294B LYS* 1.3 77.2 - - - +
296B ILE* 1.3 58.7 + - - +
298B ALA* 3.5 4.8 + - - +
299B ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 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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256B ILE* 4.7 6.5 - - + -
292B ALA* 2.8 30.2 + - + +
293B VAL 3.9 3.1 - - - +
295B SER* 1.3 74.1 - - - +
297B LYS* 1.3 55.7 + - - +
299B ALA* 3.6 2.1 + - - +
300B SER* 2.7 33.8 + - - +
310B TRP* 3.8 21.5 - - + -
328B PHE* 4.7 7.6 - - + -
329B PRO* 4.0 34.4 - - + +
331B ILE* 4.2 12.1 - - + -
353B TYR* 4.4 11.2 - - + +
370B PHE* 4.2 13.2 - - + -
372B ILE* 4.1 26.0 - - + -
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B VAL* 2.7 38.6 + - - +
294B LYS* 3.5 7.9 - - - +
296B ILE* 1.3 77.5 - - - +
298B ALA* 1.3 63.3 + - - +
300B SER* 3.1 18.6 + - - -
301B SER* 3.2 12.9 + - - -
305B PHE* 5.8 0.2 - - - -
307B ASP* 4.8 8.7 + - - +
310B TRP* 3.5 47.2 - - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS* 3.1 12.8 + - + +
295B SER* 3.5 5.1 + - - +
296B ILE 3.4 0.2 - - - -
297B LYS* 1.3 77.0 - - - +
299B ALA* 1.3 63.1 + - - +
300B SER 3.1 1.6 - - - -
301B SER* 2.9 24.8 + - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 5.9 0.7 - - + -
257B ASN* 4.8 8.1 - - + +
295B SER 3.0 18.0 + - - +
296B ILE 4.1 0.7 - - - +
297B LYS 3.3 0.6 - - - -
298B ALA* 1.3 77.7 - - - +
300B SER* 1.3 57.8 + - - +
301B SER 3.5 0.8 + - - -
302B THR* 4.6 3.6 - - - +
327B ILE* 2.9 27.1 - - - +
329B PRO* 4.1 27.1 - - + -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE 2.7 22.2 + - - -
297B LYS* 3.1 8.6 + - - -
298B ALA 3.1 0.6 - - - -
299B ALA* 1.3 79.5 - - - +
301B SER* 1.3 60.7 + - - +
302B THR* 3.2 5.2 - - - +
303B GLU* 3.1 12.6 + - - +
305B PHE* 3.5 22.0 - - - -
310B TRP* 4.1 6.9 - - - -
327B ILE* 3.6 22.2 - - - -
328B PHE* 3.8 21.7 - - - -
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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