Contacts of the helix formed by residues 284 - 296 (chain E) in PDB entry 3K6G
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 GLY 284 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B GLU* 5.9 0.6 + - - -
396B PHE* 4.3 4.7 - - - -
282E THR* 3.7 5.6 + - - -
283E ILE* 1.3 77.2 - - - +
285E MSE 1.3 60.2 + - - -
286E MSE 3.3 2.7 - - - -
287E THR* 3.1 13.4 + - - -
288E LEU* 2.8 26.9 + - - +
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Residues in contact with MSE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 4.2 9.9 - - + -
396B PHE* 3.4 60.2 + - + +
397B ARG* 4.0 28.0 - - - +
284E GLY* 1.3 70.8 - - - -
286E MSE 1.3 78.2 + - + +
288E LEU* 3.4 5.2 + - - +
289E LYS* 3.0 25.8 + - - +
305E PHE* 4.0 13.5 - - + -
309E ASP* 3.7 29.8 - - + +
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Residues in contact with MSE 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E GLY 3.3 0.6 - - - -
285E MSE 1.3 107.6 - - + +
287E THR* 1.3 60.3 + - - +
289E LYS* 3.6 32.9 - - + +
290E ALA* 3.0 27.9 + - - +
305E PHE* 4.9 1.1 - - + -
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Residues in contact with THR 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER 5.5 4.0 + - - -
310B GLU* 3.7 48.9 + - + +
311B VAL* 4.0 9.7 - - + +
314B ALA* 4.0 4.0 - - + -
283E ILE* 4.0 15.7 - - + -
284E GLY* 3.1 17.0 + - - +
286E MSE 1.3 77.0 - - - +
288E LEU* 1.3 64.2 + - - +
290E ALA* 3.2 6.1 + - - +
291E ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ILE* 4.1 22.3 - - + +
333B THR* 3.9 15.9 - - + +
336B PHE* 3.8 37.7 - - + -
337B LEU* 3.6 39.7 - - + +
341B GLY* 5.7 0.2 - - - -
396B PHE* 4.6 7.4 - - + -
283E ILE* 3.8 17.9 - - + +
284E GLY 2.8 16.4 + - - +
285E MSE 3.5 4.9 - - - +
287E THR* 1.3 77.6 - - - +
289E LYS* 1.3 56.5 + - - +
291E ALA* 3.3 6.2 + - - +
292E PHE* 2.9 29.3 + - - +
305E PHE* 4.2 1.8 - - + -
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Residues in contact with LYS 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E MSE 3.0 17.0 + - - +
286E MSE 3.6 32.5 - - + +
287E THR 3.2 0.2 - - - -
288E LEU* 1.3 77.0 - - - +
290E ALA* 1.3 56.3 + - - +
292E PHE* 3.3 1.4 + - - +
293E LYS* 2.9 48.9 + - + +
302E GLU* 2.5 45.9 + - - +
305E PHE* 3.6 39.8 - - + -
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B VAL* 3.9 23.3 - - + -
286E MSE 3.0 16.8 + - - +
287E THR* 3.2 5.1 + - - +
289E LYS* 1.3 76.7 - - - +
291E ALA* 1.3 63.0 + - - +
293E LYS* 3.4 7.0 + - - +
294E THR* 2.8 29.5 + - - +
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Residues in contact with ALA 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B VAL* 4.1 7.1 - - + +
314B ALA* 4.1 12.8 - - + -
315B ILE* 3.8 24.2 - - + -
318B ILE* 3.9 20.9 - - + -
287E THR 3.0 16.1 + - - +
288E LEU* 3.6 4.9 - - - +
289E LYS 3.3 0.2 - - - -
290E ALA* 1.3 76.3 - - - +
292E PHE* 1.3 61.8 + - - +
294E THR* 3.2 4.8 + - - -
295E LEU* 3.1 28.8 + - - +
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Residues in contact with PHE 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ILE* 5.1 1.1 - - - +
329B LEU* 3.8 31.1 - - + +
330B SER* 4.3 9.9 - - - -
333B THR* 3.5 27.1 - - + +
288E LEU 2.9 17.5 + - - +
289E LYS 3.5 3.4 - - - +
290E ALA 3.3 0.2 - - - -
291E ALA* 1.3 77.5 - - - +
293E LYS* 1.3 57.6 + - + +
295E LEU 3.3 0.7 + - - -
296E SER* 2.7 60.8 + - - -
301E SER* 3.5 22.0 - - - -
304E ALA* 3.9 15.5 - - + -
305E PHE* 3.8 32.8 - + + -
308E LEU* 3.7 21.3 - - + -
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Residues in contact with LYS 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E LYS* 2.9 36.6 + - + +
290E ALA* 3.9 6.3 - - - +
292E PHE* 1.3 84.5 - - + +
294E THR* 1.3 63.7 + - - +
296E SER* 3.8 11.1 + - - +
301E SER* 3.4 36.0 + - - +
302E GLU* 3.1 35.1 + - - +
305E PHE* 5.4 0.2 - - + -
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Residues in contact with THR 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B VAL* 4.5 5.5 - - - +
315B ILE* 3.7 24.6 - - + +
290E ALA* 2.8 20.0 + - - +
291E ALA* 3.4 9.7 - - - -
292E PHE 3.2 0.4 - - - -
293E LYS* 1.3 79.6 - - - +
295E LEU* 1.3 63.9 + - + +
296E SER 4.6 1.9 - - - +
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Residues in contact with LEU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ILE* 4.0 41.1 - - + +
318B ILE* 4.4 7.2 - - + -
319B ARG* 4.5 15.0 - - + +
322B MSE 4.1 18.2 - - + -
329B LEU* 3.8 32.8 - - + +
291E ALA 3.1 18.1 + - - +
294E THR* 1.3 83.3 - - + +
296E SER* 1.3 62.1 + - - +
297E GLY 3.7 1.2 + - - -
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Residues in contact with SER 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU* 3.6 9.8 - - - +
292E PHE* 2.7 48.4 + - - -
293E LYS 3.8 7.4 + - - +
294E THR 3.5 2.7 - - - +
295E LEU* 1.3 75.2 - - - +
297E GLY* 1.3 62.6 + - - +
298E ALA* 3.1 26.1 + - - +
301E SER* 3.9 13.2 - - - -
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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