Contacts of the helix formed by residues 284 - 297 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A PHE* 4.4 4.5 - - - -
282D THR* 3.7 6.1 + - - +
283D ILE* 1.3 77.9 - - - +
285D MSE 1.3 60.7 + - - -
286D MSE 3.4 2.5 - - - -
287D THR* 3.2 13.7 + - - -
288D LEU* 2.9 27.7 + - - +
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Residues in contact with MSE 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU* 4.2 12.3 - - + -
396A PHE* 3.6 54.1 + - + +
397A ARG* 3.7 28.7 - - - +
398A LYS 5.7 1.1 - - - +
284D GLY* 1.3 72.1 - - - -
286D MSE 1.3 76.3 + - + +
288D LEU* 3.3 5.0 + - - +
289D LYS* 3.0 21.5 + - - +
305D PHE* 4.0 9.2 - - + -
309D ASP* 3.3 40.2 - - + +
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Residues in contact with MSE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.9 19.7 - - + +
284D GLY 3.4 0.2 - - - -
285D MSE 1.3 100.5 - - + +
287D THR* 1.3 65.7 + - - +
289D LYS* 3.2 43.0 + - + +
290D ALA* 3.0 23.2 + - - +
305D PHE* 4.4 4.9 - - + -
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Residues in contact with THR 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.8 17.5 - - - +
310A GLU* 3.4 51.0 + - + +
311A VAL* 4.0 5.9 - - + +
314A ALA* 3.8 12.6 - - + -
283D ILE* 4.0 7.4 - - + -
284D GLY* 3.2 17.0 + - - +
286D MSE 1.3 77.0 - - - +
288D LEU* 1.3 65.0 + - - +
290D ALA* 3.2 5.0 + - - +
291D ALA* 2.9 22.7 + - - +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.0 22.4 - - + -
333A THR* 3.8 14.1 - - + +
336A PHE* 3.8 36.8 - - + -
337A LEU* 3.6 39.5 - - + +
341A GLY* 5.7 0.4 - - - -
396A PHE* 4.7 6.5 - - + -
283D ILE* 3.8 18.6 - - + +
284D GLY 2.9 17.2 + - - +
285D MSE 3.5 4.9 - - - +
287D THR* 1.3 78.4 - - - +
289D LYS* 1.3 57.8 + - - +
291D ALA* 3.4 4.5 + - - +
292D PHE* 2.9 29.8 + - - +
305D PHE* 4.1 3.1 - - + -
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Residues in contact with LYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D MSE 3.0 6.0 + - - +
286D MSE 3.2 46.5 - - + +
287D THR 3.2 0.2 - - - -
288D LEU* 1.3 77.2 - - - +
290D ALA* 1.3 57.7 + - - +
292D PHE* 3.3 1.4 + - - +
293D LYS* 2.9 47.5 + - + +
302D GLU* 2.6 44.9 + - - -
305D PHE* 3.6 35.1 - - + -
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Residues in contact with ALA 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.9 11.9 - - + -
311A VAL* 3.9 24.2 - - + -
286D MSE 3.0 16.8 + - - +
287D THR 3.2 4.7 + - - +
289D LYS* 1.3 75.8 - - - +
291D ALA* 1.3 54.1 + - - +
293D LYS* 3.4 9.1 + - - +
294D THR* 2.7 39.4 + - - +
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Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A VAL* 3.9 11.4 - - + +
314A ALA* 4.0 12.3 - - + -
315A ILE* 3.8 18.2 - - + -
318A ILE* 3.7 22.9 - - + -
287D THR 2.9 16.2 + - - +
288D LEU* 3.7 4.5 - - - +
290D ALA* 1.3 78.2 - - - +
292D PHE* 1.3 62.3 + - - +
294D THR* 3.3 1.6 + - - -
295D LEU* 2.9 31.1 + - - +
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Residues in contact with PHE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.9 1.3 - - - +
329A LEU* 3.7 31.5 - - + +
330A SER* 3.9 13.2 - - - -
333A THR* 3.5 28.7 - - + +
288D LEU 2.9 17.9 + - - +
289D LYS 3.6 3.4 - - - +
291D ALA* 1.3 77.8 - - - +
293D LYS* 1.3 57.1 + - + +
296D SER* 2.8 45.7 + - - -
301D SER* 3.4 30.1 - - - -
304D ALA* 4.1 15.3 - - + -
305D PHE* 3.8 31.6 - + + -
308D LEU* 3.8 22.7 - - + -
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Residues in contact with LYS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D LYS* 2.9 37.3 + - + +
290D ALA* 3.8 7.2 - - - +
292D PHE* 1.3 79.0 - - + +
294D THR* 1.3 64.5 + - - +
296D SER* 3.8 0.9 - - - -
297D GLY* 3.3 18.7 + - - -
298D ALA 4.9 0.3 + - - +
301D SER* 3.7 38.3 + - - +
302D GLU* 2.9 35.8 + - - +
305D PHE* 5.6 0.2 - - + -
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Residues in contact with THR 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A VAL* 4.3 7.1 - - - +
315A ILE* 3.8 23.3 - - + -
290D ALA* 2.7 23.6 + - - +
291D ALA 3.6 4.3 - - - -
293D LYS* 1.3 79.7 - - - +
295D LEU* 1.3 63.5 + - + +
297D GLY* 3.8 7.6 + - - -
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ILE* 3.7 38.6 - - + -
318A ILE* 3.8 32.3 - - + -
319A ARG* 4.2 20.4 - - + +
322A MSE 4.3 5.6 - - + -
329A LEU* 3.9 21.9 - - + +
291D ALA 2.9 19.0 + - - +
294D THR* 1.3 77.4 - - + +
296D SER* 1.3 66.2 + - - +
297D GLY* 3.5 0.3 + - - -
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Residues in contact with SER 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 3.5 15.2 - - - +
292D PHE* 2.8 32.3 + - - -
293D LYS 3.8 4.3 - - - -
294D THR 3.3 0.2 - - - -
295D LEU* 1.3 75.2 - - - +
297D GLY* 1.3 62.1 + - - +
298D ALA* 3.4 22.0 + - - +
301D SER* 3.9 16.3 - - - -
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Residues in contact with GLY 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D LYS 3.3 10.7 + - - -
294D THR 3.8 6.2 + - - -
295D LEU 3.4 1.8 - - - -
296D SER* 1.3 79.1 - - - +
298D ALA* 1.3 58.4 + - - +
299D GLN 4.4 0.2 + - - -
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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