Contacts of the helix formed by residues 297 - 309 (chain D) in PDB entry 3KDO
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 SER 297 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D ARG* 3.5 29.7 + - - +
123D LEU 2.9 22.4 + - - -
124D GLU* 3.7 19.8 + - - -
289D THR* 4.4 0.2 - - - -
296D ILE* 1.3 78.3 - - - +
298D MET* 1.3 60.9 + - - +
299D PHE* 2.9 20.5 + - - +
300D VAL* 3.0 23.0 + - - +
301D LEU* 3.4 4.5 + - - +
333D PHE* 4.7 4.0 - - - -
351D HIS* 4.9 1.6 + - - -
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Residues in contact with MET 298 (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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122D ARG* 4.7 1.8 - - - +
282D ARG* 3.4 40.4 - - + +
285D HIS* 4.4 6.1 - - + -
289D THR* 4.0 17.0 - - - +
296D ILE 3.6 2.2 + - - -
297D SER* 1.3 70.3 + - - +
299D PHE* 1.3 58.7 + - - +
300D VAL 3.2 0.2 - - - -
301D LEU* 3.2 28.6 + - + +
302D ALA* 2.9 32.9 + - + +
305D TYR* 5.3 1.1 - - + -
313D LEU* 4.1 22.0 - - + -
314D HIS 3.5 24.5 - - - +
315D VAL* 4.9 2.7 - - + -
333D PHE* 3.6 30.7 - - + -
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Residues in contact with PHE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLU 3.7 6.5 - - - +
125D ASP* 3.5 31.2 - - - -
297D SER* 3.0 14.4 + - - +
298D MET* 1.3 80.6 - - - +
300D VAL* 1.3 60.5 + - - +
302D ALA* 3.6 1.3 + - - -
303D LYS* 3.4 10.2 + - - +
332D GLY* 4.0 18.8 - - - -
333D PHE* 3.5 26.6 - + + -
336D LEU* 3.2 52.2 - - + +
342D TYR* 3.6 34.1 - + - -
351D HIS* 3.3 40.8 - + + +
352D LEU 5.3 0.2 - - - -
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Residues in contact with VAL 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 5.5 2.0 - - + -
123D LEU* 3.8 44.4 - - + +
124D GLU 3.9 1.8 - - - +
125D ASP* 3.8 26.0 - - - +
126D LEU* 4.3 13.5 - - + +
296D ILE* 4.0 15.0 - - + -
297D SER 3.0 9.0 + - - +
299D PHE* 1.3 75.8 - - - +
301D LEU* 1.3 67.3 + - + +
303D LYS* 3.4 6.2 + - - +
304D LEU* 3.0 43.1 + - + +
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Residues in contact with LEU 301 (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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257D VAL* 4.3 3.8 - - + -
261D TRP* 3.6 31.9 - - + -
282D ARG* 5.6 0.4 - - + -
285D HIS* 4.1 11.7 - - + -
288D PHE* 4.0 22.4 - - + -
289D THR* 3.9 24.2 - - + -
296D ILE* 4.7 9.9 - - + -
297D SER 3.4 8.9 + - - +
298D MET* 3.2 24.1 + - + +
300D VAL* 1.3 80.7 - - + +
302D ALA* 1.3 57.7 + - - +
304D LEU* 3.2 3.0 + - - -
305D TYR* 2.8 59.2 + - + +
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Residues in contact with ALA 302 (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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298D MET* 2.9 20.7 + - + +
299D PHE* 3.7 7.6 - - - +
300D VAL 3.3 0.2 - - - -
301D LEU* 1.3 76.1 - - - +
303D LYS* 1.3 63.2 + - - +
305D TYR* 3.5 1.4 + - - +
306D ARG* 3.0 18.4 + - - +
313D LEU* 3.7 15.9 - - + -
315D VAL* 5.6 0.2 - - + -
333D PHE* 4.7 15.7 - - + +
336D LEU* 4.3 8.3 - - + -
337D LEU* 3.4 32.1 - - + +
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Residues in contact with LYS 303 (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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125D ASP* 3.4 19.3 + - - +
126D LEU* 2.5 34.3 + - + +
127D TYR* 4.0 1.6 - - - +
128D PHE* 5.3 4.7 - - + +
299D PHE* 3.4 5.0 + - - +
300D VAL* 3.4 8.6 + - - +
301D LEU 3.3 0.6 - - - -
302D ALA* 1.3 79.5 - - - +
304D LEU* 1.3 62.3 + - + +
306D ARG* 3.2 5.9 + - - +
307D LEU* 2.9 52.0 + - + +
336D LEU* 3.9 32.2 - - + +
337D LEU* 5.4 0.2 - - - -
352D LEU* 5.3 1.2 + - - +
354D GLN* 2.9 41.4 - - - +
356D PHE* 4.1 12.1 - - + -
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Residues in contact with LEU 304 (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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101D LEU* 4.2 15.8 - - + +
105D LEU* 3.9 24.9 - - + -
126D LEU* 4.6 6.3 - - + -
128D PHE* 4.0 31.9 - - + -
136D PHE* 5.5 0.2 - - + -
261D TRP* 3.7 34.8 - - + -
300D VAL* 3.0 37.6 + - + +
301D LEU 3.8 2.0 - - - +
303D LYS* 1.3 80.8 - - + +
305D TYR* 1.3 59.2 + - - +
307D LEU* 3.3 10.0 + - + +
308D ILE* 2.9 35.3 + - - +
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Residues in contact with TYR 305 (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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256D VAL* 3.6 21.6 + - + -
257D VAL* 3.3 30.3 - - + +
261D TRP* 3.6 31.9 - + - -
264D LEU* 3.3 35.2 - - + -
282D ARG* 5.7 1.1 - - + -
298D MET* 5.3 1.8 - - + -
301D LEU* 2.8 56.0 + - + +
304D LEU* 1.3 68.6 - - - +
306D ARG* 1.3 63.2 + - - +
308D ILE* 3.6 2.8 + - + +
309D GLY 3.1 5.2 + - - -
310D ILE* 3.0 40.8 + - + +
313D LEU* 4.0 30.5 - - + -
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Residues in contact with ARG 306 (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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138D GLY* 3.4 0.2 - - - -
139D PRO* 3.3 16.5 - - + +
302D ALA 3.0 18.5 + - - +
303D LYS* 3.5 5.2 - - - +
305D TYR* 1.3 75.1 - - - +
307D LEU* 1.3 65.7 + - - +
309D GLY 3.1 9.5 + - - -
310D ILE 4.6 8.3 - - - -
313D LEU* 5.4 0.2 - - - +
336D LEU 2.8 31.0 + - - -
337D LEU* 3.2 29.5 + - + +
339D GLU 2.7 33.5 + - - -
340D SER* 4.3 2.2 - - - +
356D PHE* 3.5 33.7 - - + +
359D ILE* 3.1 28.0 + - + +
360D LYS 2.8 26.4 + - - +
361D ALA* 3.7 5.3 - - - +
362D ALA* 4.3 9.6 - - + -
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Residues in contact with LEU 307 (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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128D PHE* 3.7 33.9 - - + -
133D ILE* 3.9 25.6 - - + -
136D PHE* 3.2 33.9 - - + +
137D ASP 3.8 0.2 + - - -
138D GLY* 2.9 29.3 + - - -
303D LYS* 2.9 36.9 + - + +
304D LEU* 3.6 8.1 - - + +
306D ARG* 1.3 75.4 - - - +
308D ILE* 1.3 58.3 + - - +
356D PHE* 4.2 13.7 - - + -
359D ILE* 4.1 22.9 - - + -
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Residues in contact with ILE 308 (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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101D LEU* 4.1 14.8 - - + -
136D PHE* 4.2 13.2 - - + -
137D ASP* 5.0 2.1 + - - +
138D GLY 4.0 2.5 + - - +
261D TRP* 4.0 30.3 - - + +
264D LEU* 4.0 29.6 - - + +
265D ARG* 4.1 26.1 + - + +
268D ARG* 3.1 40.7 + - + +
304D LEU 2.9 21.6 + - - +
305D TYR* 3.9 5.4 - - + +
306D ARG 3.3 0.2 - - - -
307D LEU* 1.3 75.9 - - - +
309D GLY* 1.3 57.3 + - - +
310D ILE* 4.9 4.3 - - + -
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Residues in contact with GLY 309 (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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138D GLY 3.1 28.3 - - - -
139D PRO* 3.4 12.6 - - - +
140D ALA 4.4 1.4 + - - -
268D ARG* 4.1 9.5 + - - +
278D ILE* 4.0 9.0 - - - +
305D TYR 3.1 1.6 + - - -
306D ARG 3.1 6.0 + - - -
308D ILE* 1.3 79.7 - - - +
310D ILE* 1.3 66.4 + - - +
311D ASP* 3.2 11.1 + - - +
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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