Contacts of the helix formed by residues 297 - 309 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122J ARG* 3.6 32.5 + - - +
123J LEU 2.9 22.0 + - - -
124J GLU* 3.7 17.7 + - - -
289J THR* 4.3 0.2 - - - -
296J ILE* 1.3 76.8 - - - +
298J MET* 1.3 63.8 + - - +
299J PHE* 2.8 23.4 + - - +
300J VAL* 2.9 15.4 + - - +
301J LEU* 3.4 7.1 + - - +
333J PHE* 4.7 3.6 - - - -
351J HIS* 5.0 1.9 + - - -
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Residues in contact with MET 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J ARG* 4.9 0.4 - - - +
282J ARG* 3.4 37.7 - - + +
285J HIS* 4.4 6.3 - - + +
289J THR* 3.8 21.2 + - - +
296J ILE 3.5 2.8 + - - -
297J SER* 1.3 72.1 + - - +
299J PHE* 1.3 55.9 + - - +
301J LEU* 3.3 20.1 + - + -
302J ALA* 2.9 36.7 + - + +
305J TYR* 5.3 1.3 - - + -
313J LEU* 4.0 22.7 - - + -
314J HIS 3.5 24.5 - - - +
315J VAL* 4.8 4.3 - - + -
333J PHE* 3.6 30.5 - - + -
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Residues in contact with PHE 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J GLU 3.6 7.6 - - - +
125J ASP* 3.3 36.8 - - - -
297J SER* 2.8 15.7 + - - +
298J MET* 1.3 79.5 - - - +
300J VAL* 1.3 61.2 + - - +
303J LYS* 3.4 8.3 + - - +
332J GLY* 4.2 15.7 - - - -
333J PHE* 3.6 25.3 - + + -
336J LEU* 3.2 59.0 - - + +
342J TYR* 3.7 22.2 - + - -
351J HIS* 3.4 43.5 - + + +
352J LEU 5.5 0.2 - - - -
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Residues in contact with VAL 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J LEU* 5.6 1.8 - - + -
123J LEU* 3.8 46.9 - - + +
124J GLU 3.9 1.1 - - - +
125J ASP* 3.8 28.0 - - - +
126J LEU* 4.4 13.9 - - + +
296J ILE* 4.0 10.1 - - + -
297J SER 2.9 8.2 + - - +
299J PHE* 1.3 76.3 - - - +
301J LEU* 1.3 66.9 + - + +
303J LYS* 3.2 6.6 + - - +
304J LEU* 3.1 42.3 + - + +
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Residues in contact with LEU 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257J VAL* 4.3 11.0 - - + -
261J TRP* 3.5 33.0 - - + -
285J HIS* 4.2 12.3 - - + -
288J PHE* 3.7 37.9 - - + -
289J THR* 3.9 11.4 - - + -
296J ILE* 4.6 10.3 - - + -
297J SER 3.4 8.5 + - - +
298J MET* 3.3 17.8 + - - +
300J VAL* 1.3 81.9 - - + +
302J ALA* 1.3 62.9 + - - +
304J LEU* 3.3 4.0 + - - +
305J TYR* 2.9 45.2 + - + +
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Residues in contact with ALA 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298J MET* 2.9 24.7 + - + +
299J PHE* 3.9 6.3 - - - +
300J VAL 3.3 0.2 - - - -
301J LEU* 1.3 74.9 - - - +
303J LYS* 1.3 63.1 + - - +
305J TYR* 3.7 1.0 + - - +
306J ARG* 3.2 16.8 + - - +
313J LEU* 3.8 17.7 - - + -
333J PHE* 4.7 12.8 - - + -
336J LEU* 4.3 9.9 - - + -
337J LEU* 3.4 31.5 - - + +
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Residues in contact with LYS 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J ASP* 3.6 18.6 + - - +
126J LEU* 2.9 27.3 + - + +
127J TYR* 4.1 1.6 - - - +
128J PHE* 5.1 3.8 - - + -
299J PHE* 3.4 9.6 + - - +
300J VAL* 3.2 10.8 + - - +
302J ALA* 1.3 76.5 - - - +
304J LEU* 1.3 64.4 + - + +
306J ARG* 3.2 6.7 + - - +
307J LEU* 2.9 42.4 + - + +
336J LEU* 3.9 27.6 - - + +
352J LEU 5.1 1.0 + - - -
354J GLN* 2.6 50.1 - - - +
356J PHE* 4.0 15.9 - - + -
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Residues in contact with LEU 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J LEU* 4.0 14.8 - - + -
105J LEU* 3.9 27.1 - - + -
126J LEU* 4.5 5.6 - - + -
128J PHE* 3.7 35.0 - - + -
136J PHE* 5.2 0.8 - - + -
261J TRP* 3.7 37.2 - - + -
300J VAL* 3.1 30.1 + - + +
301J LEU 3.9 0.4 - - - +
303J LYS* 1.3 79.3 - - + +
305J TYR* 1.3 58.7 + - - +
307J LEU* 3.3 8.5 + - + +
308J ILE* 2.9 34.7 + - - +
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Residues in contact with TYR 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256J VAL* 3.6 21.9 + - + -
257J VAL* 3.4 31.2 - - + +
261J TRP* 3.6 33.1 - + - -
264J LEU* 3.5 33.0 - - + -
282J ARG* 5.6 1.1 - - + -
298J MET* 5.3 2.0 - - + -
301J LEU* 2.9 47.6 + - + +
302J ALA 4.1 2.7 - - - +
304J LEU* 1.3 74.3 - - - +
306J ARG* 1.3 64.7 + - - +
308J ILE* 3.7 2.4 + - + +
309J GLY 3.1 5.2 + - - -
310J ILE* 2.9 42.9 + - + +
313J LEU* 4.0 28.3 - - + -
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Residues in contact with ARG 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J GLY* 3.4 0.2 - - - -
139J PRO* 3.3 22.4 - - + +
302J ALA 3.2 18.1 + - - +
303J LYS* 3.6 4.7 - - - +
305J TYR* 1.3 75.2 - - - +
307J LEU* 1.3 65.4 + - - +
309J GLY 3.2 8.8 + - - -
310J ILE 4.5 7.4 - - - -
336J LEU 2.8 34.7 + - - -
337J LEU* 3.3 31.8 + - + +
338J ARG 4.0 1.0 + - - -
339J GLU 2.8 32.5 + - - -
340J SER* 4.3 2.6 - - - +
356J PHE* 3.4 29.2 - - + +
359J ILE* 2.9 31.1 + - + +
360J LYS 3.0 23.5 + - - +
361J ALA* 3.8 4.4 - - - +
362J ALA* 4.3 9.9 - - + -
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Residues in contact with LEU 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J PHE* 3.5 38.1 - - + -
133J ILE* 3.9 24.5 - - + -
136J PHE* 3.2 34.4 - - + +
138J GLY* 2.9 22.4 + - - -
303J LYS* 2.9 34.9 + - + +
304J LEU* 3.3 7.4 + - + +
306J ARG* 1.3 77.3 - - - +
308J ILE* 1.3 63.5 + - - +
356J PHE* 4.0 19.1 - - + -
359J ILE* 4.1 18.8 - - + -
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Residues in contact with ILE 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J LEU* 4.0 19.1 - - + -
136J PHE* 4.1 21.3 - - + -
137J ASP* 4.8 2.6 + - - +
138J GLY 3.9 4.0 + - - +
261J TRP* 4.0 20.0 - - + +
264J LEU* 4.1 29.4 - - + +
265J ARG* 4.1 27.9 - - + +
268J ARG* 3.4 37.2 + - + +
304J LEU 2.9 21.8 + - - +
305J TYR* 3.9 5.4 - - + +
307J LEU* 1.3 75.6 - - - +
309J GLY* 1.3 59.0 + - - +
310J ILE* 4.8 3.6 - - + -
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Residues in contact with GLY 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J GLY 3.3 26.5 - - - -
139J PRO* 3.4 10.5 - - - +
140J ALA 4.5 0.9 + - - -
268J ARG* 3.8 18.5 + - - +
278J ILE* 3.8 8.5 - - - +
305J TYR 3.1 2.2 + - - -
306J ARG 3.2 3.4 + - - -
308J ILE* 1.3 80.9 - - - +
310J ILE* 1.3 67.9 + - - +
311J ASP* 3.4 5.9 + - - +
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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