Contacts of the helix formed by residues 281 - 292 (chain A) in PDB entry 1KKQ
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 VAL 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A GLN* 3.4 16.2 - - + +
278A CYS* 5.5 1.6 - - - -
279A THR 5.8 0.2 - - - +
280A SER* 1.3 81.6 - - - +
282A GLU* 1.3 68.7 + - + +
283A THR 3.3 0.6 - - - +
284A VAL* 3.9 8.0 - - - +
285A THR* 2.5 34.9 + - - +
460A LEU* 4.8 8.7 - - + -
464A TYR* 6.3 2.5 - - - -
468A TYR* 6.5 0.9 - - + -
688E ILE* 3.8 36.8 - - + -
691E LYS* 4.7 7.2 - - - +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A CYS 4.7 12.1 - - - +
279A THR* 4.4 10.1 - - + +
281A VAL* 1.3 86.8 - - + +
283A THR* 1.3 64.3 + - - +
285A THR* 3.1 10.4 + - - -
286A GLU* 3.2 29.2 + - - +
334A TYR* 2.4 41.4 + - + +
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE* 5.2 1.0 - - - -
279A THR* 3.3 22.8 + - - +
280A SER* 4.2 7.0 - - - +
281A VAL 3.3 0.8 - - - +
282A GLU* 1.3 81.1 - - - +
284A VAL* 1.3 65.6 + - + +
285A THR 3.5 0.3 + - - -
286A GLU* 3.6 13.1 + - - +
287A LEU* 3.5 22.1 + - + +
317A ILE* 3.4 42.2 - - + -
775A 471 5.3 5.0 - - + -
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 3.8 25.6 - - - +
281A VAL* 3.8 7.6 + - - +
282A GLU 3.4 0.8 - - - -
283A THR* 1.3 82.9 - - + +
285A THR* 1.3 60.7 + - - +
287A LEU* 3.6 7.0 + - + +
288A THR* 2.8 27.1 + - - +
309A LEU* 5.7 0.4 - - - +
313A VAL* 4.0 28.0 - - + -
314A TYR* 6.0 2.0 - - + -
317A ILE* 4.8 1.1 - - + -
685E LEU* 4.9 9.4 - - + -
688E ILE* 4.9 8.5 - - + -
689E ILE* 3.8 36.1 - - + +
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 2.5 28.0 + - - +
282A GLU* 3.1 5.4 + - - -
284A VAL* 1.3 76.9 - - - +
286A GLU* 1.3 61.3 + - - +
287A LEU 3.2 0.4 - - - -
288A THR* 3.1 6.1 + - - -
289A GLU* 3.0 37.8 + - + +
468A TYR* 4.9 30.3 - - + -
688E ILE* 4.8 5.7 - - - +
691E LYS* 5.7 2.4 - - - -
692E ALA* 3.2 29.1 - - + +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN* 2.9 26.9 - - - +
218A PHE* 3.9 19.0 - - + -
219A ASN* 3.2 32.8 + - - +
220A MET 5.5 0.2 + - - -
282A GLU* 3.2 25.1 + - - +
283A THR* 4.1 11.8 + - - +
284A VAL 3.4 0.4 - - - -
285A THR* 1.3 77.2 - - - +
287A LEU* 1.3 56.8 + - - +
289A GLU* 4.5 5.8 - - - +
290A PHE* 2.9 31.2 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE* 3.6 20.9 - - + -
283A THR* 3.5 15.7 + - + +
284A VAL* 3.9 6.7 - - - +
285A THR 3.2 0.4 - - - -
286A GLU* 1.3 79.1 - - - +
288A THR* 1.3 58.8 + - - +
290A PHE* 4.0 6.0 - - + -
291A ALA* 3.1 26.1 + - - +
309A LEU* 3.4 11.7 - - + +
313A VAL* 3.6 24.9 - - + +
316A ALA* 3.4 24.7 - - + -
317A ILE* 4.3 13.5 - - + -
320A MET* 3.7 18.2 - - + -
379A VAL* 4.0 16.8 - - + -
383A ILE* 4.1 8.3 - - + +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A VAL* 2.8 23.9 + - - +
285A THR* 3.1 10.1 + - - -
287A LEU* 1.3 79.6 - - - +
289A GLU* 1.3 59.6 + - - +
291A ALA* 3.8 1.6 - - - +
292A LYS* 3.1 26.4 + - + +
309A LEU* 3.8 21.9 - - + +
689E ILE* 3.9 18.8 + - - +
692E ALA* 4.0 19.7 - - - +
693E LEU* 3.4 30.2 - - + +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LYS* 5.9 0.7 + - - -
217A ASN* 3.0 24.1 - - - +
285A THR* 3.0 29.3 + - + +
286A GLU* 3.9 4.7 - - - +
288A THR* 1.3 74.9 - - - +
290A PHE* 1.3 64.0 + - - +
291A ALA 3.1 1.6 - - - -
292A LYS* 3.1 28.9 + - - +
293A ALA* 3.1 14.6 + - - +
468A TYR* 6.0 2.3 - - - -
692E ALA* 3.0 25.5 - - - +
696E LYS* 3.6 28.4 - - - +
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Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.7 23.3 - - + -
213A ALA* 3.6 22.0 - - + -
214A TYR* 3.6 9.9 - - + -
217A ASN* 3.7 15.8 - - + +
218A PHE* 3.5 27.6 - + + -
286A GLU 2.9 19.4 + - - +
287A LEU* 4.0 10.5 - - + +
289A GLU* 1.3 77.0 - - - +
291A ALA* 1.3 62.9 + - - +
293A ALA* 3.4 10.8 + - - +
294A ILE* 3.1 39.0 - - + +
376A SER* 3.8 22.0 - - - -
379A VAL* 4.0 21.5 - - + -
380A ALA* 4.2 5.4 - - + -
383A ILE* 4.2 5.8 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 3.1 19.3 + - - +
288A THR 3.8 5.2 - - - +
289A GLU 3.1 0.6 - - - -
290A PHE* 1.3 77.1 - - - +
292A LYS* 1.3 57.9 + - - +
293A ALA 2.9 4.7 - - - -
294A ILE* 3.0 27.4 + - + +
297A PHE* 3.0 38.4 - - + +
309A LEU* 3.9 16.6 - - + -
383A ILE* 4.2 10.1 - - + -
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A THR 3.1 19.0 + - - +
289A GLU* 3.1 37.4 + - - +
291A ALA* 1.3 74.3 - - - +
293A ALA* 1.3 56.2 + - - +
294A ILE 3.4 2.7 - - - -
297A PHE* 3.4 20.1 - - + -
298A ALA* 4.3 17.7 - - + +
305A GLN* 4.7 4.7 - - - +
692E ALA 4.1 3.3 + - - +
693E LEU* 2.8 44.1 + - + +
694E MET* 4.6 2.2 - - - +
696E LYS* 4.5 14.1 + - - +
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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