Contacts of the helix formed by residues 280 - 292 (chain B) 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 SER 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B CYS 3.9 2.5 - - - -
277B GLN* 3.8 17.3 - - - -
278B CYS 2.7 4.2 + - - -
279B THR* 1.3 82.0 - - - +
281B VAL* 1.3 57.9 + - - +
282B GLU 3.4 2.0 - - - -
283B THR* 4.0 9.3 - - - -
284B VAL* 2.9 28.9 + - - +
317B ILE* 4.4 4.0 - - - +
776B 471 2.6 59.5 + - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLN* 3.4 19.7 + - + +
278B CYS* 3.0 6.3 + - - +
280B SER* 1.3 79.0 - - - +
282B GLU* 1.3 60.7 + - - +
284B VAL* 4.0 6.8 - - - +
285B THR* 2.8 22.3 + - - +
464B TYR* 5.9 4.0 - - + +
776B 471 4.0 21.3 - - + -
688F ILE* 4.0 27.8 - - + -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B CYS* 3.4 13.8 + - + +
279B THR* 5.1 4.0 - - - -
281B VAL* 1.3 79.1 - - - +
283B THR* 1.3 65.4 + - - +
285B THR* 3.1 15.2 + - - -
286B GLU* 3.1 31.5 + - + +
334B TYR* 3.1 33.7 + - + +
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 5.3 1.5 - - + -
279B THR* 3.1 26.8 + - - +
280B SER* 4.1 6.9 - - - +
281B VAL 4.0 0.2 - - - +
282B GLU* 1.3 77.0 - - - +
284B VAL* 1.3 65.3 + - - +
286B GLU* 3.3 16.5 + - - +
287B LEU* 3.0 28.2 + - + +
317B ILE* 3.7 35.4 - - + -
320B MET* 5.3 7.2 - - + -
776B 471 5.4 0.6 - - + -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 2.9 25.4 + - - +
281B VAL* 4.4 7.0 - - - +
282B GLU 3.3 0.4 - - - -
283B THR* 1.3 79.6 - - - +
285B THR* 1.3 59.7 + - - +
287B LEU* 3.3 6.5 + - - +
288B THR* 3.0 34.3 + - - +
313B VAL* 4.6 18.4 - - + +
317B ILE* 5.1 5.4 - - + -
776B 471 4.4 9.2 - - + +
685F LEU* 4.0 24.5 - - + -
688F ILE* 4.2 18.6 - - + -
689F ILE* 4.2 26.5 - - + +
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL 2.8 17.9 + - - -
282B GLU* 3.1 10.3 + - - -
284B VAL* 1.3 79.3 - - - +
286B GLU* 1.3 57.4 + - - +
288B THR* 3.2 7.4 + - - -
289B GLU* 3.0 34.7 + - + +
688F ILE* 4.5 9.7 - - - +
692F ALA* 3.8 22.2 - - + +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ASN* 3.1 31.4 - - + +
218B PHE* 3.8 19.9 - - + +
219B ASN* 3.8 25.4 + - - +
220B MET 5.1 1.6 + - - -
282B GLU* 3.1 30.9 + - - +
283B THR* 3.7 18.0 + - - +
285B THR* 1.3 72.0 - - - +
287B LEU* 1.3 59.9 + - - +
288B THR 3.1 0.4 - - - -
289B GLU* 3.7 8.5 - - - +
290B PHE* 2.9 30.7 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PHE* 4.0 18.1 - - + -
283B THR* 3.0 18.6 + - + +
284B VAL 3.5 5.2 - - - +
286B GLU* 1.3 78.3 - - - +
288B THR* 1.3 57.3 + - - +
290B PHE* 3.9 1.0 - - + +
291B ALA* 3.2 26.7 + - - +
309B LEU* 3.9 3.9 - - + +
313B VAL* 3.6 41.1 - - + +
316B ALA* 3.7 18.8 - - + -
317B ILE* 3.9 15.9 - - + -
320B MET* 3.9 16.4 - - + -
379B VAL* 4.2 4.3 - - + -
383B ILE* 3.6 29.8 - - + +
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B VAL* 3.0 16.0 + - - +
285B THR 3.4 9.0 - - - -
287B LEU* 1.3 77.4 - - - +
289B GLU* 1.3 63.0 - - - +
291B ALA* 3.5 2.9 - - - +
292B LYS* 3.3 21.6 + - + +
297B PHE* 5.4 0.2 - - - -
309B LEU* 3.1 32.4 - - + +
313B VAL* 5.8 0.3 - - - +
689F ILE* 3.9 14.2 - - - +
692F ALA* 3.5 30.1 - - + +
693F LEU* 3.5 21.2 - - + +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LYS* 5.7 1.2 + - - -
217B ASN* 3.1 32.3 + - - +
285B THR* 3.0 27.9 + - + +
286B GLU* 3.2 6.7 + - - +
288B THR* 1.3 76.1 - - - +
290B PHE* 1.3 66.7 + - - +
292B LYS* 3.2 30.3 + - - +
293B ALA* 3.4 8.1 + - - +
692F ALA* 3.8 11.5 - - - +
696F LYS* 3.2 31.2 - - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 3.5 32.5 - - + -
213B ALA* 3.6 21.5 - - + -
214B TYR* 3.6 17.3 - + + -
217B ASN* 3.8 13.9 + - + -
218B PHE* 3.7 25.1 - + + -
286B GLU 2.9 17.2 + - - +
287B LEU 3.9 5.4 - - - +
289B GLU* 1.3 73.6 - - - +
291B ALA* 1.3 56.9 + - - +
293B ALA* 2.7 31.0 + - - +
294B ILE* 3.3 27.9 + - + +
376B SER 3.7 20.2 - - - -
379B VAL* 3.6 26.5 - - + -
380B ALA* 4.3 3.6 - - + -
383B ILE* 4.5 5.4 - - + -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B LEU 3.2 17.6 + - - +
288B THR 3.5 7.6 - - - +
289B GLU 3.2 0.2 - - - -
290B PHE* 1.3 81.4 - - - +
292B LYS* 1.3 59.8 + - - +
294B ILE* 3.3 19.3 - - - +
297B PHE* 3.1 48.4 - - + +
309B LEU* 4.2 13.2 - - + -
383B ILE* 4.2 10.1 - - + -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B THR 3.3 10.2 + - - +
289B GLU* 3.2 24.4 + - - +
290B PHE 3.0 0.6 + - - -
291B ALA* 1.3 76.0 - - - +
293B ALA* 1.3 57.8 + - - +
294B ILE 3.2 8.1 - - - +
297B PHE* 3.8 17.7 - - + -
298B ALA* 4.1 23.4 - - + +
305B GLN* 5.6 1.8 - - - +
692F ALA 3.3 11.9 + - - -
693F LEU* 3.2 36.3 + - + +
694F MET 4.0 0.2 + - - -
696F LYS* 2.6 57.9 - - - +
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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