Contacts of the helix formed by residues 282 - 294 (chain C) 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 GLU 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C ASN* 5.9 1.0 - - - +
277C GLN 5.0 0.4 + - - -
278C CYS 4.4 12.1 - - - +
279C THR* 4.7 2.5 - - - -
280C SER 2.4 14.3 + - - +
281C VAL* 1.3 73.3 - - - +
283C THR* 1.3 62.0 + - - +
284C VAL 3.1 4.3 - - - -
285C THR* 3.1 20.8 + - - -
286C GLU* 3.4 24.5 + - - +
334C TYR* 4.1 26.5 + - + +
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Residues in contact with THR 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C PHE* 5.5 0.9 - - + -
279C THR* 4.3 15.4 + - - +
280C SER* 2.5 16.8 + - - +
282C GLU* 1.3 74.4 - - - +
284C VAL* 1.3 56.0 + - - -
285C THR 3.3 0.2 - - - -
286C GLU* 3.7 20.4 + - - +
287C LEU* 3.3 28.1 + - + +
317C ILE* 3.6 35.9 - - + -
320C MET* 5.1 8.7 - - + -
777C 471 5.6 1.0 - - - -
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C SER* 2.8 24.8 + - - +
281C VAL* 4.2 10.3 - - - +
283C THR* 1.3 77.3 - - - +
285C THR* 1.3 62.5 + - - +
287C LEU* 3.9 7.9 - - - +
288C THR* 2.8 21.9 + - - +
313C VAL* 4.4 20.4 - - + +
314C TYR* 5.7 2.2 - - + -
317C ILE* 4.5 10.5 - - + -
777C 471 5.3 4.3 - - + -
685G LEU* 4.2 22.0 - - + -
688G ILE* 4.5 7.0 - - + -
689G ILE* 3.9 30.1 - - + -
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Residues in contact with THR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 2.6 27.9 + - - +
282C GLU* 3.1 13.6 + - - -
284C VAL* 1.3 76.6 - - - +
286C GLU* 1.3 67.5 + - - +
287C LEU 3.2 0.2 - - - -
288C THR* 3.1 4.5 + - - -
289C GLU* 3.0 35.3 + - + +
688G ILE 5.6 1.4 + - - -
692G ALA* 3.7 26.0 - - + -
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ASN 3.3 22.4 - - - +
218C PHE* 3.7 19.8 - - + -
219C ASN* 2.9 38.1 + - - +
220C MET 5.3 1.0 + - - -
282C GLU* 3.6 28.0 - - - +
283C THR* 3.9 20.6 + - - +
284C VAL 3.5 0.2 - - - -
285C THR* 1.3 79.2 - - - +
287C LEU* 1.3 57.6 + - - +
289C GLU* 3.1 8.3 + - - +
290C PHE* 2.8 30.0 + - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C PHE* 3.3 27.8 - - + -
283C THR 3.3 15.9 + - - +
284C VAL* 3.9 6.7 - - - +
285C THR 3.2 0.2 - - - -
286C GLU* 1.3 81.4 - - - +
288C THR* 1.3 56.8 + - - +
290C PHE* 3.7 6.8 - - + +
291C ALA* 3.2 26.0 + - - +
309C LEU* 3.7 9.0 - - + +
313C VAL* 3.5 42.4 - - + +
316C ALA* 4.0 10.3 - - + -
317C ILE* 3.9 13.0 - - + -
320C MET* 3.7 12.6 - - + -
379C VAL* 4.1 16.4 - - + -
383C ILE* 4.2 7.4 - - + +
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Residues in contact with THR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C VAL* 2.8 18.8 + - - +
285C THR 3.1 8.3 + - - -
287C LEU* 1.3 76.2 - - - +
289C GLU* 1.3 60.8 + - - +
291C ALA* 3.4 1.4 + - - +
292C LYS* 2.9 35.7 + - + +
309C LEU* 3.2 26.0 - - + +
689G ILE* 3.9 15.2 - - - +
692G ALA* 4.0 22.5 - - + +
693G LEU* 3.2 32.8 - - + +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN* 3.5 24.9 + - + +
285C THR* 3.0 25.1 + - + +
286C GLU* 3.5 8.7 - - - +
288C THR* 1.3 76.5 - - - +
290C PHE* 1.3 63.4 + - - +
292C LYS* 3.2 28.6 + - - +
293C ALA* 3.3 20.6 + - - +
692G ALA 4.5 9.2 - - - +
696G LYS* 3.4 26.3 + - - +
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ILE* 3.5 27.6 - - + -
213C ALA* 3.5 20.4 - - + -
214C TYR* 4.1 10.5 - + + -
217C ASN* 4.1 12.1 - - + +
218C PHE* 3.4 28.9 - + + -
286C GLU 2.8 15.7 + - - +
287C LEU* 3.7 12.1 - - + +
289C GLU* 1.3 78.0 - - - +
291C ALA* 1.3 63.6 + - - +
293C ALA* 3.2 4.0 - - - +
294C ILE* 3.1 31.5 + - + +
376C SER* 3.7 24.7 - - - -
379C VAL* 3.7 23.6 - - + -
380C ALA* 4.3 12.3 - - + -
383C ILE* 4.8 2.5 - - + -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C LEU 3.2 18.4 + - - +
288C THR 3.8 3.1 - - - +
290C PHE* 1.3 73.2 - - - +
292C LYS* 1.3 55.9 + - - +
293C ALA 2.6 15.5 + - - -
294C ILE* 2.8 27.1 + - + +
297C PHE* 2.9 49.0 - - + +
309C LEU* 4.2 11.2 - - + -
383C ILE* 4.6 4.7 - - + -
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Residues in contact with LYS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C THR 2.9 24.5 + - - +
289C GLU* 3.2 28.8 + - - +
290C PHE 3.5 0.4 - - - -
291C ALA* 1.3 74.9 - - - +
293C ALA* 1.3 58.6 + - - +
294C ILE 4.5 1.7 - - - +
297C PHE* 3.6 13.7 - - + -
298C ALA* 4.3 21.7 + - + +
305C GLN* 4.9 2.9 - - - +
692G ALA 3.7 11.2 + - - -
693G LEU* 3.1 51.8 + - + +
694G MET 5.3 0.2 - - - -
696G LYS* 4.3 18.8 + - - +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ARG* 2.4 40.1 + - - +
213C ALA* 3.5 15.5 - - + -
217C ASN* 4.5 5.2 - - - +
289C GLU 3.3 12.4 + - - +
290C PHE* 3.2 11.4 - - - +
291C ALA 2.6 1.2 + - - -
292C LYS* 1.3 79.1 - - - +
294C ILE* 1.3 68.5 + - - +
295C PRO* 2.9 2.6 - - - +
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 5.7 0.4 - - + -
209C ARG* 4.0 0.9 - - - +
210C ILE* 3.8 19.3 - - + -
213C ALA* 5.0 0.4 - - - +
290C PHE* 3.1 27.5 + - + +
291C ALA* 2.8 30.4 + - + +
292C LYS 4.5 0.9 - - - +
293C ALA* 1.3 72.3 - - - +
295C PRO* 1.3 87.2 - - + +
296C GLY 3.2 0.3 + - - -
297C PHE* 2.9 21.8 + - + +
380C ALA* 4.1 22.9 - - + +
383C ILE* 5.0 4.9 - - + -
384C CYS* 4.1 22.7 - - - -
400C MET* 5.5 0.9 - - + -
404C ILE* 4.2 16.4 - - + -
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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