Contacts of the helix formed by residues 287 - 301 (chain C) in PDB entry 1KYO
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 ASP 287 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C ILE* 3.1 9.5 + - + +
286C PRO* 1.3 79.2 - - + +
288C LYS* 1.3 69.7 + - - +
289C LEU* 3.2 10.3 + - - +
290C LEU* 2.8 53.2 + - + +
291C GLY* 3.0 16.8 + - - -
138P LYS* 6.2 0.4 - - - +
161P HIS* 5.1 1.4 + - - -
195P PRO* 4.5 8.6 - - - +
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Residues in contact with LYS 288 (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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152C SER* 3.2 31.6 + - - -
153C ALA* 4.7 12.8 - - + +
282C LEU* 5.5 0.2 - - - +
287C ASP* 1.3 78.5 + - - +
289C LEU* 1.3 66.6 + - - +
291C GLY* 3.2 4.7 + - - -
292C VAL* 3.1 25.2 + - + +
160P THR 3.3 17.7 + - - +
161P HIS* 3.0 51.3 + - + +
162P LEU* 4.6 5.2 - - + -
195P PRO 3.8 11.1 + - - +
197P PRO* 4.1 20.8 - - + +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ALA* 3.5 34.8 - - + +
154C ILE* 5.6 0.2 - - - -
155C PRO* 5.0 10.5 - - + -
287C ASP* 3.2 7.9 + - - +
288C LYS* 1.3 78.4 - - - +
290C LEU* 1.3 63.6 + - + +
292C VAL* 3.2 8.1 + - + +
293C ILE* 2.8 62.1 + - + +
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ILE* 3.5 19.7 - - + -
287C ASP* 2.8 31.8 + - + +
289C LEU* 1.3 75.6 - - + +
291C GLY* 1.3 56.4 + - - +
293C ILE* 4.4 16.2 - - + -
294C THR* 2.5 46.1 + - - +
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Residues in contact with GLY 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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282C LEU* 3.7 26.9 - - - +
285C ILE* 3.7 18.7 - - - +
287C ASP 3.0 20.0 + - - -
288C LYS 3.2 1.1 + - - -
290C LEU* 1.3 74.4 - - - +
292C VAL* 1.3 57.2 + - - +
294C THR* 3.8 1.0 - - - -
295C MET* 3.0 27.9 + - - +
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Residues in contact with VAL 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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150C LEU* 4.0 30.7 - - + +
153C ALA* 3.9 22.0 - - + -
154C ILE* 6.1 2.5 - - + -
282C LEU* 3.8 17.2 - - + +
288C LYS* 3.1 22.0 - - + +
289C LEU* 3.2 4.9 + - + +
291C GLY* 1.3 71.0 - - - +
293C ILE* 1.3 73.6 + - + +
295C MET* 3.2 3.0 + - - +
296C PHE* 3.1 42.9 + - + -
161P HIS* 5.9 1.1 - - - +
162P LEU* 5.5 4.9 - - + -
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Residues in contact with ILE 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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289C LEU* 2.8 51.4 + - + +
290C LEU* 3.9 14.6 - - + +
292C VAL* 1.3 80.5 - - + +
294C THR* 1.3 60.4 + - - +
296C PHE* 3.4 5.3 + - - +
297C ALA* 2.9 30.7 + - + +
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Residues in contact with THR 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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281C ILE* 4.0 12.3 - - + -
285C ILE* 3.7 25.8 - - + +
290C LEU* 2.5 36.7 + - - +
291C GLY 3.8 3.4 - - - -
293C ILE* 1.3 75.2 - - - +
295C MET* 1.3 56.2 + - - +
297C ALA* 3.3 5.6 - - - +
298C ALA* 3.0 23.4 + - - +
356C THR* 4.8 3.1 - - + -
360C PHE* 3.3 28.1 - - + -
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Residues in contact with MET 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LEU* 3.9 18.8 - - + -
278C PHE* 3.7 30.7 - - + +
281C ILE* 4.4 5.6 - - - +
282C LEU* 4.0 17.3 - - + +
291C GLY 3.0 18.6 + - - +
292C VAL* 3.6 4.0 - - - +
293C ILE 3.2 0.2 - - - -
294C THR* 1.3 74.4 - - - +
296C PHE* 1.3 71.0 + - + +
298C ALA* 2.9 23.2 + - - +
299C ILE* 3.4 6.8 + - + +
505C SMA 3.3 73.1 - - + -
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Residues in contact with PHE 296 (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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122C THR* 6.1 4.3 - - + -
150C LEU* 4.8 18.8 - - + -
151C PHE* 4.8 22.4 - + - -
292C VAL* 3.1 38.4 + - + +
293C ILE* 3.9 6.1 - - - +
295C MET* 1.3 79.3 - - + +
297C ALA* 1.3 57.7 + - - +
299C ILE* 2.9 15.2 + - + +
300C LEU* 2.9 41.9 + - + +
505C SMA 3.7 40.6 - - + -
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Residues in contact with ALA 297 (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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293C ILE* 2.9 21.6 + - + +
294C THR* 3.3 11.2 - - - +
296C PHE* 1.3 76.6 - - - +
298C ALA* 1.3 56.1 + - - +
299C ILE 3.0 0.2 + - - -
300C LEU* 3.1 8.2 + - - +
301C VAL* 2.7 36.6 + - - +
360C PHE* 3.8 15.0 - - + -
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE* 4.4 9.5 - - + -
281C ILE* 3.7 29.4 - - + -
294C THR 3.0 11.7 + - - +
295C MET* 2.9 16.2 + - - +
297C ALA* 1.3 75.8 - - - +
299C ILE* 1.3 60.1 + - - +
301C VAL* 3.4 7.2 - - - +
302C LEU* 4.7 1.0 - - - +
359C TYR* 2.5 33.1 + - + +
360C PHE* 3.4 14.8 - - + -
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Residues in contact with ILE 299 (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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118C VAL* 4.7 8.5 - - + +
121C PHE* 4.2 17.7 - - + -
122C THR* 4.0 24.7 - - + +
125C ILE* 4.5 20.2 - - + -
278C PHE* 3.8 30.5 - - + -
295C MET* 4.2 5.6 - - + +
296C PHE* 2.9 15.2 + - + +
298C ALA* 1.3 78.0 - - - +
300C LEU* 1.3 69.4 + - + +
302C LEU* 3.2 28.0 + - - +
505C SMA 4.3 28.3 - - + +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 5.5 5.6 - - + -
296C PHE* 2.9 31.6 + - + +
297C ALA* 4.0 6.5 - - - +
299C ILE* 1.3 77.2 - - + +
301C VAL* 1.3 55.3 + - - +
302C LEU 2.8 12.4 + - - -
303C LEU* 2.9 46.9 + - + +
304C VAL 4.3 0.3 + - - -
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ALA* 2.7 23.2 + - + +
298C ALA* 3.4 19.3 - - - +
300C LEU* 1.3 71.5 - - - +
302C LEU* 1.3 59.0 + - + +
303C LEU 3.1 0.4 - - - -
304C VAL* 2.9 47.2 - - + +
305C LEU 4.2 0.7 + - - -
359C TYR* 4.0 8.3 - - + +
360C PHE* 4.2 18.8 - - + -
363C PHE* 3.9 38.6 - - + -
364C LEU* 4.2 12.8 - - + -
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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