Contacts of the helix formed by residues 270 - 288 (chain A) in PDB entry 3KXK
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A THR 4.0 0.6 + - - -
269A PHE* 1.3 76.9 - - - +
271A GLU* 1.3 61.1 + - - +
272A ASN* 4.2 2.3 + - - +
273A LEU* 3.4 31.7 + - - +
274A LEU* 2.9 27.4 + - - +
312A LYS* 4.9 7.6 - - - +
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Residues in contact with GLU 271 (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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270A SER* 1.3 79.3 - - - +
272A ASN* 1.3 74.7 + - - +
274A LEU* 3.3 5.5 + - - +
275A ILE* 3.1 28.2 + - + +
311A LYS* 3.5 25.5 + - - +
312A LYS* 5.3 4.1 - - - +
315A LEU* 3.9 21.6 - - + +
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Residues in contact with ASN 272 (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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270A SER* 3.6 2.9 + - - +
271A GLU* 1.3 96.3 + - - +
273A LEU* 1.3 60.1 + - + +
275A ILE* 3.3 16.6 + - - +
276A GLU* 2.9 29.7 + - - +
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Residues in contact with LEU 273 (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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269A PHE* 3.6 32.1 - - + -
270A SER* 3.4 24.7 + - - +
271A GLU 3.3 0.4 - - - -
272A ASN* 1.3 79.5 - - + +
274A LEU* 1.3 58.0 + - - +
276A GLU* 3.2 16.0 + - + +
277A THR* 2.8 34.0 + - - -
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Residues in contact with LEU 274 (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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265A ILE* 3.5 23.8 - - + -
266A ASP 3.5 24.2 - - - +
267A SER* 4.5 2.0 - - - -
269A PHE* 3.6 8.7 - - + +
270A SER 2.9 20.0 + - - +
271A GLU* 3.5 4.5 - - - +
273A LEU* 1.3 74.5 - - - +
275A ILE* 1.3 60.9 + - - +
277A THR* 3.2 3.4 + - - -
278A LEU* 2.9 29.4 + - + +
299A LEU* 4.3 4.7 - - + -
312A LYS* 3.6 41.7 - - + +
315A LEU* 5.1 10.5 - - + -
316A VAL* 3.7 24.0 - - + -
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Residues in contact with ILE 275 (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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271A GLU* 3.1 17.6 + - + +
272A ASN* 3.5 22.7 - - - +
274A LEU* 1.3 76.6 - - - +
276A GLU* 1.3 58.5 + - - +
278A LEU* 3.3 1.9 + - - +
279A GLN* 2.8 44.0 + - - +
315A LEU* 3.6 38.8 - - + -
319A LEU* 3.5 24.6 - - + +
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Residues in contact with GLU 276 (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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238A ARG* 2.9 37.5 + - - -
269A PHE* 5.9 0.7 - - - -
272A ASN 2.9 17.4 + - - +
273A LEU* 3.5 17.0 - - + +
275A ILE* 1.3 78.0 - - - +
277A THR* 1.3 66.2 + - - +
279A GLN* 3.9 7.9 - - - +
280A SER* 2.7 54.5 + - - +
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Residues in contact with THR 277 (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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187A TYR* 3.8 25.2 - - + -
238A ARG* 4.2 5.9 + - - +
265A ILE* 4.6 15.5 - - + -
266A ASP* 5.0 4.0 - - + +
269A PHE* 3.5 37.4 - - + -
273A LEU 2.8 20.2 + - - -
274A LEU* 3.6 7.4 - - - -
276A GLU* 1.3 86.4 + - - +
278A LEU* 1.3 54.3 + - - +
280A SER* 3.7 1.7 - - - -
281A SER* 2.8 40.2 + - - +
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Residues in contact with LEU 278 (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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263A LEU* 4.4 2.0 - - + -
265A ILE* 3.9 32.2 - - + +
274A LEU* 2.9 19.2 + - + +
275A ILE* 3.7 4.5 - - - +
277A THR* 1.3 76.9 - - - +
279A GLN* 1.3 62.7 + - - +
281A SER* 3.2 3.1 + - - -
282A PHE* 3.1 49.2 + - + -
297A VAL* 4.8 1.1 - - + -
315A LEU* 5.7 0.2 - - + -
316A VAL* 3.9 19.3 - - + +
319A LEU* 3.7 35.9 - - + -
320A SER* 3.4 29.8 - - - +
323A LEU* 4.0 4.3 - - + -
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Residues in contact with GLN 279 (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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275A ILE* 2.8 35.9 + - + +
276A GLU* 3.9 5.8 - - - +
278A LEU* 1.3 73.9 - - - +
280A SER* 1.3 57.8 + - - +
282A PHE* 3.4 2.4 + - - +
283A GLU* 2.9 32.9 + - + +
323A LEU* 3.9 28.0 - - + +
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Residues in contact with SER 280 (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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187A TYR* 3.4 21.1 - - - -
276A GLU* 2.7 47.0 + - - +
277A THR* 3.7 3.8 - - - -
279A GLN* 1.3 73.7 - - - +
281A SER* 1.3 57.5 + - - +
283A GLU* 3.2 6.9 + - - +
284A ILE* 2.8 38.9 + - - +
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Residues in contact with SER 281 (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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186A GLY* 5.3 0.3 - - - -
187A TYR* 3.7 17.7 - - - -
236A PHE* 4.1 13.6 - - - -
263A LEU* 3.7 29.7 - - - +
264A VAL 5.3 0.7 + - - -
265A ILE* 3.8 11.3 - - - +
277A THR 2.8 24.3 + - - -
278A LEU 3.2 6.3 + - - -
280A SER* 1.3 77.4 - - - +
282A PHE* 1.3 57.4 + - - +
284A ILE* 3.4 2.6 + - - +
285A LEU* 3.0 33.3 + - - +
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Residues in contact with PHE 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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263A LEU* 3.7 17.5 - - + -
278A LEU* 3.1 49.3 + - + +
279A GLN 4.0 2.9 - - - +
281A SER* 1.3 73.2 - - - +
283A GLU* 1.3 61.1 + - - +
285A LEU* 3.3 15.6 + - + +
286A ARG* 2.9 29.2 + - - +
295A ILE* 4.3 8.1 - - + -
297A VAL* 4.0 8.1 - - + -
320A SER* 3.8 14.6 - - - -
323A LEU* 3.9 25.6 - - + +
324A TYR* 3.4 42.7 - + + -
327A ILE* 3.8 23.1 - - + -
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Residues in contact with GLU 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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279A GLN* 2.9 22.1 + - + +
280A SER* 3.5 9.0 - - - +
282A PHE* 1.3 77.4 - - - +
284A ILE* 1.3 58.5 + - + +
286A ARG* 2.8 45.6 + - - +
287A GLU* 2.9 50.7 + - - +
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Residues in contact with ILE 284 (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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187A TYR* 3.5 26.5 - - + +
236A PHE* 3.6 47.3 - - + -
237A ILE 5.7 2.2 - - - +
248A PHE* 6.1 0.4 - - + -
252A LEU* 3.8 15.7 - - + -
280A SER* 2.8 23.0 + - - +
281A SER 3.7 4.0 - - - +
283A GLU* 1.3 72.9 - - + +
285A LEU* 1.3 63.1 + - - +
287A GLU* 3.0 27.0 + - + +
288A ILE* 3.0 16.5 + - + +
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Residues in contact with LEU 285 (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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185A VAL* 3.9 18.2 - - + -
236A PHE* 3.5 22.9 - - + -
261A LEU* 4.3 18.4 - - + -
263A LEU* 4.3 22.0 - - + -
281A SER 3.0 25.0 + - - +
282A PHE* 3.3 28.2 + - + +
284A ILE* 1.3 75.4 - - - +
286A ARG* 1.3 55.9 + - - +
288A ILE* 3.2 23.2 - - + +
290A VAL* 3.0 39.3 + - + +
295A ILE* 5.0 8.7 - - + -
324A TYR* 5.9 4.5 - - + -
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Residues in contact with ARG 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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282A PHE 2.9 12.9 + - - +
283A GLU* 2.8 44.1 + - - +
285A LEU* 1.3 77.5 - - - +
287A GLU* 1.3 78.7 + - - +
289A GLY* 3.1 14.6 + - - -
290A VAL 4.4 9.3 - - - +
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Residues in contact with GLU 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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249A PHE* 3.7 26.6 - - + -
283A GLU* 2.9 50.1 + - - +
284A ILE* 3.5 18.2 - - + +
286A ARG* 1.3 89.3 - - - +
288A ILE* 1.3 61.3 + - + +
289A GLY* 3.1 1.6 + - - -
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Residues in contact with ILE 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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236A PHE* 5.2 0.2 - - + -
249A PHE* 4.2 14.5 - - + -
252A LEU* 3.8 49.4 - - + +
253A SER* 4.0 23.6 + - - +
255A ALA* 4.5 7.9 - - + -
256A LYS* 3.1 29.4 + - + +
284A ILE* 3.0 11.6 + - + +
285A LEU* 3.2 35.4 - - + +
287A GLU* 1.3 75.9 - - + +
289A GLY* 1.3 56.5 + - - +
290A VAL* 3.6 22.0 - - + -
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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