Contacts of the helix formed by residues 255 - 267 (chain C) in PDB entry 1KXT
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 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C ASP 4.6 2.3 - - - +
244C SER* 5.1 1.0 + - - -
253C VAL 3.3 1.0 + - - -
254C THR* 1.3 72.1 - - - +
256C PHE* 1.3 56.2 + - - +
257C LYS* 3.0 44.4 + - + +
258C TYR* 2.9 42.6 + - + +
259C GLY 4.0 0.9 + - - -
286C PHE* 3.6 9.8 - - + -
287C MET* 3.0 49.0 + - + +
292C ALA* 4.4 12.1 - - + -
293C LEU 3.1 14.7 + - - +
294C VAL* 4.6 3.0 - - + -
295C PHE* 4.1 7.9 - - - +
333C TYR* 4.2 11.9 - - + +
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Residues in contact with PHE 256 (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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233C GLU* 4.2 10.1 - - + -
234C VAL 3.8 12.1 + - - -
235C ILE* 3.8 26.2 - - + -
236C ASP 4.9 3.3 + - - +
237C LEU* 3.8 18.8 - - + +
254C THR* 3.3 31.5 + - - -
255C GLU* 1.3 72.8 + - - +
257C LYS* 1.3 63.9 + - - +
258C TYR 3.2 0.2 + - - -
259C GLY* 3.4 3.1 + - - +
260C ALA* 3.2 23.2 + - - +
295C PHE* 3.9 14.4 - + - -
298C ASN* 3.4 30.1 - - - -
300C ASP* 5.8 1.3 - - + -
301C ASN* 3.6 17.7 - - - -
307C ALA* 3.3 30.3 - - + +
312C ILE* 5.5 0.3 - - - +
4004C CL 3.8 11.4 - - + -
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ASP* 2.5 50.1 + - - +
237C LEU* 3.8 11.4 - - + +
238C GLY* 3.9 4.4 - - - +
244C SER* 4.8 5.1 + - - -
255C GLU* 3.3 24.9 + - - +
256C PHE* 1.3 78.8 - - - +
258C TYR* 1.3 64.8 + - - +
260C ALA* 3.4 2.3 + - - -
261C LYS* 2.9 32.1 + - + +
285C GLY 4.1 12.3 - - - +
286C PHE* 3.7 24.5 - - + -
96D PRO* 4.6 5.6 - - - +
97D GLY* 3.3 40.8 - - - +
98D SER* 5.3 0.9 - - - -
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C GLU* 2.9 24.4 + - + +
257C LYS* 1.3 80.5 - - - +
259C GLY* 1.3 60.1 + - - +
261C LYS* 3.8 1.4 - - - +
262C LEU* 2.9 52.3 + - + +
280C TRP* 2.7 35.5 + + - -
286C PHE* 3.9 15.0 - + - -
294C VAL* 3.3 29.6 - - + -
295C PHE 4.1 10.3 - - - +
327C PHE* 4.3 3.1 - - - -
328C MET* 3.8 35.4 + - + +
331C HIS* 4.4 4.5 - - - +
333C TYR* 3.5 32.1 + + + -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C GLU 4.0 1.4 + - - -
256C PHE* 3.4 5.5 + - - +
258C TYR* 1.3 82.2 - - - +
260C ALA* 1.3 56.1 + - - +
262C LEU* 4.6 2.9 - - - -
263C GLY* 3.0 25.6 + - - -
295C PHE* 3.6 13.9 + - - -
296C VAL* 3.5 25.2 - - - +
312C ILE* 3.6 15.1 - - - +
313C LEU 5.4 0.2 + - - -
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Residues in contact with ALA 260 (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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237C LEU* 4.6 3.1 - - + -
256C PHE 3.2 18.0 + - - +
257C LYS 3.9 3.1 - - - +
259C GLY* 1.3 76.5 - - - +
261C LYS* 1.3 60.8 + - - +
264C THR* 3.0 27.2 + - - -
308C GLY* 3.7 25.1 - - - +
311C SER* 3.6 8.0 + - - +
312C ILE* 3.8 9.9 - - + +
98D SER* 4.1 22.2 - - - +
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Residues in contact with LYS 261 (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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257C LYS* 2.9 23.3 + - - +
260C ALA* 1.3 77.0 - - - +
262C LEU* 1.3 64.8 + - - +
264C THR* 3.3 7.1 + - - +
265C VAL* 3.2 27.6 + - - +
272C GLU* 5.6 2.9 - - - +
280C TRP* 3.8 20.9 - - + -
284C TRP* 4.1 37.2 + - + -
286C PHE* 3.9 14.4 - - + -
33D PRO* 5.4 5.1 - - - +
50D ARG* 6.4 0.2 - - - +
97D GLY* 3.1 32.1 + - - +
98D SER* 3.7 20.4 - - - +
100D GLY* 4.4 10.0 - - - -
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Residues in contact with LEU 262 (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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258C TYR* 2.9 44.2 + - + +
259C GLY* 4.2 3.6 - - - +
261C LYS* 1.3 75.7 - - - +
263C GLY* 1.3 63.9 + - - +
265C VAL* 3.1 6.4 + - - +
266C VAL* 2.9 46.3 + - + +
277C LEU* 5.3 6.5 - - + -
280C TRP* 3.7 16.5 - - + -
296C VAL* 4.1 17.7 - - + -
324C ALA* 3.5 32.1 - - + +
327C PHE* 4.7 13.9 - - + -
328C MET* 4.5 2.5 - - + -
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Residues in contact with GLY 263 (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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259C GLY 3.0 17.6 + - - -
262C LEU* 1.3 77.6 - - - +
264C THR* 1.3 55.1 + - - +
266C VAL* 4.0 0.3 - - - +
267C ARG* 3.0 35.9 + - - +
296C VAL* 6.1 1.9 - - - +
311C SER 3.2 22.2 - - - -
313C LEU* 4.1 18.6 - - - -
324C ALA* 5.7 0.4 - - - -
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Residues in contact with THR 264 (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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260C ALA 3.0 16.4 + - - -
261C LYS* 3.3 12.4 + - - +
262C LEU 3.2 0.8 - - - -
263C GLY* 1.3 77.7 - - - +
265C VAL* 1.3 59.4 + - - +
267C ARG* 3.8 3.0 - - - -
268C LYS 3.1 2.6 + - - -
269C TRP* 2.9 52.3 + - + +
272C GLU* 3.9 13.2 - - + +
311C SER* 3.3 18.7 + - - -
100D TYR* 3.9 31.2 - - + -
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Residues in contact with VAL 265 (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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261C LYS 3.2 15.0 - - - +
262C LEU* 3.1 6.8 + - - +
264C THR* 1.3 75.3 - - - +
266C VAL* 1.3 61.3 + - + +
268C LYS* 2.8 27.4 + - - +
272C GLU* 3.8 21.0 - - + +
273C LYS 3.1 36.1 - - - +
274C MET* 3.8 12.7 + - + +
277C LEU* 4.3 19.7 - - + -
284C TRP* 3.8 28.5 - - + -
415C ASN* 4.8 0.9 - - - +
431C ASN* 4.5 0.3 + - - -
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Residues in contact with VAL 266 (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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262C LEU* 2.9 41.5 + - + +
265C VAL* 1.3 71.4 - - + +
267C ARG* 1.3 60.1 + - - +
268C LYS* 2.9 6.1 - - - +
274C MET* 5.0 17.0 - - + -
277C LEU* 5.7 1.8 - - + -
313C LEU* 3.7 14.8 - - + -
320C LEU* 3.7 39.7 - - + +
323C ILE* 4.8 9.9 - - + -
324C ALA* 3.8 12.3 - - + +
327C PHE* 6.1 1.3 - - + -
431C ASN* 3.2 25.3 + - - +
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Residues in contact with ARG 267 (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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263C GLY 3.0 23.1 + - - +
264C THR 4.0 0.9 - - - +
266C VAL* 1.3 75.0 - - - +
268C LYS* 1.3 70.6 + - - +
269C TRP* 3.3 57.4 + - + +
310C SER 3.2 12.9 + - - -
311C SER 2.8 20.2 + - - -
312C ILE 2.6 26.9 + - - -
313C LEU* 3.4 22.5 - - + +
317C ASP* 3.0 30.5 + - - -
320C LEU* 4.2 13.7 - - + +
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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