Contacts of the helix formed by residues 255 - 268 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASP 4.5 3.1 - - - +
244E SER* 5.4 0.2 + - - -
253E VAL 3.4 0.6 + - - -
254E THR* 1.3 68.3 - - - +
256E PHE* 1.3 62.1 + - - +
257E LYS* 3.2 39.3 + - + +
258E TYR* 3.2 32.1 + - + +
259E GLY 4.3 1.0 + - - -
286E PHE* 3.5 11.2 - - + -
287E MET* 2.9 54.9 + - + +
292E ALA* 4.3 8.3 - - + -
293E LEU 3.1 15.6 + - - +
294E VAL* 4.5 2.4 - - + -
295E PHE* 4.4 8.8 - - - +
333E TYR* 4.2 11.0 - - + +
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Residues in contact with PHE 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E GLU* 4.2 18.6 - - + -
234E VAL 3.2 24.4 + - - -
235E ILE* 3.6 23.8 - - + -
236E ASP 4.8 3.0 + - - +
237E LEU* 3.5 20.7 - - + +
254E THR* 3.0 27.0 + - - -
255E GLU* 1.3 69.5 + - - +
257E LYS* 1.3 63.9 + - - +
258E TYR 3.1 2.6 + - - -
259E GLY* 3.8 2.7 + - - +
260E ALA* 3.5 20.6 + - - +
295E PHE* 3.5 32.5 - + - -
298E ASN* 4.2 10.3 - - - -
300E ASP* 6.2 0.2 - - + -
301E ASN* 4.1 11.4 - - - -
307E ALA* 3.4 33.3 - - + +
4006E CL 4.3 7.0 - - + -
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Residues in contact with LYS 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E ASP* 3.5 30.9 + - - +
237E LEU* 3.7 14.4 - - + -
238E GLY* 4.5 2.0 - - - +
244E SER* 6.1 0.4 - - - -
255E GLU* 3.1 25.5 + - - +
256E PHE* 1.3 78.5 - - - +
258E TYR* 1.3 63.9 + - - +
260E ALA* 3.6 2.4 - - - +
261E LYS* 3.0 31.5 + - + +
284E TRP 5.8 0.2 - - - +
285E GLY 3.4 23.5 + - - +
286E PHE* 4.0 15.7 - - + -
287E MET 5.7 0.2 - - - +
32F TYR* 5.6 0.2 - - - -
96F PRO* 3.9 11.7 - - - +
97F GLY* 3.3 40.8 - - - +
98F SER* 5.2 1.6 - - - +
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Residues in contact with TYR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E GLU* 3.2 22.7 + - + +
256E PHE 3.1 0.4 - - - -
257E LYS* 1.3 79.5 - - - +
259E GLY* 1.3 66.9 + - - +
262E LEU* 3.0 48.1 + - + +
280E TRP* 3.1 39.8 + + - -
286E PHE* 3.9 13.5 - + - -
294E VAL* 3.7 25.1 - - + +
295E PHE 3.9 12.8 - - - +
327E PHE* 4.6 0.7 - - - -
328E MET* 3.2 48.2 + - + +
331E HIS* 4.7 2.9 - - - +
333E TYR* 3.6 28.2 + + + -
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Residues in contact with GLY 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E GLU 4.3 1.0 + - - -
256E PHE* 3.8 4.4 + - - +
258E TYR* 1.3 83.5 - - - +
260E ALA* 1.3 56.9 + - - +
262E LEU* 4.1 3.5 - - - +
263E GLY* 3.0 26.2 + - - -
295E PHE* 3.6 20.7 + - - -
296E VAL* 3.8 22.0 - - - +
312E ILE* 4.5 9.2 - - - -
313E LEU 5.2 0.2 + - - -
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E LEU* 4.6 2.0 - - + -
256E PHE 3.5 18.6 + - - +
257E LYS* 3.6 5.4 - - - +
258E TYR 3.2 0.8 - - - -
259E GLY* 1.3 77.9 - - - +
261E LYS* 1.3 62.3 + - - +
263E GLY* 3.9 0.2 - - - -
264E THR* 3.0 26.1 + - - -
308E GLY* 3.9 25.6 - - - +
311E SER* 3.5 13.7 + - - +
312E ILE* 4.7 3.2 - - - +
98F SER* 3.9 20.4 - - - +
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Residues in contact with LYS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E LYS* 3.0 21.0 + - + +
260E ALA* 1.3 75.1 - - - +
262E LEU* 1.3 67.7 + - - +
264E THR* 3.1 14.0 + - + +
265E VAL* 3.0 26.2 + - - +
272E GLU* 5.6 3.6 - - - +
280E TRP* 4.2 17.9 - - + -
284E TRP* 4.3 34.8 + - + -
286E PHE* 4.4 7.8 - - + -
33F PRO* 6.0 3.6 - - - +
50F ARG* 6.0 1.4 - - - +
97F GLY 3.1 18.8 + - - -
98F SER* 3.2 31.0 - - - -
100F TYR* 3.7 23.2 - - + +
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Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E TYR* 3.0 47.4 + - + +
259E GLY* 4.1 4.5 - - - +
261E LYS* 1.3 76.3 - - - +
263E GLY* 1.3 62.0 + - - +
265E VAL* 3.3 3.8 + - + +
266E VAL* 3.1 36.2 + - + +
277E LEU* 4.2 17.9 - - + -
280E TRP* 3.4 21.0 - - + -
296E VAL* 5.0 5.4 - - + -
324E ALA* 3.8 31.6 - - + +
327E PHE* 3.9 22.9 - - + -
328E MET* 4.5 0.7 - - + -
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Residues in contact with GLY 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E GLY 3.0 17.2 + - - -
260E ALA 3.9 0.4 - - - -
261E LYS 3.2 0.2 - - - -
262E LEU* 1.3 78.3 - - - +
264E THR* 1.3 61.2 + - - +
266E VAL* 4.1 1.2 - - - +
267E ARG* 3.2 28.8 + - - +
296E VAL* 6.2 1.5 - - - +
311E SER 3.2 23.6 - - - -
313E LEU* 4.3 16.2 - - - -
324E ALA* 5.9 0.2 - - - -
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Residues in contact with THR 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E ALA 3.0 15.7 + - - -
261E LYS* 3.1 16.2 + - + +
263E GLY* 1.3 76.9 - - - +
265E VAL* 1.3 57.9 + - - +
267E ARG* 3.8 2.7 - - - +
268E LYS* 3.0 19.9 + - - -
269E TRP* 3.0 32.1 + - + +
272E GLU* 3.8 21.2 - - + +
311E SER* 3.6 17.5 + - - -
100F TYR* 3.8 33.8 - - + -
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Residues in contact with VAL 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LYS 3.0 14.8 + - - +
262E LEU* 3.8 7.2 - - + +
263E GLY 3.2 0.4 - - - -
264E THR* 1.3 75.2 - - - +
266E VAL* 1.3 59.4 + - + +
268E LYS* 2.7 32.4 + - - +
272E GLU* 3.7 28.9 - - + +
273E LYS 3.9 5.8 - - - +
274E MET* 3.6 35.3 + - + +
277E LEU* 3.7 35.0 - - + -
284E TRP* 4.1 11.0 - - + -
431E ASN* 4.3 1.0 + - - -
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Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.1 24.4 + - + +
265E VAL* 1.3 77.8 - - + +
267E ARG* 1.3 59.7 + - - +
268E LYS* 3.1 3.6 - - - -
274E MET* 5.5 8.7 - - - -
277E LEU* 5.9 0.9 - - + -
313E LEU* 3.9 9.9 - - + -
320E LEU* 3.9 43.0 - - + +
323E ILE* 4.6 15.9 - - + -
324E ALA* 3.9 26.5 - - + +
327E PHE* 6.1 0.9 - - + -
431E ASN* 3.3 28.3 + - - +
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Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E GLY 3.2 20.7 + - - +
264E THR 4.0 2.0 - - - +
266E VAL* 1.3 74.5 - - - +
268E LYS* 1.3 72.4 + - - +
269E TRP* 3.4 53.8 + - + +
310E SER 3.5 13.8 + - - -
311E SER* 3.1 16.9 + - - +
312E ILE 3.3 17.4 + - - -
313E LEU* 3.2 31.8 - - + +
317E ASP* 3.2 26.1 + - - -
320E LEU* 4.6 17.7 - - + +
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Residues in contact with LYS 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E THR 3.0 2.8 + - - -
265E VAL 2.7 21.4 + - - +
266E VAL 3.9 6.1 - - - -
267E ARG* 1.3 84.8 - - - +
269E TRP* 1.3 64.5 + - - +
270E SER 4.1 0.3 + - - -
271E GLY* 4.3 4.2 + - - -
272E GLU 3.6 16.9 - - - +
415E ASN* 3.5 31.0 - - - +
431E ASN* 2.6 48.1 + - - +
432E ASP* 4.6 3.4 - - - +
433E ASP* 4.6 15.4 + - - -
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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