Contacts of the helix formed by residues 255 - 268 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASP 4.1 5.0 - - - +
244A SER* 4.9 0.9 + - - -
253A VAL 3.3 1.4 + - - -
254A THR* 1.3 69.5 - - - +
256A PHE* 1.3 62.8 + - - +
257A LYS* 3.0 40.6 + - + +
258A TYR* 3.2 34.9 - - + +
259A GLY 4.3 0.7 + - - -
286A PHE* 3.7 9.1 - - + -
287A MET* 3.0 52.7 + - + +
292A ALA* 4.3 8.3 - - + -
293A LEU 3.2 14.8 + - - +
294A VAL* 4.7 2.2 - - + -
295A PHE* 4.3 9.4 - - - +
333A TYR* 4.2 12.8 - - + +
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Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU* 4.2 8.5 - - + -
234A VAL 3.4 15.0 - - - -
235A ILE* 3.5 27.8 - - + -
236A ASP 4.8 3.0 + - - +
237A LEU* 3.4 29.4 - - + +
254A THR* 2.9 34.4 + - - -
255A GLU* 1.3 69.4 + - - +
257A LYS* 1.3 63.4 + - - +
258A TYR 3.1 2.6 + - - -
259A GLY* 3.8 3.5 + - - +
260A ALA* 3.4 16.1 + - - +
295A PHE* 3.5 30.3 - + - -
298A ASN* 4.2 11.2 - - - -
300A ASP* 6.1 0.7 - - + -
301A ASN* 3.9 14.6 - - - -
307A ALA* 3.6 26.5 - - + +
4002A CL 4.1 16.2 - - + -
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP* 2.8 50.5 + - - +
237A LEU* 3.7 8.9 - - + +
238A GLY* 3.9 6.3 - - - +
244A SER* 5.3 1.4 + - - -
255A GLU* 3.0 27.5 + - - +
256A PHE* 1.3 78.8 - - - +
258A TYR* 1.3 63.4 + - - +
260A ALA* 3.5 1.6 + - - +
261A LYS* 3.0 34.9 + - + +
285A GLY 3.9 20.4 - - - +
286A PHE* 3.8 16.6 - - + -
32B TYR* 5.6 0.4 - - - -
96B PRO* 4.0 8.4 - - - +
97B GLY* 3.1 39.7 - - - +
98B SER* 5.2 0.9 - - - -
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Residues in contact with TYR 258 (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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255A GLU* 3.2 23.2 + - + +
257A LYS* 1.3 79.9 - - - +
259A GLY* 1.3 66.4 + - - +
260A ALA 3.2 0.2 + - - -
262A LEU* 2.9 37.6 + - + +
280A TRP* 3.2 43.8 + + - -
286A PHE* 3.8 17.2 - + - -
294A VAL* 3.6 24.6 - - + +
295A PHE 3.6 14.1 - - - +
296A VAL* 5.2 0.9 - - + -
328A MET* 3.1 54.9 + - + +
331A HIS* 4.9 1.6 - - - +
333A TYR* 3.8 23.8 + + + +
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Residues in contact with GLY 259 (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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255A GLU 4.3 0.8 + - - -
256A PHE* 3.8 5.3 + - - +
257A LYS 3.6 0.2 - - - -
258A TYR* 1.3 83.9 - - - +
260A ALA* 1.3 61.0 + - - +
262A LEU* 4.4 3.1 - - - +
263A GLY* 3.1 20.1 + - - -
295A PHE* 3.8 12.7 + - - -
296A VAL* 3.5 28.0 - - - +
301A ASN* 6.2 1.1 - - - -
312A ILE* 4.4 12.1 - - - +
313A LEU 5.3 0.2 + - - -
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Residues in contact with ALA 260 (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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237A LEU* 4.4 3.4 - - + -
256A PHE 3.4 18.3 + - - +
257A LYS 3.8 2.9 - - - +
258A TYR 3.1 0.8 - - - -
259A GLY* 1.3 78.0 - - - +
261A LYS* 1.3 64.1 + - - +
264A THR* 3.2 26.6 + - - -
307A ALA 4.9 0.7 - - - +
308A GLY* 4.3 19.7 - - - -
311A SER* 3.4 13.9 + - - +
312A ILE* 4.7 4.0 - - - +
98B SER* 3.5 24.5 - - - +
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Residues in contact with LYS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LYS* 3.0 22.9 + - - +
258A TYR 3.8 2.0 - - - +
260A ALA* 1.3 76.9 - - - +
262A LEU* 1.3 57.1 + - - +
264A THR* 3.5 6.8 + - - -
265A VAL* 3.1 33.4 + - - +
272A GLU* 6.0 0.9 - - - +
280A TRP* 4.0 17.7 - - + -
284A TRP* 3.8 39.1 + - + -
286A PHE* 3.9 11.3 - - + -
33B PRO* 5.7 4.0 - - - +
50B ARG* 5.9 1.8 - - - +
97B GLY* 3.2 36.7 + - - +
98B SER* 3.5 20.2 - - - +
100B GLY* 4.5 7.4 - - + -
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Residues in contact with LEU 262 (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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258A TYR* 2.9 37.8 + - + +
259A GLY* 4.4 3.4 - - - +
261A LYS* 1.3 76.1 - - - +
263A GLY* 1.3 67.5 + - - +
265A VAL* 3.2 4.7 + - + -
266A VAL* 2.9 46.9 + - + +
277A LEU* 4.5 18.6 - - + -
280A TRP* 3.8 20.6 - - + -
296A VAL* 4.7 6.5 - - + -
313A LEU* 5.4 0.2 - - - -
324A ALA* 3.8 34.3 - - + +
327A PHE* 4.5 12.8 - - + -
328A MET* 4.7 1.1 - - + -
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Residues in contact with GLY 263 (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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259A GLY 3.1 16.6 + - - -
260A ALA 4.0 0.4 - - - -
262A LEU* 1.3 77.1 - - - +
264A THR* 1.3 57.9 + - - +
266A VAL* 4.1 0.5 - - - +
267A ARG* 2.9 36.4 + - - +
296A VAL* 6.3 1.7 - - - +
311A SER 3.2 22.9 - - - -
313A LEU* 4.2 17.5 - - - -
324A ALA* 5.9 0.2 - - - -
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Residues in contact with THR 264 (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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260A ALA 3.2 13.7 + - - -
261A LYS* 3.7 10.3 - - - -
262A LEU 3.2 0.2 - - - -
263A GLY* 1.3 75.7 - - - +
265A VAL* 1.3 62.3 + - - +
267A ARG* 3.3 5.4 + - - +
268A LYS* 3.0 18.0 + - - -
269A TRP* 3.2 34.9 + - + +
272A GLU* 3.7 14.1 - - + +
311A SER* 3.5 19.1 + - - -
100B TYR* 3.7 30.2 - - + -
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Residues in contact with VAL 265 (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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261A LYS 3.1 18.1 + - - +
262A LEU* 3.2 7.2 + - + +
264A THR* 1.3 77.5 - - - +
266A VAL* 1.3 60.9 + - - +
268A LYS* 2.9 25.5 + - - +
272A GLU* 3.7 33.0 - - - +
273A LYS 4.0 6.1 - - - +
274A MET* 3.8 19.0 + - + +
277A LEU* 3.6 47.3 - - + -
284A TRP* 3.9 11.7 - - + -
431A ASN* 4.5 1.2 + - - -
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Residues in contact with VAL 266 (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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262A LEU* 2.9 41.9 + - + +
265A VAL* 1.3 75.7 - - + +
267A ARG* 1.3 60.0 + - - +
268A LYS* 3.1 2.0 - - - +
274A MET* 5.0 9.0 - - - -
277A LEU* 5.5 0.7 - - + -
313A LEU* 3.8 22.7 - - + -
320A LEU* 3.8 31.9 - - + +
323A ILE* 4.5 17.0 - - + -
324A ALA* 4.1 13.9 - - + +
327A PHE* 5.9 1.6 - - + -
431A ASN* 3.1 26.3 + - - +
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Residues in contact with ARG 267 (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 GLY 2.9 19.2 + - - +
264A THR 3.8 3.8 - - - +
266A VAL* 1.3 75.6 - - - +
268A LYS* 1.3 73.8 + - - +
269A TRP* 3.3 56.9 + - + +
310A SER 3.1 13.7 + - - -
311A SER 2.9 22.9 + - - -
312A ILE 3.0 24.0 + - - -
313A LEU* 3.4 23.8 - - + +
317A ASP* 3.4 27.3 + - - +
320A LEU* 4.2 13.7 - - + +
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Residues in contact with LYS 268 (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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264A THR 3.0 2.1 + - - -
265A VAL 2.9 17.0 + - - +
266A VAL 3.1 3.3 - - - -
267A ARG* 1.3 83.3 - - - +
269A TRP* 1.3 63.3 + - - +
271A GLY* 4.6 3.5 + - - -
272A GLU 3.8 15.6 - - - +
320A LEU* 6.2 2.0 - - - -
415A ASN* 3.5 28.3 - - - +
431A ASN* 2.7 54.4 + - - +
432A ASP* 4.6 1.8 - - - +
433A ASP* 3.9 20.8 + - - -
44B GLU* 5.1 1.7 - - - +
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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