Contacts of the helix formed by residues 250 - 266 (chain A) in PDB entry 1VK4
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PHE* 5.2 0.7 - - - -
248A LYS 3.8 0.8 + - - -
249A MSE 1.3 76.7 - - - +
251A ILE* 1.3 61.2 + - - +
252A GLU* 3.7 7.7 + - - +
253A LYS* 3.1 30.1 + - - +
254A ALA* 2.9 27.0 + - - +
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Residues in contact with ILE 251 (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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200A ILE* 4.2 20.9 - - + -
211A VAL* 3.8 29.6 - - + -
213A ASP* 3.8 31.0 - - + +
217A TYR* 3.6 31.9 - - + +
240A PHE* 4.2 8.7 - - + -
244A PHE* 4.0 22.2 - - + -
249A MSE 3.7 0.4 + - - -
250A SER* 1.3 73.2 - - - +
252A GLU* 1.3 63.1 + - - +
254A ALA* 3.8 2.1 - - - +
255A THR* 2.7 30.6 + - - -
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Residues in contact with GLU 252 (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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217A TYR* 3.7 34.8 - - + -
250A SER* 3.2 7.7 + - - +
251A ILE* 1.3 84.7 - - - +
253A LYS* 1.3 68.0 + - + +
255A THR* 3.3 3.8 + - - -
256A LYS* 2.7 55.1 + - + +
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Residues in contact with LYS 253 (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 MSE 3.9 19.5 - - + +
250A SER* 3.1 20.9 + - - +
252A GLU* 1.3 85.6 - - + +
254A ALA* 1.3 57.5 + - - +
256A LYS* 3.4 16.7 + - + +
257A PHE* 2.9 29.1 + - - +
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Residues in contact with ALA 254 (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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240A PHE* 3.7 27.5 - - + +
243A GLY* 4.1 3.4 - - - -
244A PHE* 3.8 30.5 - - + +
249A MSE 4.0 10.5 - - + +
250A SER 2.9 17.1 + - - +
251A ILE 3.8 1.3 - - - +
253A LYS* 1.3 73.3 - - - +
255A THR* 1.3 60.2 + - - +
257A PHE* 3.6 2.1 - - - +
258A ALA* 2.9 29.8 + - - +
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Residues in contact with THR 255 (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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209A VAL* 4.0 16.0 - - + +
211A VAL* 3.4 31.5 - - + +
217A TYR* 3.5 35.1 - - - +
218A GLU 4.2 9.2 - - - +
219A ALA* 3.9 0.2 - - - +
240A PHE* 3.7 8.2 - - - -
251A ILE 2.7 22.0 + - - -
252A GLU 3.5 5.2 - - - -
253A LYS 3.3 0.2 - - - -
254A ALA* 1.3 73.4 - - - +
256A LYS* 1.3 67.5 + - - +
258A ALA* 3.3 5.0 + - - +
259A ALA* 3.2 21.1 + - - +
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Residues in contact with LYS 256 (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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218A GLU 4.9 10.3 - - - +
219A ALA* 3.9 17.2 - - + +
252A GLU* 2.7 48.2 + - + +
253A LYS* 3.8 20.3 - - + +
254A ALA 3.4 0.2 - - - -
255A THR* 1.3 77.3 - - - +
257A PHE* 1.3 57.3 + - - +
259A ALA* 3.4 3.5 + - - +
260A ALA* 3.0 27.4 + - - +
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Residues in contact with PHE 257 (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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37A LEU* 4.1 22.7 - - + -
239A ALA 3.4 26.9 - - - -
242A VAL* 4.2 7.6 - - + -
243A GLY* 4.0 19.5 - - - -
247A LYS* 5.5 4.3 - - + -
249A MSE 3.7 28.7 - - + -
253A LYS 2.9 18.6 + - - +
254A ALA 3.6 3.8 - - - +
256A LYS* 1.3 72.9 - - - +
258A ALA* 1.3 61.0 + - - +
260A ALA* 3.2 6.4 + - - +
261A VAL* 2.9 49.4 + - + +
280A ILE* 3.7 28.9 - - + -
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Residues in contact with ALA 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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202A LEU* 5.5 0.7 - - + -
209A VAL* 5.2 2.0 - - + -
236A CYS* 3.5 31.4 - - - +
239A ALA* 3.7 13.1 - - - +
240A PHE* 3.7 16.6 - - + +
254A ALA 2.9 17.9 + - - +
255A THR* 3.3 6.9 + - - +
257A PHE* 1.3 77.2 - - - +
259A ALA* 1.3 56.4 + - - +
261A VAL* 3.4 2.8 + - - +
262A THR* 2.8 32.8 + - - -
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Residues in contact with ALA 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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209A VAL* 4.3 3.6 - - + +
219A ALA* 3.4 36.3 - - + +
220A SER 3.5 18.4 - - - +
221A PHE* 3.7 18.0 - - + +
236A CYS* 4.6 1.0 - - - -
255A THR 3.2 6.4 + - - +
256A LYS 3.7 4.0 - - - +
258A ALA* 1.3 73.2 - - - +
260A ALA* 1.3 58.4 + - - +
262A THR* 3.2 2.8 + - - -
263A SER* 2.9 31.9 + - - -
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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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256A LYS 3.0 14.0 + - - +
257A PHE* 3.2 10.5 + - - +
259A ALA* 1.3 75.8 - - - +
261A VAL* 1.3 63.1 + - - +
263A SER* 3.3 7.0 + - - +
264A VAL* 3.1 29.3 + - + +
280A ILE* 3.7 28.0 - - + +
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Residues in contact with VAL 261 (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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33A THR* 4.2 3.8 - - + -
37A LEU* 4.2 3.4 - - + -
235A THR* 4.0 14.6 - - + -
239A ALA* 3.6 30.3 - - + -
257A PHE* 2.9 38.1 + - + +
260A ALA* 1.3 74.8 - - - +
262A THR* 1.3 63.0 + - - +
264A VAL* 3.3 8.7 - - - +
265A LYS* 3.2 21.0 + - - +
272A LEU* 4.2 25.6 - - + -
280A ILE* 3.9 22.4 - - + -
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Residues in contact with THR 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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221A PHE* 3.7 22.7 - - + -
232A ARG* 3.8 35.0 - - + +
235A THR* 4.1 9.0 - - + -
236A CYS* 3.1 25.9 + - - +
258A ALA 2.8 19.0 + - - -
259A ALA 3.6 4.0 - - - -
261A VAL* 1.3 76.1 - - - +
263A SER* 1.3 63.1 + - - +
265A LYS* 3.3 2.5 + - + +
266A MSE 3.0 37.9 + - + +
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Residues in contact with SER 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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220A SER 4.4 1.0 + - - -
221A PHE* 3.1 12.9 - - - +
222A ARG* 3.0 42.6 + - - +
259A ALA 2.9 13.8 + - - -
260A ALA* 3.7 7.4 - - - -
262A THR* 1.3 75.5 - - - +
264A VAL* 1.3 64.3 + - - +
266A MSE 3.2 9.1 + - - -
267A ARG* 3.5 14.1 + - - +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ALA* 3.1 15.8 + - + +
261A VAL 3.3 14.4 - - - +
263A SER* 1.3 76.9 - - - +
265A LYS* 1.3 61.7 + - - +
267A ARG* 3.0 38.6 + - - +
268A HIS* 3.8 1.2 - - - -
272A LEU* 3.7 20.0 - - + -
276A ASP* 3.8 20.5 - - + +
279A ALA* 3.6 37.2 - - + +
280A ILE* 3.9 17.7 - - + +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A MSE 4.6 1.6 - - - -
227A GLU 5.1 0.2 + - - -
228A GLY 3.0 15.0 + - - -
230A THR 3.2 27.3 + - - -
231A GLY* 4.4 7.4 - - - +
232A ARG* 4.7 0.7 - - - +
235A THR* 3.8 29.4 - - + +
261A VAL 3.2 16.2 + - - +
262A THR 3.7 2.5 - - - +
264A VAL* 1.3 77.9 - - - +
266A MSE 1.3 68.7 + - + +
267A ARG 3.1 5.4 + - - -
268A HIS* 2.8 46.9 + - - +
270A GLY 2.6 37.4 + - - +
271A PRO* 4.1 0.9 - - + -
272A LEU* 3.8 22.7 - - + +
276A ASP* 4.3 2.5 - - - -
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Residues in contact with MSE 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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206A ALA 5.6 1.3 - - - +
221A PHE* 3.5 36.8 - - + -
222A ARG* 3.6 26.7 - - - +
223A SER* 3.4 20.7 - - - +
224A TRP* 3.0 20.4 + - - -
225A SER 4.3 0.2 + - - -
228A GLY* 3.3 24.3 - - - +
229A ARG* 3.9 19.5 - - - +
232A ARG* 3.7 27.8 - - + -
262A THR* 3.0 20.7 + - + +
263A SER 3.2 3.9 + - - -
265A LYS* 1.3 80.6 - - + +
267A ARG* 1.3 59.0 + - - +
268A HIS 3.2 2.4 + - - -
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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