Contacts of the helix formed by residues 258 - 276 (chain D) in PDB entry 4LEY
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 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251D PHE* 2.8 24.6 + - - +
253D GLU* 3.1 27.1 + - - -
256D VAL* 3.9 2.9 + - - -
257D LEU* 1.3 72.7 - - - +
259D ALA* 1.3 63.2 + - - +
260D THR* 3.5 7.8 + - - -
261D LYS* 3.2 31.5 + - - +
262D MET* 3.3 22.2 + - - +
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Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D LEU* 3.4 7.7 + - - +
258D SER* 1.3 72.1 - - - +
260D THR* 1.3 59.2 + - - +
262D MET* 3.5 6.9 + - - +
263D LEU* 2.9 33.8 + - + +
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Residues in contact with THR 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D SER* 3.3 7.1 + - - +
259D ALA* 1.3 80.5 - - - +
261D LYS* 1.3 57.4 + - + +
263D LEU* 3.5 7.1 + - - +
264D SER* 2.6 43.7 + - - +
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Residues in contact with LYS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D HIS 4.2 15.2 + - - +
251D PHE* 3.8 22.2 - - + -
252D LEU 3.9 8.1 + - - -
253D GLU* 3.4 40.6 + - - +
258D SER* 3.2 20.8 + - - +
260D THR* 1.3 76.7 - - + +
262D MET* 1.3 60.9 + - - +
264D SER* 3.1 9.1 + - - -
265D LYS* 2.9 26.0 + - - +
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Residues in contact with MET 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D PHE* 3.1 26.2 - - + -
218D LEU* 4.0 19.1 - - + -
220D VAL* 5.4 3.1 - - + -
248D LEU* 3.7 31.6 - - + -
251D PHE* 3.6 32.4 - - + -
257D LEU* 4.2 24.0 - - + -
258D SER 3.3 15.2 + - - +
259D ALA* 3.8 6.5 - - - +
261D LYS* 1.3 77.7 - - - +
263D LEU* 1.3 58.3 + - - +
265D LYS 3.4 0.3 + - - -
266D PHE* 3.0 25.2 + - - +
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Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ALA 2.9 20.2 + - - +
260D THR* 3.7 7.6 - - - +
262D MET* 1.3 74.7 - - - +
264D SER* 1.3 58.9 + - - +
266D PHE* 3.4 20.2 - - + +
267D ARG* 2.9 42.1 + - + +
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Residues in contact with SER 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D THR* 2.6 27.6 + - - +
261D LYS* 3.1 12.5 + - - -
263D LEU* 1.3 75.7 - - - +
265D LYS* 1.3 56.3 + - - +
267D ARG* 3.3 9.4 + - - +
268D LYS* 2.9 28.7 + - - +
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Residues in contact with LYS 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D GLU* 2.6 35.1 + - - +
189D PHE* 3.7 14.4 - - + -
251D PHE* 3.6 28.8 - - + -
261D LYS 2.9 9.3 + - - +
262D MET 3.8 1.1 - - - +
264D SER* 1.3 72.4 - - - +
266D PHE* 1.3 66.2 + - - +
268D LYS* 3.0 29.3 + - + +
269D ILE* 2.9 40.2 + - + +
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Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D MET* 3.7 26.6 - - + +
189D PHE* 3.4 35.3 - + + -
192D VAL* 5.0 2.2 - - + -
216D PHE* 3.5 42.2 - + + -
262D MET 3.0 18.0 + - - +
263D LEU* 3.4 22.0 - - + +
265D LYS* 1.3 76.5 - - - +
267D ARG* 1.3 58.6 + - - +
269D ILE* 3.4 4.5 + - - +
270D ILE* 2.9 52.8 + - + +
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Residues in contact with ARG 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D LEU* 2.9 27.0 + - + +
264D SER* 3.5 7.4 - - - +
266D PHE* 1.3 75.3 - - + +
268D LYS* 1.3 61.3 + - - +
270D ILE* 3.3 9.0 + - + +
271D LYS* 2.9 57.9 + - + +
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D SER 2.9 14.3 + - - +
265D LYS* 3.0 33.2 + - + +
267D ARG* 1.3 76.7 - - - +
269D ILE* 1.3 59.1 + - - +
271D LYS* 3.1 13.2 + - - +
272D GLU* 2.9 61.1 + - + +
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Residues in contact with ILE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ARG* 3.5 50.3 + - + +
182D MET* 4.1 16.6 - - + -
187D SER* 4.2 13.2 - - - +
188D GLU* 4.5 3.1 - - - +
189D PHE* 3.7 31.2 - - + -
265D LYS* 2.9 35.1 + - + +
266D PHE 3.6 5.8 - - - +
268D LYS* 1.3 75.9 - - + +
270D ILE* 1.3 58.0 + - - +
272D GLU* 3.3 9.3 + - - +
273D GLU* 3.0 27.9 + - - +
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LEU* 4.5 25.8 - - + -
182D MET* 3.9 17.3 - - + -
216D PHE* 5.6 3.1 - - + -
266D PHE* 2.9 51.2 + - + +
267D ARG* 3.7 7.9 - - - +
269D ILE* 1.3 75.8 - - - +
271D LYS* 1.3 58.6 + - + +
273D GLU* 3.3 1.4 + - - +
274D VAL* 2.9 48.6 + - + +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ARG* 2.9 48.1 + - + +
268D LYS* 3.3 11.4 - - + +
270D ILE* 1.3 76.5 - - + +
272D GLU* 1.3 58.8 + - + +
274D VAL* 3.4 5.8 + - - +
275D LYS* 2.9 29.7 + - - +
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Residues in contact with GLU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ARG* 3.6 23.3 + - - +
185D ARG* 4.9 2.9 + - - -
268D LYS* 2.9 55.0 + - + +
269D ILE* 3.6 8.5 - - - +
270D ILE 3.3 0.2 - - - -
271D LYS* 1.3 77.9 - - + +
273D GLU* 1.3 60.3 + - - +
275D LYS* 3.4 21.4 - - - +
276D GLU* 3.7 14.4 - - - +
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Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ARG* 3.0 42.2 + - + +
178D LEU* 3.7 25.1 - - + -
181D ARG* 3.2 44.4 + - + +
185D ARG* 5.4 1.2 + - - -
269D ILE 3.0 16.9 + - - +
270D ILE* 4.7 0.2 - - - -
272D GLU* 1.3 73.3 - - - +
274D VAL* 1.3 66.1 + - - +
276D GLU* 3.3 17.0 + - - +
277D ILE* 3.4 12.7 + - - +
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D VAL* 5.4 3.8 - - + -
178D LEU* 4.0 15.7 - - + -
270D ILE* 2.9 36.5 + - + +
271D LYS* 3.8 6.1 - - - +
273D GLU* 1.3 74.0 - - - +
275D LYS* 1.3 64.5 + - - +
276D GLU 3.2 0.9 + - - -
277D ILE* 3.3 30.3 + - + +
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Residues in contact with LYS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D LYS 2.9 18.1 + - - +
272D GLU* 3.4 13.0 - - - +
273D GLU 3.2 0.2 - - - -
274D VAL* 1.3 78.6 - - - +
276D GLU* 1.3 71.6 + - - +
277D ILE 3.6 2.6 + - - +
278D LYS* 3.0 21.8 + - - +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ARG* 3.5 21.6 + - - +
272D GLU 3.7 13.4 - - - +
273D GLU* 3.3 12.4 + - - +
274D VAL 3.1 1.0 - - - -
275D LYS* 1.3 98.2 - - - +
277D ILE* 1.3 62.7 - - - +
278D LYS* 3.4 29.1 + - - +
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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