Contacts of the helix formed by residues 259 - 270 (chain E) in PDB entry 4LQL
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 259 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218E VAL* 3.9 24.0 - - + +
255E TYR 4.1 16.4 - - - +
256E GLN* 4.0 13.5 - - - +
257E LEU 2.9 0.4 - - - -
258E ARG* 1.3 78.8 - - - +
260E TYR* 1.3 66.5 + - - +
261E LEU 3.1 1.6 - - - -
262E GLY 3.3 0.9 + - - -
263E ILE* 2.9 32.0 + - + +
285E LEU* 5.3 6.1 - - + -
287E GLN* 5.1 10.1 - - - +
289E PRO* 4.7 22.0 - - + -
292E ALA* 4.3 7.2 - - + -
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Residues in contact with TYR 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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257E LEU* 3.9 16.1 - - + +
259E GLU* 1.3 77.3 - - - +
261E LEU* 1.3 65.8 + - + +
263E ILE* 3.5 5.4 + - - +
264E LYS* 3.1 28.0 + - + +
292E ALA* 3.5 32.7 - - + +
295E LEU* 3.8 38.1 - - + -
296E LEU* 4.1 5.4 - - + +
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Residues in contact with LEU 261 (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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221E ILE* 3.8 29.3 - - + +
225E GLU* 3.4 29.4 - - + +
226E ILE* 5.6 0.2 - - - -
229E ALA* 3.7 19.7 - - + -
257E LEU* 3.4 21.7 + - + +
258E ARG* 4.7 0.7 - - - +
259E GLU 3.1 0.8 - - - -
260E TYR* 1.3 88.5 - - + +
262E GLY* 1.3 58.2 + - - +
263E ILE 3.3 0.4 - - - -
264E LYS* 3.8 27.0 + - + +
265E LYS* 3.2 21.3 + - - +
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Residues in contact with GLY 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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214E LEU* 4.3 1.9 - - - +
217E VAL* 2.9 39.6 - - - +
218E VAL* 4.6 6.5 - - - -
221E ILE* 3.6 16.5 - - - +
258E ARG 3.8 6.5 + - - -
259E GLU 3.3 4.1 + - - -
261E LEU* 1.3 76.6 - - - +
263E ILE* 1.3 63.4 + - - +
265E LYS* 3.9 2.7 - - - -
266E PHE* 3.3 10.4 + - - +
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Residues in contact with ILE 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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181E PHE* 4.7 11.7 - - + -
214E LEU* 4.1 27.4 - - + -
218E VAL* 5.5 1.3 - - + -
259E GLU* 2.9 20.7 + - + +
260E TYR* 3.7 4.9 - - - +
262E GLY* 1.3 77.3 - - - +
264E LYS* 1.3 53.8 + - - +
266E PHE* 2.8 9.4 + - - +
267E LEU* 2.4 43.3 + - + +
275E PHE* 5.2 7.0 - - + -
289E PRO* 6.5 1.6 - - + -
296E LEU* 4.0 20.0 - - + -
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Residues in contact with LYS 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 TYR* 3.1 16.8 + - + +
261E LEU* 3.9 27.9 - - + +
263E ILE* 1.3 77.5 - - - +
265E LYS* 1.3 56.4 + - - +
267E LEU* 4.0 8.5 - - - -
268E ASP* 2.7 38.3 + - + +
296E LEU* 4.1 15.1 - - + +
301E TYR* 4.0 15.0 - - + +
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Residues in contact with LYS 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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217E VAL* 4.1 12.6 - - + -
221E ILE* 5.6 2.2 - - + -
261E LEU 3.2 16.2 + - - +
262E GLY* 3.9 7.6 - - - +
263E ILE 3.1 0.4 - - - -
264E LYS* 1.3 82.3 - - - +
266E PHE* 1.3 52.7 + - - +
268E ASP* 3.4 1.8 - - - +
269E ASP* 2.6 48.4 + - - +
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Residues in contact with PHE 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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179E ALA* 3.4 26.5 - - + -
181E PHE* 3.6 20.4 - + - -
209E TYR* 3.5 34.3 - + + -
213E GLU* 4.5 18.4 - - + -
214E LEU* 4.3 14.4 - - + -
217E VAL* 4.4 20.1 - - + +
262E GLY 3.3 12.4 + - - +
263E ILE* 2.8 13.5 + - - +
265E LYS* 1.3 74.9 - - - +
267E LEU* 1.3 65.6 + - + +
269E ASP* 2.7 27.3 + - + -
270E ASN* 2.9 26.7 + - + -
272E TYR* 4.9 0.2 - + - -
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Residues in contact with LEU 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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179E ALA* 5.3 0.4 - - + -
181E PHE* 4.3 9.6 - - + -
263E ILE* 2.4 44.4 + - + +
264E LYS* 3.9 3.4 - - - +
266E PHE* 1.3 82.6 - - + +
268E ASP* 1.3 58.2 + - - +
271E GLY* 3.0 5.9 + - - -
272E TYR* 2.6 51.4 + - + +
273E ASP 4.4 0.3 + - - -
275E PHE* 3.7 40.2 - - + +
296E LEU* 4.5 5.4 - - + -
301E TYR* 3.3 40.2 - - + -
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Residues in contact with ASP 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 LYS* 2.7 26.9 + - + +
265E LYS* 3.4 1.6 - - - +
267E LEU* 1.3 73.1 - - - +
269E ASP* 1.3 62.8 + - - +
271E GLY* 3.8 7.7 + - - +
301E TYR* 3.1 28.0 - - - -
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Residues in contact with ASP 269 (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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265E LYS* 2.6 33.9 + - - +
266E PHE* 2.7 12.4 + - + +
268E ASP* 1.3 71.8 - - - +
270E ASN* 1.3 58.2 + - - +
271E GLY* 3.0 7.2 + - - -
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Residues in contact with ASN 270 (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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186A ARG* 5.8 3.8 - - - +
177E LYS* 4.6 13.2 + - - +
209E TYR* 5.3 6.7 - - + -
266E PHE* 2.9 25.6 + - + +
269E ASP* 1.3 74.8 - - - +
271E GLY* 1.3 61.6 + - - +
272E TYR* 3.5 20.8 - - + -
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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