Contacts of the helix formed by residues 256 - 270 (chain C) 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 GLN 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C ASN 2.7 14.7 + - - +
253C VAL* 3.5 15.0 - - + +
254C ARG 3.3 0.4 - - - -
255C TYR* 1.3 79.0 - - - +
257C LEU* 1.3 58.2 + - - +
258C ARG 3.0 4.9 - - - -
259C GLU* 2.9 30.5 + - - +
260C TYR 3.8 1.6 + - - -
287C GLN* 3.3 14.8 - - - +
291C LEU* 5.3 5.4 - - + -
292C ALA* 3.9 8.3 - - + +
377C ALA* 3.8 18.8 - - + +
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ILE* 4.6 11.0 - - + +
229C ALA* 5.2 5.4 - - + -
230C TYR* 5.5 3.6 - - - +
253C VAL 3.4 12.7 + - - +
254C ARG* 4.2 4.2 + - - +
255C TYR 3.8 0.2 - - - -
256C GLN* 1.3 73.2 - - - +
258C ARG* 1.3 54.0 + - - +
259C GLU 3.0 5.4 - - - -
260C TYR* 3.9 11.2 - - + +
261C LEU* 2.9 54.7 + - + +
292C ALA* 5.1 1.8 - - - +
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C VAL* 3.2 30.4 - - + +
221C ILE* 3.2 26.4 - - + +
226C ILE* 4.6 14.5 - - + +
254C ARG 4.2 5.2 + - - +
255C TYR* 4.0 23.3 - - + +
256C GLN 3.0 1.0 - - - +
257C LEU* 1.3 77.0 - - - +
259C GLU* 1.3 57.7 + - + +
262C GLY 3.7 1.4 + - - -
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Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C VAL* 4.4 16.8 - - + +
255C TYR 4.7 6.7 - - - +
256C GLN* 2.9 18.3 + - - +
258C ARG* 1.3 77.9 - - + +
260C TYR* 1.3 56.4 + - - +
261C LEU 3.1 0.9 - - - -
262C GLY* 2.9 2.4 + - - -
263C ILE* 2.8 41.6 + - + +
285C LEU* 5.6 9.4 - - + -
286C GLU* 5.9 3.8 - - + +
287C GLN* 4.2 22.9 - - + +
289C PRO* 4.9 14.8 - - + -
292C ALA* 4.1 9.4 - - + -
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Residues in contact with TYR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LEU* 3.4 11.1 + - + +
259C GLU* 1.3 77.2 - - - +
261C LEU* 1.3 69.5 + - + +
263C ILE* 4.0 4.4 - - - +
264C LYS* 3.0 44.7 + - + +
292C ALA* 3.4 40.6 - - + +
295C LEU* 4.9 11.0 - - + -
296C LEU* 4.7 9.5 - - + +
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 3.6 20.6 - - + +
225C GLU* 5.3 4.9 - - + +
226C ILE* 3.8 26.5 - - + +
229C ALA* 4.0 21.1 - - + -
257C LEU* 2.9 42.9 + - + +
260C TYR* 1.3 85.6 - - + +
262C GLY* 1.3 56.8 - - - +
264C LYS* 4.7 11.6 - - + +
265C LYS* 3.1 19.9 + - - +
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LEU* 4.0 8.7 - - - +
217C VAL* 4.0 7.1 - - - +
218C VAL* 4.3 9.6 - - - -
221C ILE* 3.5 16.9 - - - +
258C ARG 4.2 2.7 - - - -
259C GLU 2.9 6.2 + - - -
261C LEU* 1.3 79.5 - - - +
263C ILE* 1.3 56.0 + - - +
265C LYS* 3.2 7.8 - - - +
266C PHE* 2.8 32.2 + - - +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LEU* 4.0 28.2 - - + +
259C GLU* 2.8 20.5 + - + +
260C TYR* 4.0 0.9 - - - +
262C GLY* 1.3 72.6 - - - +
264C LYS* 1.3 53.7 + - - +
266C PHE* 2.6 6.7 + - - -
267C LEU* 2.2 47.3 + - + +
275C PHE* 4.3 25.1 - - + -
289C PRO* 6.0 5.8 - - + -
296C LEU* 3.7 20.2 - - + -
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Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C TYR* 3.0 25.6 + - + +
261C LEU* 4.7 11.0 - - + -
263C ILE* 1.3 77.1 - - - +
265C LYS* 1.3 51.9 + - - +
267C LEU* 3.0 10.2 - - - +
268C ASP* 2.6 37.6 + - + +
296C LEU* 3.9 21.1 - - + +
299C ASP* 5.6 8.5 - - - -
301C TYR* 3.3 28.6 + - + +
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C VAL* 4.8 7.2 - - + -
221C ILE* 5.7 1.6 - - + -
261C LEU 3.1 24.0 + - - +
262C GLY* 3.2 11.0 - - - +
264C LYS* 1.3 77.9 - - - +
266C PHE* 1.3 51.4 - - - +
268C ASP* 2.6 8.7 + - - +
269C ASP* 2.2 51.4 + - - -
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ALA* 4.9 13.9 - - + -
209C TYR* 4.2 28.5 - + + -
213C GLU* 4.9 15.3 - - + -
214C LEU* 4.3 20.6 - - + -
217C VAL* 4.6 21.3 - - + +
262C GLY 2.8 18.0 + - - +
263C ILE* 2.6 11.1 + - - +
265C LYS* 1.3 72.8 - - - +
267C LEU* 1.3 67.6 + - + +
268C ASP 3.0 0.4 + - - -
269C ASP* 4.1 9.2 - - + -
270C ASN* 2.9 49.5 + - + +
271C GLY 3.6 1.9 + - - -
272C TYR* 5.5 5.3 - + - +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ALA* 4.0 8.5 - - + -
263C ILE* 2.2 47.6 + - + +
264C LYS* 3.0 8.8 - - - +
266C PHE* 1.3 73.6 - - + +
268C ASP* 1.3 56.1 + - - +
272C TYR* 3.0 52.6 + - + +
273C ASP 5.4 0.2 - - - +
274C ALA 4.3 2.2 - - - +
275C PHE* 3.5 48.9 - - + +
296C LEU* 4.2 6.7 - - + -
301C TYR* 3.8 25.0 + - + -
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Residues in contact with ASP 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LYS* 2.6 18.3 + - + +
265C LYS* 2.6 12.6 + - - +
267C LEU* 1.3 74.1 - - - +
269C ASP* 1.3 68.7 + - - +
270C ASN 3.5 0.6 + - - -
271C GLY* 3.5 10.5 + - - -
301C TYR* 5.4 3.6 - - - +
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Residues in contact with ASP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C VAL* 5.9 4.0 - - - -
265C LYS* 2.2 46.7 + - - +
266C PHE* 4.1 6.7 - - + -
268C ASP* 1.3 70.5 - - - +
270C ASN* 1.3 62.0 + - + +
271C GLY* 4.5 0.3 - - - -
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Residues in contact with ASN 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C PHE* 2.9 46.2 + - + +
269C ASP* 1.3 76.2 - - + +
271C GLY* 1.3 60.5 + - - +
272C TYR* 5.2 3.1 - - + -
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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