Contacts of the helix formed by residues 265 - 278 (chain A) in PDB entry 5LXG
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A HIS 3.7 3.6 + - - +
264A ARG* 1.3 72.2 - - - +
266A THR* 1.3 57.6 + - - +
267A ARG* 3.3 4.5 - - - -
268A ALA* 2.9 37.0 + - + +
269A GLY 3.7 1.4 + - - -
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Residues in contact with THR 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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252A VAL* 5.3 6.3 - - + -
264A ARG* 3.4 28.0 + - - +
265A GLN* 1.3 72.0 + - - +
267A ARG* 1.4 59.4 + - - +
268A ALA 2.9 2.5 - - - -
269A GLY* 2.6 25.6 + - - +
270A VAL* 3.1 19.3 + - + +
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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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209A TYR* 3.5 56.4 + - - -
249A ALA* 5.5 1.5 - - - +
252A VAL* 3.0 34.4 + - + +
253A ALA* 4.6 21.8 + - + +
255A TRP* 5.7 2.4 - - - +
264A ARG* 5.3 1.0 + - - +
265A GLN* 3.3 2.2 - - - -
266A THR* 1.4 75.2 - - - +
268A ALA* 1.3 58.4 + - - +
270A VAL* 3.2 5.8 + - - +
271A PHE* 3.0 28.6 + - + +
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Residues in contact with ALA 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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265A GLN* 2.9 37.6 + - + +
267A ARG* 1.3 80.4 - - - +
269A GLY* 1.3 52.0 + - - +
271A PHE* 3.2 20.6 + - + +
272A LEU* 2.7 37.1 + - - +
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Residues in contact with GLY 269 (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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265A GLN 3.7 1.6 + - - -
266A THR* 2.6 20.9 + - - +
268A ALA* 1.3 71.0 - - - +
270A VAL* 1.3 54.8 + - - -
272A LEU* 3.2 14.1 + - - +
273A GLY* 3.0 22.5 + - - -
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Residues in contact with VAL 270 (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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245A LEU* 3.2 16.4 - - + +
248A SER* 2.5 23.3 - - - +
249A ALA* 3.0 42.6 - - + +
252A VAL* 3.8 16.6 - - + -
266A THR* 3.1 13.1 + - + +
267A ARG 3.2 7.6 + - - +
269A GLY* 1.3 73.5 - - - +
271A PHE* 1.3 64.9 + - - +
273A GLY* 3.0 13.1 + - - +
274A LEU* 3.3 13.3 + - - +
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Residues in contact with PHE 271 (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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216A ILE* 6.0 5.4 - - + -
249A ALA* 5.3 2.7 - - - +
267A ARG* 3.0 17.6 + - + +
268A ALA* 3.2 24.0 + - + +
270A VAL* 1.3 75.4 - - - +
272A LEU* 1.3 67.0 + - + +
274A LEU* 3.2 27.4 + - + +
275A GLY* 3.5 8.6 + - - -
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Residues in contact with LEU 272 (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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268A ALA 2.7 17.9 + - - +
269A GLY* 3.2 17.5 - - - +
270A VAL 3.1 0.2 - - - -
271A PHE* 1.3 80.7 - - + +
273A GLY* 1.3 59.1 + - - +
274A LEU 3.3 0.2 + - - -
275A GLY* 3.5 1.1 + - - -
276A LEU* 2.5 79.9 + - + +
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Residues in contact with GLY 273 (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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245A LEU* 3.2 26.2 - - - +
269A GLY 3.0 13.0 + - - -
270A VAL 3.0 7.2 + - - -
272A LEU* 1.3 77.2 - - - +
274A LEU* 1.3 51.7 + - - +
276A LEU* 4.7 3.8 - - - -
277A SER* 2.8 38.6 + - - -
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Residues in contact with LEU 274 (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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213A ALA* 4.0 25.8 - - + +
216A ILE* 3.8 45.3 - - + -
217A MET* 5.6 1.1 - - + -
220A PHE* 3.8 18.4 - - - -
242A VAL* 4.7 6.5 - - + +
245A LEU* 3.5 40.6 - - + +
246A GLY* 3.8 5.4 - - - +
249A ALA* 4.2 6.3 - - + -
270A VAL 3.6 9.9 - - - +
271A PHE* 3.2 15.2 + - + +
273A GLY* 1.3 73.9 - - - +
275A GLY* 1.3 65.5 + - - +
277A SER* 3.7 7.1 + - - -
278A GLY 3.7 7.1 + - - -
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Residues in contact with GLY 275 (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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216A ILE* 5.6 1.9 - - - +
220A PHE* 5.8 0.8 - - - -
271A PHE* 3.5 9.7 + - - -
272A LEU* 3.5 4.7 + - - -
274A LEU* 1.3 79.3 - - - +
276A LEU* 1.3 64.8 + - - +
278A GLY* 3.5 12.5 + - - -
279A VAL* 4.1 8.7 + - - +
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Residues in contact with LEU 276 (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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272A LEU* 2.5 58.6 + - + +
273A GLY* 4.1 3.8 - - - +
275A GLY* 1.3 76.6 - - - +
277A SER* 1.4 64.7 + - - +
278A GLY 3.1 2.2 - - - -
279A VAL* 3.2 24.2 + - + +
280A VAL* 4.1 7.3 + - - +
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Residues in contact with SER 277 (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 PHE* 5.3 0.2 - - - -
238A TYR* 4.8 2.3 + - - -
241A ILE* 3.8 22.2 - - - +
242A VAL* 3.8 21.6 - - - +
245A LEU* 3.9 14.1 - - - -
273A GLY 2.8 23.4 + - - -
274A LEU* 4.0 5.8 - - - -
275A GLY 3.5 0.2 - - - -
276A LEU* 1.4 71.7 - - - +
278A GLY* 1.3 50.2 + - - +
279A VAL 3.4 0.2 + - - -
280A VAL* 3.7 6.1 + - - +
281A PRO* 2.5 34.4 - - - +
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Residues in contact with GLY 278 (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 PHE* 4.2 22.8 - - - -
223A TRP* 4.5 2.8 - - - -
274A LEU 3.7 4.0 + - - -
275A GLY 3.5 8.8 + - - -
276A LEU 3.1 0.8 - - - -
277A SER* 1.3 79.1 - - - +
279A VAL* 1.3 48.9 + - - +
281A PRO* 2.9 19.8 - - - +
282A THR* 2.5 29.8 + - - +
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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