Contacts of the helix formed by residues 250 - 260 (chain D) in PDB entry 1Y8Q
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 ASP 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D THR* 3.5 22.6 + - - +
248D GLY 3.3 1.3 - - - -
249D TYR* 1.3 76.2 - - - +
251D PRO* 1.3 75.8 - - - +
252D VAL* 3.4 12.6 + - - +
253D LYS* 2.9 49.8 + - + +
254D LEU* 2.9 27.1 + - - +
330D ARG* 4.4 1.8 + - - +
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Residues in contact with PRO 251 (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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249D TYR 3.3 9.6 - - - +
250D ASP* 1.3 90.0 - - - +
252D VAL* 1.3 57.0 + - + +
254D LEU* 3.7 1.4 - - - +
255D PHE* 2.8 37.3 + - - +
284D TRP* 5.5 1.8 - - + -
322D PHE* 4.0 3.8 - - + -
323D SER* 3.5 43.5 - - - +
326D ILE* 4.1 19.5 - - + -
327D GLU* 4.3 15.7 - - + +
330D ARG* 3.9 9.0 - - - +
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Residues in contact with VAL 252 (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 ASP* 3.3 11.0 + - - +
251D PRO* 1.3 75.0 - - + +
253D LYS* 1.3 59.7 + - + +
255D PHE* 3.5 5.3 - - - +
256D THR* 2.7 52.5 + - - +
284D TRP* 4.1 46.7 - - + +
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Residues in contact with LYS 253 (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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243D TRP* 3.7 15.2 - - + +
247D THR* 4.1 26.0 + - + +
250D ASP* 2.9 43.3 + - + +
252D VAL* 1.3 79.3 - - + +
254D LEU* 1.3 63.0 + - - +
256D THR* 3.7 5.3 - - - -
257D LYS* 2.9 26.5 + - - +
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Residues in contact with LEU 254 (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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196D LEU* 4.2 24.0 - - + -
243D TRP* 3.4 31.9 - - + -
244D ALA* 4.0 19.7 - - + -
247D THR* 5.1 1.8 - - - +
249D TYR* 4.1 22.7 - - + -
250D ASP 2.9 21.6 + - - +
251D PRO 3.7 2.9 - - - +
253D LYS* 1.3 76.7 - - - +
255D PHE* 1.3 63.8 + - - +
257D LYS* 3.8 0.3 - - - +
258D LEU* 2.9 35.5 + - + +
322D PHE* 4.5 5.2 - - + -
326D ILE* 3.5 33.0 - - + -
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Residues in contact with PHE 255 (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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251D PRO 2.8 22.4 + - - +
252D VAL 3.5 4.5 - - - +
254D LEU* 1.3 74.2 - - - +
256D THR* 1.3 61.3 + - - +
259D PHE* 2.8 57.3 + + + +
282D LEU* 4.2 29.2 - - + -
283D ASP 4.0 4.5 - - - -
284D TRP* 3.4 62.8 - + + -
287D VAL* 4.9 5.8 - - + -
319D ALA* 4.2 13.9 - - + -
322D PHE* 3.9 20.6 - + + -
361D LEU* 3.6 24.2 - - + -
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Residues in contact with THR 256 (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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252D VAL* 2.7 38.1 + - - +
253D LYS* 3.7 5.6 - - - -
255D PHE* 1.3 80.0 - - - +
257D LYS* 1.3 60.7 + - - +
260D LYS* 3.1 40.8 + - - +
261D ASP* 3.0 36.8 + - - +
282D LEU 5.5 0.4 - - - -
283D ASP* 6.6 0.2 - - - +
284D TRP* 4.9 4.6 + - - +
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Residues in contact with LYS 257 (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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207D SER* 4.0 16.8 + - - -
240D THR* 5.5 6.1 - - - +
243D TRP* 3.2 52.3 - - + -
253D LYS 2.9 8.1 + - - +
254D LEU 3.8 0.2 - - - +
256D THR* 1.3 77.3 - - - +
258D LEU* 1.3 64.7 + - + +
261D ASP* 3.6 18.1 - - + +
262D ASP* 2.7 72.3 + - - +
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Residues in contact with LEU 258 (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 TRP* 4.4 15.0 - - + -
192D LEU* 3.4 47.1 - - + -
196D LEU* 4.9 2.2 - - + -
206D VAL* 4.1 16.2 - - + -
207D SER* 5.6 1.8 - - - +
240D THR* 5.4 4.9 - - + -
243D TRP* 5.1 2.2 - - + -
254D LEU* 2.9 35.2 + - + +
257D LYS* 1.3 91.4 - - + +
259D PHE* 1.3 74.1 + - + +
260D LYS 3.6 0.2 - - - -
262D ASP* 3.4 26.6 - - - +
263D ILE* 4.2 8.7 - - - +
322D PHE* 4.6 9.9 - - + -
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Residues in contact with PHE 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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188D TRP* 3.8 24.9 - + - -
192D LEU* 5.2 0.2 - - + -
255D PHE* 2.8 50.3 + + + +
256D THR 4.0 0.2 - - - -
258D LEU* 1.3 81.5 - - + +
260D LYS* 1.3 52.7 + - - +
263D ILE* 3.6 13.9 - - - +
281D PRO 3.6 1.9 - - - -
282D LEU* 2.7 43.7 + - + +
322D PHE* 3.8 26.0 - + - -
358D ALA* 3.8 21.5 - - - -
361D LEU* 3.5 39.7 - - + -
362D ARG* 4.0 4.9 - - + -
365D ILE* 3.7 21.8 - - + +
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Residues in contact with LYS 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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256D THR* 3.1 33.3 + - - +
258D LEU 3.6 2.0 - - - -
259D PHE* 1.3 76.5 - - - +
261D ASP* 1.3 65.9 + - - +
262D ASP 3.0 0.9 - - - -
263D ILE* 2.9 1.9 + - - +
264D ARG* 2.6 66.2 + - + +
281D PRO* 4.0 17.3 - - + -
282D LEU 3.0 27.8 - - - +
283D ASP* 2.9 31.5 + - + +
284D TRP 5.3 0.2 - - - +
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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