Contacts of the helix formed by residues 258 - 268 (chain D) in PDB entry 1USK
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 ASN 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D TYR* 2.9 33.0 + - - +
255D ASP* 3.0 20.9 + - - +
257D ALA* 1.3 77.4 - - - +
259D GLN* 1.3 63.4 + - - +
260D GLY 3.2 2.9 - - - -
261D ILE* 3.2 12.2 + - - +
262D VAL* 3.1 23.2 + - + +
278D TRP* 3.7 15.4 - - + -
314D VAL* 2.9 54.8 + - - +
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Residues in contact with GLN 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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253D ASP 3.9 17.0 - - - +
254D GLN* 5.3 2.8 + - - +
255D ASP 3.7 7.1 + - - +
256D PRO* 3.4 20.3 + - + +
257D ALA 3.3 2.8 - - - -
258D ASN* 1.3 77.2 - - - +
260D GLY* 1.3 60.1 + - - +
261D ILE 3.4 0.2 - - - -
262D VAL* 3.6 14.8 - - + +
263D ASP* 3.1 38.7 + - - +
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Residues in contact with GLY 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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257D ALA 4.5 3.2 + - - -
258D ASN 3.2 1.2 - - - -
259D GLN* 1.3 77.4 - - - +
261D ILE* 1.3 62.0 + - - +
263D ASP* 3.6 9.3 + - - +
264D ALA* 3.3 19.8 + - - +
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Residues in contact with ILE 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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28D GLN* 4.3 7.6 - - + -
32D ASP* 4.0 7.9 - - - +
257D ALA 5.7 0.7 - - - +
258D ASN* 3.2 15.3 + - - +
260D GLY* 1.3 75.4 - - - +
262D VAL* 1.3 65.2 + - - +
264D ALA* 3.3 7.1 + - - +
265D LEU* 3.1 32.0 + - + +
277D VAL* 5.9 0.7 - - + -
278D TRP* 3.5 23.6 - - + -
281D TYR* 3.6 38.4 - - + +
314D VAL* 3.6 30.7 - - + -
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Residues in contact with VAL 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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253D ASP* 3.8 26.0 - - + +
258D ASN 3.1 16.5 + - - +
259D GLN* 3.6 22.2 - - - +
260D GLY 3.3 0.2 - - - -
261D ILE* 1.3 76.8 - - - +
263D ASP* 1.3 65.3 + - - +
265D LEU* 3.6 1.9 + - - +
266D LYS* 3.1 39.2 + - + +
272D PRO* 4.3 20.2 - - + +
278D TRP* 3.6 21.3 - - + -
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Residues in contact with ASP 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 GLN* 3.1 25.6 + - - +
260D GLY* 3.8 8.5 - - - +
261D ILE 3.3 0.4 - - - -
262D VAL* 1.3 79.7 - - - +
264D ALA* 1.3 61.4 + - - +
266D LYS* 3.5 10.9 + - - +
267D ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 264 (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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28D GLN* 3.4 32.1 - - - +
32D ASP* 5.6 0.7 - - - +
260D GLY 3.3 12.6 + - - +
261D ILE* 3.3 10.3 + - - +
263D ASP* 1.3 80.9 - - - +
265D LEU* 1.3 60.5 + - - +
267D ALA* 3.3 7.8 + - - +
268D ASP* 3.3 26.2 + - - +
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Residues in contact with LEU 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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24D ASN* 4.1 34.5 - - + +
28D GLN* 4.5 15.9 - - + +
261D ILE* 3.1 31.4 + - + +
262D VAL 4.1 3.4 - - - +
264D ALA* 1.3 77.7 - - - +
266D LYS* 1.3 60.4 + - - +
268D ASP* 3.2 6.9 + - - +
269D LYS 3.1 5.9 + - - -
270D LYS* 2.9 50.3 + - + +
271D ASP 5.1 1.1 - - - +
272D PRO* 4.0 20.0 - - + -
277D VAL* 3.6 26.5 - - + -
278D TRP* 4.7 2.9 - - + -
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Residues in contact with LYS 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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262D VAL* 3.1 32.7 + - + +
263D ASP* 3.8 11.7 - - - +
264D ALA 3.4 0.2 - - - -
265D LEU* 1.3 76.1 - - - +
267D ALA* 1.3 57.5 + - - +
269D LYS* 3.2 24.6 + - - +
270D LYS 4.1 5.6 - - - +
272D PRO* 3.8 29.7 - - + +
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Residues in contact with ALA 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 ASP 3.0 17.2 + - - +
264D ALA* 3.6 8.7 - - - +
265D LEU 3.2 0.6 - - - -
266D LYS* 1.3 72.5 - - - +
268D ASP* 1.3 62.0 + - - +
269D LYS* 3.1 14.6 + - - +
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Residues in contact with ASP 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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28D GLN* 4.0 13.0 - - - +
31D LYS* 4.5 13.5 + - - -
264D ALA* 3.3 12.4 + - - +
265D LEU* 3.2 9.1 + - - +
267D ALA* 1.3 80.2 - - - +
269D LYS* 1.3 70.4 + - - +
270D LYS* 3.4 35.7 + - + +
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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