Contacts of the helix formed by residues 258 - 268 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C TYR* 3.0 28.2 + - - +
255C ASP* 3.0 17.8 + - - +
257C ALA* 1.3 81.6 - - - +
259C GLN* 1.3 58.8 + - - +
260C GLY 3.2 2.9 - - - -
261C ILE* 3.3 8.2 + - - +
262C VAL* 3.1 29.4 + - + +
278C TRP* 3.6 25.7 - - + -
314C VAL* 2.9 50.5 + - - +
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Residues in contact with GLN 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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253C ASP 3.5 18.4 + - - +
254C GLN* 4.8 2.4 - - - -
255C ASP 3.8 10.4 - - - +
256C PRO* 3.3 19.1 + - + +
257C ALA 3.3 0.8 - - - -
258C ASN* 1.3 76.5 - - - +
260C GLY* 1.3 61.8 + - - +
262C VAL* 3.3 30.8 - - - +
263C ASP* 2.9 43.4 + - - +
266C LYS* 5.2 3.0 - - - +
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Residues in contact with GLY 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 ALA 4.6 3.2 + - - -
258C ASN 3.2 1.0 - - - -
259C GLN* 1.3 76.5 - - - +
261C ILE* 1.3 59.0 + - - +
263C ASP* 3.5 7.0 + - - +
264C ALA* 3.2 26.2 + - - +
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Residues in contact with ILE 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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28C GLN* 4.2 8.1 - - + -
32C ASP* 4.0 7.9 - - - +
257C ALA 5.4 1.6 - - - +
258C ASN* 3.3 14.9 + - - +
260C GLY* 1.3 74.6 - - - +
262C VAL* 1.3 65.9 + - - +
264C ALA* 3.5 5.9 + - - +
265C LEU* 3.2 32.8 + - + +
277C VAL* 5.7 0.9 - - + -
278C TRP* 3.5 23.6 - - + -
281C TYR* 3.4 47.3 - - + +
314C VAL* 3.6 22.9 - - + -
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP* 3.6 26.9 - - + +
258C ASN 3.1 19.5 + - - +
259C GLN* 3.3 32.3 - - - +
260C GLY 3.3 0.2 - - - -
261C ILE* 1.3 77.4 - - - +
263C ASP* 1.3 62.2 + - - +
265C LEU* 3.4 4.0 + - - +
266C LYS* 3.0 49.6 + - + +
272C PRO* 4.3 17.6 - - + +
278C TRP* 3.8 17.7 - - + -
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Residues in contact with ASP 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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259C GLN* 2.9 30.3 + - - +
260C GLY* 4.0 6.1 - - - +
262C VAL* 1.3 83.0 - - - +
264C ALA* 1.3 60.0 + - - +
266C LYS* 3.9 11.8 + - - +
267C ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 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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28C GLN* 3.7 28.7 - - - +
260C GLY 3.2 17.7 + - - +
261C ILE* 3.8 7.0 - - - +
262C VAL 3.3 0.4 - - - -
263C ASP* 1.3 77.7 - - - +
265C LEU* 1.3 61.3 - - - +
267C ALA* 3.4 7.8 + - - +
268C ASP* 3.3 28.3 + - - +
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Residues in contact with LEU 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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24C ASN* 4.2 29.2 - - + +
28C GLN* 4.6 12.6 - - + +
261C ILE* 3.2 33.9 + - + +
262C VAL 3.7 3.6 - - - +
264C ALA* 1.3 77.3 - - - +
266C LYS* 1.3 59.3 + - - +
268C ASP* 3.0 18.5 + - - +
269C LYS 3.1 0.2 + - - -
270C LYS* 3.0 52.5 + - + +
271C ASP 5.2 2.9 - - - +
272C PRO* 4.0 21.3 - - + -
277C VAL* 3.8 24.9 - - + -
278C TRP* 4.7 2.7 - - + -
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Residues in contact with LYS 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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339B ASP* 5.1 3.8 - - - +
259C GLN* 5.2 2.8 - - - +
262C VAL* 3.0 37.0 + - + +
263C ASP* 4.0 11.8 + - - +
265C LEU* 1.3 75.3 - - - +
267C ALA* 1.3 61.3 + - - +
269C LYS* 3.2 22.0 + - - +
270C LYS 4.1 8.3 - - - +
272C PRO* 4.2 24.5 - - + +
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Residues in contact with ALA 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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263C ASP 3.0 19.6 + - - +
264C ALA* 3.4 10.3 - - - +
265C LEU 3.2 0.2 - - - -
266C LYS* 1.3 78.3 - - - +
268C ASP* 1.3 59.6 + - - +
269C LYS* 3.2 10.1 + - - +
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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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242B GLU* 4.5 5.2 - - - +
338B ALA* 5.3 0.3 - - - +
28C GLN* 3.8 14.7 - - - +
31C LYS* 4.9 11.3 + - - -
264C ALA* 3.3 13.0 + - - +
265C LEU* 3.0 11.1 + - - +
267C ALA* 1.3 77.3 - - - +
269C LYS* 1.3 68.8 + - - +
270C LYS* 3.4 30.1 - - + +
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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