Contacts of the helix formed by residues 252 - 261 (chain C) in PDB entry 5U03
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 ARG 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245C HIS* 6.1 1.3 - - - -
247C VAL* 3.8 25.6 - - + +
248C SER* 3.0 29.2 + - - +
249C SER 2.9 14.1 + - - +
250C ILE 2.9 0.2 + - - -
251C TYR* 1.3 111.2 + - + +
253C VAL* 1.3 56.4 + - - +
254C PRO 3.5 0.7 - - - -
255C LEU* 3.2 13.7 + - + +
256C LEU* 2.9 27.0 + - - +
289C ALA* 5.4 2.2 - - - +
292C TYR 5.6 0.4 - - - -
293C ASP* 2.7 34.1 + - - -
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Residues in contact with VAL 253 (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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18C ILE* 4.4 9.6 - - + -
19C ILE* 3.9 23.6 - - + -
22C SER* 3.4 23.3 - - - +
244C VAL* 4.5 8.5 - - + -
247C VAL* 3.9 24.9 - - + -
250C ILE* 2.8 20.7 + - - +
252C ARG* 1.3 72.7 - - - +
254C PRO* 1.3 68.6 - - + +
255C LEU 3.0 1.3 - - - -
256C LEU* 2.9 7.8 + - + +
257C LEU* 2.8 27.3 + - + +
601C ATP 4.1 15.7 - - + +
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Residues in contact with PRO 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER* 3.8 20.4 - - - +
26C ILE* 4.3 19.5 - - + -
77C PHE* 4.4 2.0 - - + -
250C ILE 3.3 9.2 - - - +
251C TYR* 3.3 12.6 - - - +
253C VAL* 1.3 95.9 - - + +
255C LEU* 1.3 54.2 + - - +
257C LEU* 3.3 6.8 + - + +
258C GLU 3.0 20.8 + - - -
280C LYS* 3.3 22.3 + - - +
285C TRP* 4.2 40.4 - - + +
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Residues in contact with LEU 255 (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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251C TYR* 4.1 16.8 - - + +
252C ARG* 3.2 13.4 + - + +
253C VAL 3.0 0.6 - - - -
254C PRO* 1.3 73.6 - - - +
256C LEU* 1.3 68.4 + - - +
258C GLU* 3.0 23.2 + - - +
259C GLU* 2.9 29.2 + - + +
280C LYS* 4.9 1.8 - - - +
282C LEU* 4.4 13.7 - - + -
285C TRP* 3.9 28.0 - - + +
286C LYS* 4.5 8.3 - - + +
289C ALA* 3.8 28.9 - - + -
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Residues in contact with LEU 256 (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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243C CYS 3.7 12.3 - - - +
244C VAL* 3.8 38.6 - - + -
245C HIS* 3.8 39.5 - - + +
247C VAL* 4.6 5.2 - - + -
252C ARG 2.9 14.4 + - - +
253C VAL* 3.3 9.9 - - - +
255C LEU* 1.3 76.6 - - - +
257C LEU* 1.3 68.2 + - + +
259C GLU* 2.9 30.4 + - - +
260C GLN* 2.9 31.6 + - + +
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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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19C ILE* 4.8 9.9 - - + +
22C SER* 3.7 24.7 - - - -
23C VAL* 3.9 18.4 - - + -
26C ILE* 3.7 22.7 - - + -
215C VAL* 6.0 2.2 - - + -
242C ILE* 4.6 5.2 - - + -
244C VAL* 4.5 13.9 - - + -
253C VAL* 2.8 25.4 + - + +
254C PRO 3.6 6.5 - - - +
256C LEU* 1.3 82.7 - - + +
258C GLU* 1.3 51.3 + - - +
260C GLN* 3.1 6.7 + - - +
261C GLY 2.7 29.6 + - - -
262C VAL* 3.4 36.6 + - + +
263C VAL* 5.8 0.2 - - - -
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Residues in contact with GLU 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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254C PRO 3.0 7.6 + - - +
255C LEU* 3.0 16.0 + - - +
257C LEU* 1.3 73.5 - - - +
259C GLU* 1.3 66.4 + - + +
261C GLY* 2.9 15.2 + - - +
263C VAL* 5.5 3.6 - - - -
278C PRO* 5.9 1.6 - - - +
279C ARG* 3.7 29.2 + - - +
280C LYS* 3.0 43.5 + - - +
282C LEU* 3.4 34.1 - - - +
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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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245C HIS* 5.8 1.6 + - - -
255C LEU* 2.9 20.5 + - + +
256C LEU* 2.9 22.9 + - - +
258C GLU* 1.3 78.0 - - + +
260C GLN* 1.3 68.3 + - - +
261C GLY* 4.4 0.5 - - - -
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Residues in contact with GLN 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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227C LYS* 5.3 11.1 + - - +
239C GLU* 5.0 13.0 - - - +
241C VAL 4.5 4.0 - - - +
242C ILE* 4.0 25.0 - - + +
243C CYS* 4.1 17.0 + - - +
256C LEU* 2.9 34.6 + - + +
257C LEU* 3.3 9.0 - - - +
258C GLU 3.1 0.2 - - - -
259C GLU* 1.3 84.4 + - - +
261C GLY* 1.3 61.6 + - - +
262C VAL* 3.5 15.7 + - + +
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Residues in contact with GLY 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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239C GLU* 4.4 5.6 - - - +
257C LEU 2.7 10.3 + - - -
258C GLU* 2.9 14.3 + - - -
259C GLU 4.4 0.7 - - - -
260C GLN* 1.3 77.5 - - - +
262C VAL* 1.3 64.1 + - - +
263C VAL* 3.0 5.8 + - - -
264C ASP* 3.2 24.8 + - - +
265C TYR* 3.3 9.9 + - - +
279C ARG* 5.1 7.4 - - - -
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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