Contacts of the helix formed by residues 250 - 261 (chain C) in PDB entry 1X1O
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 THR 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C TYR* 3.9 5.6 - - - -
248C ASN* 3.0 14.6 + - - +
249C MET* 1.3 73.3 - - - +
251C LEU* 1.3 74.5 + - - +
252C GLU* 3.6 9.4 + - + +
253C ARG* 3.2 39.8 - - + +
254C ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 251 (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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120C LEU* 5.4 6.1 - - + -
123C ALA* 5.2 13.9 - - + -
124C TYR* 3.9 36.1 + - + +
127C ALA* 4.7 5.4 - - - +
250C THR* 1.3 89.0 + - - +
252C GLU* 1.3 56.2 + - - +
254C ALA* 4.1 0.2 - - - +
255C LYS* 3.4 26.9 + - - +
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Residues in contact with GLU 252 (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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250C THR* 3.1 9.4 + - + +
251C LEU* 1.3 77.6 - - - +
253C ARG* 1.3 60.7 + - + +
254C ALA 3.0 4.9 - - - -
255C LYS* 3.3 18.0 - - - +
256C ALA* 2.9 33.4 + - + +
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Residues in contact with ARG 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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224C ASN* 4.3 21.6 + - - +
225C PHE 4.2 16.6 + - - +
230C LEU* 4.9 4.2 - - - +
248C ASN* 3.4 40.3 + - - +
249C MET* 4.0 28.7 - - + +
250C THR* 3.2 25.6 - - + +
252C GLU* 1.3 78.7 - - + +
254C ALA* 1.3 58.8 + - - +
256C ALA* 3.9 8.9 - - - +
257C ALA* 3.5 18.9 + - - +
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Residues in contact with ALA 254 (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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124C TYR* 3.8 26.9 - - + -
128C LEU* 3.8 9.4 - - + +
249C MET* 4.7 4.7 - - + -
250C THR 2.9 18.3 + - - +
251C LEU 4.1 2.2 - - - +
253C ARG* 1.3 77.6 - - - +
255C LYS* 1.3 66.3 + - - +
256C ALA 3.0 1.3 - - - -
257C ALA* 3.1 6.1 + - - +
258C ALA* 3.0 20.1 + - - +
265C VAL* 3.9 23.5 - - + +
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Residues in contact with LYS 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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127C ALA* 4.3 8.5 - - + +
128C LEU* 3.5 32.5 - - - +
251C LEU 3.4 14.8 + - - +
252C GLU* 3.3 24.2 - - - +
254C ALA* 1.3 80.1 - - - +
256C ALA* 1.3 65.7 + - - +
258C ALA* 3.3 3.5 + - - +
259C GLU* 2.8 57.4 + - + +
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Residues in contact with ALA 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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227C LEU* 5.0 14.7 - - + +
230C LEU* 5.0 3.1 - - + -
252C GLU* 2.9 21.9 + - + +
253C ARG* 3.9 9.9 - - - +
254C ALA 3.0 0.2 - - - -
255C LYS* 1.3 88.0 - - + +
257C ALA* 1.3 53.5 + - - +
259C GLU* 2.8 10.7 + - - +
260C ALA* 2.7 34.9 + - - +
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Residues in contact with ALA 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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230C LEU* 3.8 26.4 - - + +
245C ALA* 4.0 12.8 - - + -
253C ARG 3.5 11.9 + - - +
254C ALA* 3.1 9.5 + - - +
256C ALA* 1.3 78.5 - - - +
258C ALA* 1.3 62.5 + - - +
260C ALA* 3.0 3.8 + - - +
261C GLY 3.0 17.8 + - - -
262C VAL* 3.1 26.3 + - + +
265C VAL* 3.9 8.7 - - + -
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Residues in contact with ALA 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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128C LEU* 3.2 39.7 - - + +
131C THR* 3.3 25.1 - - + +
132C LYS* 5.1 0.7 + - - +
133C ALA* 3.3 29.0 - - + +
254C ALA 3.0 4.9 + - - -
255C LYS 3.4 4.5 - - - +
256C ALA 3.1 0.2 - - - -
257C ALA* 1.3 77.0 - - - +
259C GLU* 1.3 60.6 + - - +
261C GLY* 3.3 12.1 + - - -
262C VAL* 3.7 1.9 - - - +
265C VAL* 4.5 0.2 - - - +
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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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128C LEU* 6.3 1.1 - - - -
129C ALA 5.3 0.9 - - - +
131C THR* 3.4 20.8 - - - +
255C LYS* 2.8 53.5 + - + +
256C ALA* 2.8 12.0 + - - +
258C ALA* 1.3 74.2 - - - +
260C ALA* 1.3 61.3 + - - +
261C GLY* 3.0 6.4 + - - -
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Residues in contact with ALA 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 LEU* 4.5 7.4 - - + -
230C LEU* 3.3 29.2 - - + +
231C ARG* 3.8 28.1 - - + +
234C VAL* 3.1 18.7 - - - +
256C ALA 2.7 14.3 + - - +
257C ALA 3.0 11.0 + - - +
259C GLU* 1.3 72.0 - - - +
261C GLY* 1.3 57.6 + - - +
262C VAL 3.7 0.2 - - - -
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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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132C LYS* 3.1 24.2 + - - -
234C VAL* 4.0 15.8 - - - +
257C ALA 3.0 2.8 + - - -
258C ALA 3.3 8.9 + - - -
259C GLU 3.0 5.5 - - - -
260C ALA* 1.3 80.0 - - - +
262C VAL* 1.3 70.8 + - - +
263C ASP* 4.5 1.6 - - - +
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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