Contacts of the helix formed by residues 246 - 259 (chain C) in PDB entry 1XSK
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 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C GLY* 4.7 0.9 - - - -
244C GLY 3.3 0.2 - - - -
245C PRO* 1.3 91.6 - - + +
247C PRO* 1.3 76.3 - - + +
248C LYS 4.2 1.1 - - - -
249C ALA* 2.9 27.0 + - - +
250C VAL* 2.9 16.3 + - - +
596C PRO* 4.7 15.3 - - + -
3007C SO4 2.7 36.3 + - - +
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Residues in contact with PRO 247 (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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201C MET* 3.2 28.5 - - + +
202C THR 4.7 7.0 - - - +
203C ASN* 5.5 1.6 - - - -
205C GLY* 5.1 4.0 - - - +
245C PRO 4.6 1.8 - - - +
246C THR* 1.3 87.0 - - - +
248C LYS* 1.3 61.5 + - - +
250C VAL* 3.3 6.9 + - + +
251C LEU* 3.1 28.4 + - - +
592C MET* 3.8 27.6 - - + +
593C MET* 4.1 22.9 - - + +
596C PRO* 3.7 23.1 - - + -
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Residues in contact with LYS 248 (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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246C THR* 3.2 1.8 + - - -
247C PRO* 1.3 77.7 - - - +
249C ALA* 1.3 57.5 + - - +
251C LEU* 3.4 9.2 + - - +
252C ASP* 2.9 28.2 + - - +
583C ARG* 3.6 21.3 + - - +
585C THR* 4.1 24.4 + - + +
589C ARG* 4.2 5.2 - - - +
593C MET* 3.8 30.3 - - + +
594C GLU* 2.8 45.2 + - - +
612C ASP* 3.6 13.1 + - - -
3007C SO4 3.4 24.8 + - - +
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Residues in contact with ALA 249 (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 ASP 4.2 2.5 - - - -
244C GLY 3.3 26.0 - - - +
245C PRO* 4.2 1.8 - - + -
246C THR* 2.9 22.7 + - - +
248C LYS* 1.3 77.5 - - - +
250C VAL* 1.3 66.0 + - - +
252C ASP* 3.1 5.1 + - - +
253C ARG* 3.0 27.1 + - - +
583C ARG* 3.6 14.3 - - - +
3007C SO4 4.6 2.9 - - - +
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Residues in contact with VAL 250 (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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199C PHE* 4.0 17.0 - - + -
201C MET* 4.4 9.9 - - + -
205C GLY* 3.7 18.4 - - - +
206C TYR* 3.9 5.4 - - - +
207C GLY* 3.6 26.9 - - - +
242C ILE* 3.8 10.2 - - + +
243C ASP 3.8 7.6 - - - +
244C GLY* 3.4 20.0 - - - +
246C THR 2.9 16.2 + - - +
247C PRO* 3.5 9.9 - - + +
249C ALA* 1.3 76.4 - - - +
251C LEU* 1.3 51.5 + - - +
253C ARG* 3.2 5.2 + - - +
254C TYR* 2.8 32.4 + - - +
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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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199C PHE* 4.4 9.4 - - + -
201C MET* 4.1 16.8 - - - -
247C PRO 3.1 18.1 + - - +
248C LYS* 3.8 6.1 - - - +
250C VAL* 1.3 76.0 - - - +
252C ASP* 1.3 60.8 + - - +
254C TYR* 4.0 6.7 - - + -
255C THR* 2.7 36.2 + - + +
501C GLY 3.7 17.0 - - - +
502C LEU* 4.2 11.7 - - - +
504C GLY* 3.8 30.3 - - - +
583C ARG 3.9 1.3 - - - -
584C GLY 4.0 11.4 - - - +
585C THR* 5.3 0.9 - - - -
586C PRO* 4.1 9.0 - - + -
593C MET* 4.1 26.9 - - + -
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Residues in contact with ASP 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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248C LYS 2.9 15.3 + - - +
249C ALA* 3.1 10.0 + - - +
251C LEU* 1.3 77.5 - - - +
253C ARG* 1.3 64.8 + - + +
256C ARG* 3.1 15.1 + - - +
260C ARG* 2.6 47.2 + - - -
583C ARG* 3.1 50.4 + - - +
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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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61C GLN* 5.6 1.5 - - + +
62C GLU* 3.3 51.1 + - - +
63C GLY* 3.7 19.1 - - - -
64C ILE* 4.3 7.4 - - + +
242C ILE* 3.6 17.5 - - + -
243C ASP* 2.6 42.8 + - - +
244C GLY 2.8 19.0 + - - -
249C ALA* 3.0 15.8 + - - +
250C VAL 3.6 2.5 - - - +
252C ASP* 1.3 76.5 - - + +
254C TYR* 1.3 60.0 + - - +
256C ARG* 3.1 14.6 + - - +
257C PHE* 2.8 32.4 + - - +
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Residues in contact with TYR 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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197C ILE* 3.5 22.7 - - - +
199C PHE* 3.5 49.3 - + + +
209C LEU* 4.3 9.4 - - + -
242C ILE* 3.9 15.2 - - + +
250C VAL 2.8 20.1 + - - +
251C LEU* 3.3 9.4 + - + +
253C ARG* 1.3 73.9 - - - +
255C THR* 1.3 54.5 + - + +
257C PHE* 3.2 6.5 + + - +
258C THR* 2.8 69.2 + - + -
470C VAL* 4.1 16.5 - - - +
473C GLN* 4.3 5.9 + - - -
503C SER 3.5 21.6 + - - -
504C GLY* 3.9 18.2 - - - -
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Residues in contact with THR 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 LEU 2.7 26.8 + - - +
254C TYR* 1.3 73.7 - - + +
256C ARG* 1.3 60.3 + - - +
258C THR* 4.1 1.3 - - - -
259C GLY* 2.7 51.2 + - - +
260C ARG* 2.7 35.7 + - - +
261C PRO* 4.2 2.5 - - + -
473C GLN* 4.5 1.1 - - - +
504C GLY* 3.8 33.9 - - - +
584C GLY* 3.5 22.9 - - - +
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Residues in contact with ARG 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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61C GLN* 3.7 32.4 + - - +
85C ASN* 2.9 26.3 + - - +
252C ASP* 3.1 26.2 + - - +
253C ARG* 3.5 12.7 - - - +
255C THR* 1.3 76.9 + - - +
257C PHE* 1.3 57.9 + - - +
260C ARG* 3.4 34.2 - - - +
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Residues in contact with PHE 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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60C PRO* 3.7 16.6 - - + -
61C GLN* 4.1 14.1 - - + +
64C ILE* 3.8 20.2 - - + -
84C LEU* 3.6 25.3 - - + -
85C ASN* 2.7 55.3 + - - -
86C ILE* 4.3 1.6 - - + -
209C LEU* 3.8 22.4 - - + -
240C PHE* 3.7 43.3 - + + -
242C ILE* 4.5 8.7 - - + -
253C ARG 2.8 16.2 + - - +
254C TYR* 3.4 4.5 - + - +
256C ARG* 1.3 79.2 - - - +
258C THR* 1.3 65.5 + - + +
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Residues in contact with THR 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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83C PRO* 3.8 15.8 - - - +
84C LEU* 3.8 26.0 - - + -
85C ASN* 4.2 3.7 + - - -
209C LEU* 4.0 5.6 - - + -
254C TYR* 2.8 52.2 + - + +
257C PHE* 1.3 75.8 - - + +
259C GLY* 1.3 55.6 + - - +
470C VAL* 3.8 21.5 - - + -
471C GLY* 3.6 16.3 - - - -
473C GLN* 2.9 24.3 + - - -
474C LYS* 4.5 4.3 - - - +
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Residues in contact with GLY 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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85C ASN* 4.1 6.8 - - - +
255C THR* 2.7 27.7 + - - +
257C PHE 3.8 0.6 - - - -
258C THR* 1.3 76.8 + - - +
260C ARG* 1.3 61.8 + - - -
473C GLN* 2.9 27.1 + - - +
474C LYS* 3.7 20.9 - - - -
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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