Contacts of the helix formed by residues 246 - 259 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D GLY* 4.6 0.7 - - - -
244D GLY 3.4 0.2 - - - -
245D PRO* 1.3 88.8 - - + +
247D PRO* 1.3 76.2 - - - +
248D LYS* 3.6 2.8 + - - -
249D ALA* 2.9 20.3 + - + +
250D VAL* 3.1 15.3 + - - +
596D PRO* 4.9 12.3 - - + -
3004D SO4 2.9 40.9 + - - +
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Residues in contact with PRO 247 (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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201D MET* 3.3 29.6 - - + +
202D THR 4.7 7.0 - - - +
203D ASN* 5.4 2.9 - - - +
205D GLY* 4.9 4.7 - - - +
245D PRO 4.4 2.2 - - - +
246D THR* 1.3 84.9 - - - +
248D LYS* 1.3 63.0 + - - +
250D VAL* 3.2 9.1 + - + +
251D LEU* 3.2 25.8 + - - +
592D MET* 4.1 19.7 - - + +
593D MET* 4.2 21.3 - - + +
596D PRO* 3.6 29.4 - - + -
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Residues in contact with LYS 248 (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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246D THR* 3.2 3.1 + - - +
247D PRO* 1.3 78.5 - - - +
249D ALA* 1.3 58.4 + - - +
251D LEU* 3.6 8.4 + - - +
252D ASP* 3.0 25.6 + - - +
583D ARG* 3.5 16.2 + - - +
585D THR* 4.2 24.0 + - + +
589D ARG* 4.4 4.0 - - - +
593D MET* 3.8 34.5 - - + +
594D GLU* 2.6 42.5 + - - +
612D ASP* 3.6 14.3 + - - -
3004D SO4 3.5 31.9 + - - +
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Residues in contact with ALA 249 (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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243D ASP 4.3 0.2 - - - -
244D GLY* 3.2 29.2 - - - +
245D PRO* 4.8 1.3 - - + -
246D THR* 2.9 20.9 + - - +
248D LYS* 1.3 75.3 - - - +
250D VAL* 1.3 67.9 + - - +
252D ASP* 3.1 6.6 + - - +
253D ARG* 3.0 28.3 + - - +
583D ARG* 3.9 8.1 - - - +
3004D SO4 3.8 4.9 + - - +
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Residues in contact with VAL 250 (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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199D PHE* 3.9 17.0 - - + -
201D MET* 4.5 8.3 - - + -
205D GLY 3.3 33.7 - - - +
206D TYR* 3.7 5.8 - - - +
207D GLY* 3.6 26.5 - - - +
242D ILE* 3.8 11.1 - - + +
243D ASP 3.9 6.7 - - - -
244D GLY* 3.4 11.0 - - - +
246D THR 3.1 9.9 + - - +
247D PRO* 3.2 9.8 + - + +
249D ALA* 1.3 76.6 - - - +
251D LEU* 1.3 52.7 + - - +
253D ARG* 3.0 4.7 + - - +
254D TYR* 2.7 32.9 + - - +
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Residues in contact with LEU 251 (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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199D PHE* 4.2 15.5 - - + -
201D MET* 4.1 8.3 - - + -
247D PRO 3.2 15.8 + - - +
248D LYS* 3.9 6.3 - - - +
250D VAL* 1.3 78.8 - - - +
252D ASP* 1.3 52.5 + - - +
254D TYR* 4.1 5.4 - - + -
255D THR* 2.6 40.9 + - - +
501D GLY 3.6 18.4 - - - +
502D LEU* 4.1 11.7 - - - +
504D GLY* 3.7 31.0 - - - +
583D ARG 3.9 1.8 - - - -
584D GLY 3.8 12.3 - - - +
585D THR* 5.2 0.9 - - - -
586D PRO* 4.0 13.0 - - + -
593D MET* 3.7 26.9 - - + -
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Residues in contact with ASP 252 (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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248D LYS 3.0 16.1 + - - +
249D ALA* 3.3 13.2 - - - +
250D VAL 3.1 0.2 - - - -
251D LEU* 1.3 77.4 - - - +
253D ARG* 1.3 63.1 + - + +
255D THR* 3.8 0.4 - - - -
256D ARG* 3.2 15.3 + - - +
260D ARG* 2.9 34.8 + - - -
583D ARG* 2.9 48.3 + - - +
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Residues in contact with ARG 253 (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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61D GLN* 5.4 1.9 - - + +
62D GLU* 3.0 50.1 + - - +
63D GLY* 3.4 20.3 - - - -
64D ILE* 4.1 9.7 - - + +
107D ASN 6.1 0.4 - - - +
242D ILE* 3.6 15.0 - - + -
243D ASP* 2.6 41.2 + - - -
244D GLY 2.9 21.2 + - - -
249D ALA* 3.0 14.5 + - - +
250D VAL 3.0 2.9 + - - +
252D ASP* 1.3 77.7 - - + +
254D TYR* 1.3 59.3 + - - +
256D ARG* 3.2 11.3 + - - +
257D PHE* 2.8 32.8 + - - +
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Residues in contact with TYR 254 (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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197D ILE* 3.6 21.0 - - - +
199D PHE* 3.5 46.9 - + + -
209D LEU* 4.1 10.5 - - + -
242D ILE* 3.8 21.9 - - + +
250D VAL 2.7 19.7 + - - +
251D LEU* 3.9 7.4 - - + +
253D ARG* 1.3 73.7 - - - +
255D THR* 1.3 61.2 + - + +
257D PHE* 3.2 4.7 + + - +
258D THR* 2.8 62.5 + - + -
470D VAL* 3.8 16.6 - - - +
473D GLN* 4.4 8.9 + - - -
503D SER 3.6 19.4 + - - -
504D GLY* 4.0 17.9 - - - -
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Residues in contact with THR 255 (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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85D ASN* 4.9 0.2 + - - -
251D LEU* 2.6 25.4 + - - +
254D TYR* 1.3 75.8 - - + +
256D ARG* 1.3 60.2 + - - +
257D PHE 3.1 1.1 - - - -
258D THR* 4.2 1.6 - - - -
259D GLY* 2.7 47.3 + - - +
260D ARG* 2.9 34.8 + - - +
261D PRO* 4.1 2.9 - - + -
473D GLN* 4.9 0.7 - - + -
504D GLY* 3.7 34.3 - - - +
584D GLY* 3.6 20.4 - - - +
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Residues in contact with ARG 256 (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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61D GLN* 3.5 30.6 + - - +
85D ASN* 3.0 25.8 + - - +
252D ASP* 3.2 21.1 + - - +
253D ARG* 3.6 10.9 - - - +
255D THR* 1.3 77.4 + - - +
257D PHE* 1.3 58.5 + - - +
260D ARG* 3.6 35.4 - - - +
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Residues in contact with PHE 257 (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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60D PRO* 3.5 31.9 - - + -
61D GLN* 4.0 13.0 - - + -
64D ILE* 3.6 20.4 - - + -
84D LEU* 3.5 34.0 - - + -
85D ASN* 2.8 48.0 + - - -
86D ILE* 4.5 0.9 - - + -
209D LEU* 3.9 14.8 - - + -
240D PHE* 3.8 33.2 - + + -
242D ILE* 4.5 8.5 - - + -
253D ARG 2.8 16.4 + - - +
254D TYR* 3.4 4.5 - - - +
256D ARG* 1.3 79.7 - - - +
258D THR* 1.3 66.6 + - + +
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Residues in contact with THR 258 (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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83D PRO* 3.7 19.3 - - - +
84D LEU* 4.0 9.9 - - + -
85D ASN* 4.4 2.5 - - - -
209D LEU* 3.9 15.3 - - + -
254D TYR* 2.8 48.4 + - + +
257D PHE* 1.3 78.6 - - + +
259D GLY* 1.3 56.3 + - - +
470D VAL* 3.7 28.5 - - + -
471D GLY* 3.5 18.2 - - - -
473D GLN* 3.0 18.3 + - - -
474D LYS* 4.4 3.5 - - - +
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Residues in contact with GLY 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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85D ASN* 4.2 7.7 - - - +
255D THR* 2.7 34.1 + - - +
257D PHE 3.7 1.0 - - - -
258D THR* 1.3 76.2 + - - +
260D ARG* 1.3 60.4 + - - -
473D GLN* 3.1 20.5 + - - +
474D LYS* 3.6 20.2 - - - -
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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