Contacts of the helix formed by residues 246 - 259 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205E GLY* 4.7 0.9 - - - -
244E GLY 3.3 0.4 - - - -
245E PRO* 1.3 92.5 - - + +
247E PRO* 1.3 75.0 - - + +
248E LYS 4.2 0.7 - - - -
249E ALA* 2.8 19.8 + - - +
250E VAL* 3.0 15.5 + - - +
593E MET 6.1 0.2 - - - -
596E PRO* 4.7 15.9 - - + -
597E ASP* 6.1 0.4 - - - +
3006E SO4 2.7 42.6 + - - +
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Residues in contact with PRO 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E MET* 3.3 31.0 - - + +
202E THR 4.8 5.8 - - - +
203E ASN* 5.5 2.2 - - - -
205E GLY* 5.0 4.7 - - - +
245E PRO 4.5 1.6 - - - +
246E THR* 1.3 86.1 - - - +
248E LYS* 1.3 62.4 + - - +
250E VAL 3.2 1.4 + - - -
251E LEU* 3.0 25.1 + - - +
592E MET* 3.6 36.3 - - + +
593E MET* 4.0 24.7 - - + +
596E PRO* 3.7 20.0 - - + -
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Residues in contact with LYS 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E THR* 3.2 1.6 + - - -
247E PRO* 1.3 78.6 - - - +
249E ALA* 1.3 56.9 + - - +
251E LEU* 3.6 8.2 + - - +
252E ASP* 3.0 26.3 + - - +
583E ARG* 3.6 24.1 + - - +
585E THR* 4.2 21.2 + - + +
589E ARG* 3.6 14.3 - - - +
593E MET* 3.8 33.2 - - + +
594E GLU* 2.8 41.6 + - - +
612E ASP* 3.7 9.1 + - - +
3006E SO4 3.1 25.4 + - - +
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Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E ASP 4.3 1.8 - - - -
244E GLY 3.3 25.1 - - - +
245E PRO* 4.2 2.2 - - + -
246E THR* 2.8 22.1 + - - +
248E LYS* 1.3 75.9 - - - +
250E VAL* 1.3 68.6 + - - +
252E ASP* 3.4 5.1 + - - +
253E ARG* 3.2 27.5 + - - +
583E ARG* 4.0 9.2 - - - +
3006E SO4 4.0 7.2 + - - +
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Residues in contact with VAL 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E PHE* 3.9 14.1 - - + -
201E MET* 3.4 26.9 - - + -
205E GLY 3.6 13.7 - - - +
206E TYR* 3.8 10.8 - - - -
207E GLY* 3.7 24.0 - - - +
242E ILE* 4.0 10.0 - - + +
243E ASP 3.8 7.2 - - - +
244E GLY* 3.5 19.1 - - - +
246E THR 3.0 17.9 + - - +
249E ALA* 1.3 77.2 - - - +
251E LEU* 1.3 58.7 + - - +
253E ARG* 3.0 5.5 + - - +
254E TYR* 2.8 26.9 + - - +
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Residues in contact with LEU 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E PHE* 4.1 15.3 - - + -
201E MET* 4.1 13.0 - - - -
247E PRO 3.0 20.2 + - - +
248E LYS* 3.9 6.3 - - - +
250E VAL* 1.3 76.6 - - - +
252E ASP* 1.3 58.4 + - - +
254E TYR* 4.2 4.0 - - + -
255E THR* 2.9 35.7 + - + +
501E GLY 3.6 17.0 - - - +
502E LEU* 3.9 13.5 - - + +
504E GLY* 3.9 28.3 - - - +
583E ARG 3.7 1.6 - - - -
584E GLY 3.9 12.3 - - - +
585E THR* 5.3 0.7 - - - -
586E PRO* 3.9 18.4 - - + -
593E MET* 4.2 17.0 - - + -
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Residues in contact with ASP 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E LYS 3.0 18.7 + - - +
249E ALA* 3.6 8.7 - - - +
250E VAL 3.1 0.4 - - - -
251E LEU* 1.3 77.0 - - - +
253E ARG* 1.3 59.1 + - + +
256E ARG* 3.0 18.1 + - - +
260E ARG* 2.8 45.4 + - - -
582E ALA 4.1 0.3 - - - +
583E ARG* 3.0 43.2 + - - +
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Residues in contact with ARG 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E GLN* 5.3 0.7 + - + +
62E GLU* 3.2 52.1 + - - +
63E GLY* 3.7 17.9 - - - -
64E ILE* 4.2 8.0 - - + +
107E ASN* 6.0 0.4 + - - -
242E ILE* 3.5 17.7 - - + -
243E ASP* 2.8 41.7 + - - -
244E GLY 2.8 21.2 + - - -
249E ALA* 3.2 11.6 + - - +
250E VAL 3.0 3.2 + - - +
252E ASP* 1.3 75.9 - - + +
254E TYR* 1.3 60.9 + - - +
256E ARG* 3.1 11.4 + - - +
257E PHE* 2.8 32.7 + - - +
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Residues in contact with TYR 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E ILE* 3.4 24.1 - - - +
199E PHE* 3.7 46.4 - + + +
209E LEU* 4.3 9.6 - - + -
242E ILE* 3.8 20.7 - - + +
250E VAL 2.8 19.0 + - - +
251E LEU* 3.9 7.6 - - + +
253E ARG* 1.3 74.0 - - - +
255E THR* 1.3 55.3 + - + +
257E PHE* 3.1 5.3 + + - +
258E THR* 2.7 71.0 + - + +
470E VAL* 4.1 13.7 - - - +
473E GLN* 4.5 6.9 + - - -
503E SER 3.6 19.5 + - - -
504E GLY* 4.0 16.4 - - - -
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Residues in contact with THR 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E LEU 2.9 24.2 + - - +
254E TYR* 1.3 78.5 - - + +
256E ARG* 1.3 61.3 + - - +
258E THR* 4.4 0.7 - - - -
259E GLY* 2.8 47.2 + - - +
260E ARG* 2.7 37.0 + - - +
261E PRO* 4.2 2.9 - - + -
473E GLN* 4.9 0.4 - - - +
504E GLY* 3.9 31.4 - - - +
583E ARG 3.6 4.2 + - - -
584E GLY* 3.6 19.7 - - - +
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Residues in contact with ARG 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E GLN* 3.3 28.3 + - - +
85E ASN* 3.0 21.3 + - - +
252E ASP* 3.0 21.6 + - - +
253E ARG* 3.5 8.9 - - - +
255E THR* 1.3 78.7 + - - +
257E PHE* 1.3 58.6 + - - +
260E ARG* 3.5 35.9 - - - +
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Residues in contact with PHE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E PRO* 3.6 33.9 - - + -
61E GLN* 3.7 14.3 - - + +
64E ILE* 3.9 18.2 - - + -
84E LEU* 3.7 25.2 - - + -
85E ASN* 2.8 53.9 + - - -
86E ILE* 4.3 1.6 - - + -
209E LEU* 3.7 23.1 - - + -
240E PHE* 3.8 31.0 - + + -
242E ILE* 4.8 7.9 - - + -
253E ARG 2.8 16.6 + - - +
254E TYR* 3.3 4.0 - - - +
256E ARG* 1.3 77.7 - - - +
258E THR* 1.3 71.3 + - + +
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Residues in contact with THR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PRO* 3.8 17.6 - - - +
84E LEU* 4.5 6.3 - - + +
85E ASN* 4.5 1.6 - - - -
209E LEU* 4.0 10.8 - - + -
254E TYR* 2.7 54.4 + - + +
257E PHE* 1.3 89.6 - - + +
259E GLY* 1.3 55.3 + - - +
470E VAL* 3.9 19.5 - - + -
471E GLY* 3.5 17.8 - - - -
473E GLN* 2.9 18.9 + - - -
474E LYS* 4.5 4.2 + - - +
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Residues in contact with GLY 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASN* 4.2 7.9 - - - +
255E THR* 2.8 30.6 + - - +
257E PHE 3.6 1.4 - - - -
258E THR* 1.3 76.2 + - - +
260E ARG* 1.3 60.8 + - - -
473E GLN* 2.8 27.6 + - - +
474E LYS* 3.7 19.1 - - - -
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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