Contacts of the strand formed by residues 236 - 243 (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 TYR 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ARG* 3.3 45.6 + - + +
69C ILE 3.3 6.5 - - - +
70C GLU* 3.4 27.1 - - + +
72C PHE 5.5 1.3 - - - +
77C ASN* 3.7 35.2 - - + +
81C HIS* 4.9 13.9 + - - -
150C MET* 3.6 6.4 - - - +
211C ASN* 5.1 3.3 + - - -
212C HIS* 3.5 28.8 + + - -
232C VAL* 4.3 0.5 - - - +
234C SER* 2.7 39.8 + - - -
235C GLU* 1.3 82.6 - - + +
237C LEU* 1.3 63.8 + - - +
238C GLU* 4.0 13.5 - - + -
435C LYS* 5.4 7.6 - - - -
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Residues in contact with LEU 237 (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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67C VAL 3.4 2.8 - - - +
68C ARG* 3.5 0.2 - - - -
69C ILE* 2.8 49.9 + - + +
150C MET* 3.6 17.5 - - + +
151C PHE* 3.6 38.4 - - - +
152C GLU* 3.7 16.2 - - + +
210C VAL* 4.0 13.9 - - + -
212C HIS* 3.5 24.2 - - + +
230C PHE* 4.2 12.1 - - + +
231C SER* 5.7 0.2 - - - -
232C VAL* 3.8 11.9 - - + +
236C TYR* 1.3 75.2 - - - +
238C GLU* 1.3 60.6 + - - +
239C TYR* 4.4 10.5 - - + -
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Residues in contact with GLU 238 (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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58C PHE* 3.7 20.4 - - + -
67C VAL 3.3 10.1 - - - +
68C ARG* 2.8 43.0 + - + +
210C VAL* 3.8 1.9 - - - +
211C ASN* 2.8 56.4 + - + +
212C HIS* 3.1 15.5 + - + +
236C TYR* 4.0 16.4 - - + -
237C LEU* 1.3 74.4 - - - +
239C TYR* 1.3 65.1 + - - +
240C PHE* 4.0 12.2 - - + -
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Residues in contact with TYR 239 (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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65C VAL 3.9 0.2 - - - +
66C GLY* 3.5 2.4 - - - -
67C VAL* 2.8 59.3 + - + +
69C ILE* 4.4 6.7 - - + -
120C LEU* 3.8 8.3 - - - +
122C PHE* 3.7 32.9 - + - -
152C GLU* 2.7 41.6 + - + -
154C LEU* 4.0 18.6 - - + +
208C VAL* 4.4 4.9 - - + -
209C LEU 3.3 13.7 - - - +
210C VAL* 4.0 9.0 - - + -
211C ASN 4.1 0.9 - - - +
230C PHE* 4.0 26.0 - + + -
237C LEU* 4.4 6.3 - - + -
238C GLU* 1.3 77.3 - - - +
240C PHE* 1.3 63.8 + - - +
241C VAL* 4.1 11.0 - - + -
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Residues in contact with PHE 240 (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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58C PHE* 4.0 13.9 - + - -
60C PRO* 3.6 23.3 - - + -
64C ILE* 3.6 24.0 - - + -
65C VAL 3.5 2.0 - - - -
66C GLY* 3.5 22.7 - - - -
84C LEU* 5.2 1.6 - - + -
86C ILE* 5.7 5.2 - - + -
208C VAL* 2.9 27.0 - - - -
209C LEU* 2.8 26.2 + - + +
211C ASN* 3.7 32.3 - - + -
238C GLU* 4.0 18.2 - - + -
239C TYR* 1.3 76.4 - - - +
241C VAL* 1.3 62.7 + - - +
242C ILE* 3.7 6.5 + - + +
257C PHE* 3.7 28.5 - + + -
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Residues in contact with VAL 241 (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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64C ILE* 3.6 2.8 - - - +
65C VAL* 3.1 30.4 + - + +
108C LEU* 3.4 24.9 - - + +
122C PHE* 3.4 51.8 - - + -
129C ILE* 4.5 7.9 - - + -
130C THR* 4.8 2.5 - - + -
154C LEU* 4.9 7.2 - - + -
206C TYR* 4.4 16.2 - - + -
207C GLY 3.5 8.7 - - - +
208C VAL* 4.4 2.7 - - + -
239C TYR* 4.1 12.8 - - + -
240C PHE* 1.3 73.0 - - - +
242C ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 242 (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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63C GLY 3.9 2.0 - - - -
64C ILE* 3.9 21.5 - - + -
199C PHE* 3.9 24.9 - - + -
206C TYR* 3.3 8.7 - - - +
207C GLY 2.6 42.0 + - - +
209C LEU* 4.5 5.8 - - + -
240C PHE* 3.9 14.4 - - + +
241C VAL* 1.3 79.0 - - - +
243C ASP* 1.3 64.8 + - - +
250C VAL* 3.8 16.6 - - + +
253C ARG* 3.6 30.1 - - + -
254C TYR* 3.9 21.8 - - + +
257C PHE* 4.5 8.5 - - + -
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Residues in contact with ASP 243 (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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63C GLY* 3.0 23.7 + - - +
107C ASN* 4.2 14.7 + - - +
108C LEU* 4.1 19.6 + - + +
124C ARG* 2.4 54.3 + - - +
129C ILE* 4.9 2.4 - - - +
205C GLY 4.4 0.2 - - - -
206C TYR* 4.8 1.8 - - - -
241C VAL 4.1 0.4 + - - -
242C ILE* 1.3 74.9 - - - +
244C GLY* 1.3 66.8 + - - +
245C PRO* 4.8 1.9 - - - +
250C VAL* 3.8 11.2 - - - -
253C ARG* 2.6 36.3 + - - +
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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