Contacts of the strand formed by residues 236 - 243 (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 TYR 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ARG* 3.7 42.1 + - + +
69D ILE 3.3 7.0 - - - +
70D GLU* 3.4 24.0 - - + +
72D PHE 5.7 0.7 - - - +
77D ASN* 3.5 36.3 - - + +
81D HIS* 4.9 8.0 + - - -
150D MET* 3.5 5.6 - - - +
211D ASN 5.1 3.7 + - - -
212D HIS* 3.3 31.0 + + - -
232D VAL* 4.2 0.9 - - - +
234D SER* 2.9 33.2 + - - -
235D GLU* 1.3 85.0 - - + +
237D LEU* 1.3 68.6 + - - +
238D GLU* 4.2 9.2 - - + -
435D LYS* 4.3 15.6 + - - -
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Residues in contact with LEU 237 (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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67D VAL 3.7 0.9 - - - +
68D ARG* 3.5 0.7 - - - -
69D ILE* 2.9 46.4 + - + +
150D MET* 3.7 16.8 - - + +
151D PHE* 3.7 36.6 - - - +
152D GLU* 3.7 17.5 - - + +
210D VAL* 3.9 16.4 - - + -
212D HIS* 3.4 24.2 - - + +
230D PHE* 3.8 12.8 - - + +
231D SER 5.8 0.2 - - - -
232D VAL* 3.9 11.7 - - + +
236D TYR* 1.3 75.1 - - - +
238D GLU* 1.3 63.1 + - - +
239D TYR* 4.3 10.3 - - + -
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Residues in contact with GLU 238 (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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58D PHE* 3.8 16.7 - - + -
67D VAL 3.1 10.3 - - - +
68D ARG* 2.8 44.2 + - + +
210D VAL* 3.9 0.5 - - - -
211D ASN* 2.9 56.0 + - + +
212D HIS* 3.0 13.7 + - - +
236D TYR* 4.2 12.3 - - + -
237D LEU* 1.3 75.0 - - - +
239D TYR* 1.3 62.6 + - - +
240D PHE* 3.5 19.7 - - + -
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Residues in contact with TYR 239 (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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65D VAL 4.0 0.2 - - - +
66D GLY* 3.6 1.4 - - - -
67D VAL* 2.8 55.4 + - + +
69D ILE* 4.8 7.9 - - + -
120D LEU* 3.8 9.7 - - - +
122D PHE* 3.7 30.3 - + - -
152D GLU* 2.7 41.0 + - + -
154D LEU* 3.9 21.5 - - + +
208D VAL* 4.5 4.7 - - + -
209D LEU 3.3 12.1 - - - +
210D VAL* 4.2 6.7 - - - -
230D PHE* 3.8 29.6 - + + -
237D LEU* 4.3 9.2 - - + -
238D GLU* 1.3 75.5 - - - +
240D PHE* 1.3 64.9 + - - +
241D VAL* 4.2 10.3 - - + -
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Residues in contact with PHE 240 (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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58D PHE* 3.7 19.5 - + - -
60D PRO* 3.8 14.4 - - + -
64D ILE* 3.8 21.1 - - + -
65D VAL 3.6 2.0 - - - -
66D GLY* 3.3 33.7 - - - -
84D LEU* 3.9 13.2 - - + -
86D ILE* 5.7 3.4 - - + -
208D VAL* 3.1 8.2 - - - -
209D LEU* 2.9 45.5 + - + +
211D ASN* 3.7 28.5 - - + -
238D GLU* 3.5 22.7 - - + -
239D TYR* 1.3 74.7 - - - +
241D VAL* 1.3 62.4 + - - +
242D ILE* 3.5 5.0 + - + +
257D PHE* 3.8 21.8 - + + -
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D ILE* 3.4 5.0 - - - +
65D VAL* 2.9 34.9 + - + +
108D LEU* 3.4 22.1 - - + +
122D PHE* 3.4 51.1 - - + -
129D ILE* 4.9 3.4 - - + -
130D THR* 4.9 3.6 - - + -
154D LEU* 5.0 6.3 - - + -
206D TYR* 4.5 16.6 - - + -
207D GLY 3.5 8.1 - - - +
208D VAL* 4.6 2.5 - - + -
239D TYR* 4.2 15.0 - - + -
240D PHE* 1.3 73.8 - - - +
242D ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 242 (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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63D GLY 3.9 2.2 - - - -
64D ILE* 4.1 20.2 - - + -
108D LEU* 4.5 1.1 - - - -
199D PHE* 3.9 13.5 - - + -
206D TYR* 3.3 8.4 - - - +
207D GLY 2.7 42.2 + - - +
209D LEU* 4.6 5.2 - - + -
240D PHE* 3.7 12.8 - - + +
241D VAL* 1.3 77.6 - - - +
243D ASP* 1.3 62.1 + - - +
250D VAL* 3.8 18.5 - - + +
253D ARG* 3.6 31.0 - - + -
254D TYR* 3.8 34.8 - - + -
257D PHE* 4.5 7.6 - - + -
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Residues in contact with ASP 243 (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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63D GLY* 3.1 24.0 + - - +
107D ASN* 4.4 13.5 + - - +
108D LEU* 4.0 22.3 + - + +
124D ARG* 2.3 52.4 + - - +
129D ILE* 4.6 3.1 - - - +
205D GLY 4.4 0.9 - - - -
206D TYR* 4.6 2.2 - - - -
242D ILE* 1.3 75.2 - - - +
244D GLY* 1.3 63.3 + - - +
245D PRO* 4.4 1.7 - - - +
250D VAL* 3.9 9.9 - - - -
253D ARG* 2.6 37.0 + - - +
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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