Contacts of the strand formed by residues 236 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.6 38.2 + - + -
69A ILE 3.2 13.7 - - - +
70A GLU* 4.0 19.3 - - + +
72A PHE 5.7 1.1 - - - +
77A ASN* 3.4 37.3 - - - +
81A HIS* 4.9 7.6 + - - -
150A MET* 3.7 6.6 - - - +
211A ASN 4.9 3.3 + - - -
212A HIS* 3.4 32.5 + + - -
232A VAL* 4.1 0.5 - - - +
234A SER* 2.8 36.9 + - - -
235A GLU* 1.3 83.0 - - + +
237A LEU* 1.3 66.8 + - - +
238A GLU* 4.2 10.8 - - + -
435A LYS* 4.2 15.9 + - - -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL 3.5 2.8 - - - +
68A ARG* 3.5 0.7 - - - +
69A ILE* 2.9 42.8 + - + +
150A MET* 3.6 18.8 - - + +
151A PHE* 3.7 22.0 - - - +
152A GLU* 3.6 31.6 - - + +
210A VAL* 3.9 16.6 - - + -
212A HIS* 3.3 24.0 - - + +
230A PHE* 4.2 12.8 - - + +
231A SER* 5.8 0.4 - - - -
232A VAL* 4.0 10.8 - - + +
236A TYR* 1.3 75.0 - - - +
238A GLU* 1.3 61.5 + - - +
239A TYR* 4.2 10.8 - - + -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.5 22.8 - - + -
67A VAL 3.2 10.1 - - - +
68A ARG* 3.3 41.5 + - + +
210A VAL* 3.7 1.0 - - - +
211A ASN* 2.8 57.3 + - + +
212A HIS* 3.0 14.6 + - + +
236A TYR* 4.2 16.1 - - + -
237A LEU* 1.3 75.5 - - - +
239A TYR* 1.3 65.1 + - - +
240A PHE* 3.9 11.7 - - + -
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Residues in contact with TYR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL 3.9 0.7 - - - +
66A GLY* 3.7 1.0 - - - -
67A VAL* 2.8 56.2 + - + +
69A ILE* 4.4 7.4 - - + -
120A LEU* 3.8 8.5 - - - +
122A PHE* 3.7 30.8 - + - -
152A GLU* 2.5 43.1 + - + -
154A LEU* 3.9 15.0 - - + +
208A VAL* 5.0 3.4 - - + -
209A LEU 3.2 13.0 - - - +
210A VAL* 3.9 10.1 - - + -
211A ASN 4.2 0.4 - - - +
230A PHE* 3.8 24.2 - + + -
237A LEU* 4.2 9.0 - - + -
238A GLU* 1.3 77.6 - - - +
240A PHE* 1.3 66.4 + - - +
241A VAL* 4.0 14.6 - - + -
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.8 25.1 - + - -
60A PRO* 3.6 20.9 - - + -
64A ILE* 3.7 26.2 - - + -
65A VAL 3.5 2.5 - - - -
66A GLY* 3.5 13.9 - - - -
84A LEU* 3.9 13.5 - - + -
86A ILE* 5.9 2.9 - - + -
208A VAL* 3.1 7.9 - - - -
209A LEU* 2.8 46.5 + - + +
211A ASN* 3.6 29.6 - - + -
238A GLU* 3.9 18.2 - - + -
239A TYR* 1.3 75.4 - - - +
241A VAL* 1.3 63.1 + - - +
242A ILE* 3.8 6.3 + - + +
257A PHE* 3.7 22.2 - + + -
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.5 2.8 - - - +
65A VAL* 3.0 32.4 + - + +
108A LEU* 3.3 28.1 - - + +
122A PHE* 3.5 47.1 - - + -
129A ILE* 4.8 2.2 - - + -
130A THR* 4.8 2.5 - - + -
154A LEU* 4.9 7.4 - - + -
206A TYR* 4.5 18.6 - - + -
207A GLY 3.5 7.9 - - - +
208A VAL* 4.5 2.7 - - + +
239A TYR* 4.0 15.3 - - + -
240A PHE* 1.3 74.7 - - - +
242A ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLY 4.0 2.2 - - - -
64A ILE* 4.1 20.2 - - + -
108A LEU* 4.6 0.4 - - - -
199A PHE* 4.0 15.9 - - + -
206A TYR* 3.2 8.6 - - - +
207A GLY 2.7 39.1 + - - +
209A LEU* 4.4 9.0 - - + +
240A PHE* 4.0 13.2 - - + +
241A VAL* 1.3 78.9 - - - +
243A ASP* 1.3 63.0 + - - +
250A VAL* 3.8 16.9 - - + +
253A ARG* 3.5 32.3 - - + -
254A TYR* 3.9 32.8 - - + +
257A PHE* 4.9 7.0 - - + -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLY* 3.2 22.8 + - - +
107A ASN* 4.1 13.7 + - - +
108A LEU* 3.9 20.2 - - + +
124A ARG* 2.4 54.6 + - - +
129A ILE* 4.6 2.9 - - - +
205A GLY 4.2 1.1 - - - -
206A TYR* 4.6 3.1 - - - -
242A ILE* 1.3 75.3 - - - +
244A GLY* 1.3 63.9 + - - +
245A PRO* 4.4 1.9 - - - +
250A VAL* 3.9 9.8 - - - -
253A ARG* 2.5 35.9 + - - +
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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