Contacts of the strand formed by residues 196 - 202 (chain B) 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 ASN 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 5.5 0.5 + - - -
168B ARG* 2.9 37.5 + - - +
180B GLU 3.2 10.7 - - - +
181B THR* 3.5 18.1 - - - -
182B TRP 3.2 22.6 + - - +
183B ASN* 2.8 31.2 + - - +
193B ALA* 3.0 26.1 + - - -
195B LYS* 1.3 71.0 - - - +
197B ILE* 1.3 74.2 + - - +
198B PRO* 4.2 4.7 - - - +
438B ASN* 4.9 5.6 - - - +
468B ALA 3.7 7.1 + - - +
469B SER* 4.1 5.4 + - - -
470B VAL 4.7 0.2 + - - -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.0 27.8 + - - +
166B GLY* 3.9 20.4 - - - +
181B THR* 4.0 4.6 - - - +
195B LYS* 4.5 3.1 - - + +
196B ASN* 1.3 85.6 - - - +
198B PRO* 1.3 62.1 - - - +
199B PHE* 2.8 24.9 + - + -
254B TYR* 3.4 24.2 - - - +
468B ALA 4.8 1.3 - - - +
469B SER* 3.6 29.2 - - - +
470B VAL* 3.7 10.3 - - + +
473B GLN* 5.5 0.2 - - - +
503B SER* 4.2 10.5 - - - +
505B PHE* 3.8 28.9 - - + -
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Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.4 30.7 - - + +
181B THR* 3.8 27.8 - - + +
196B ASN 4.2 3.8 - - - +
197B ILE* 1.3 79.3 - - - +
199B PHE* 1.3 58.2 + - - +
208B VAL 3.8 1.4 - - - +
209B LEU* 3.5 5.4 - - + -
210B VAL* 2.9 50.4 + - + +
212B HIS 4.3 2.7 - - - +
216B VAL* 4.3 4.3 - - + -
218B PHE* 3.9 20.1 - - + -
470B VAL* 3.8 11.4 - - + -
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 2.8 29.1 + - - +
166B GLY 4.6 0.2 + - - -
197B ILE* 2.8 23.2 + - + -
198B PRO* 1.3 75.0 - - - +
200B TYR* 1.3 77.2 + - - +
201B MET* 4.3 6.7 - - + -
207B GLY* 4.3 1.8 - - - -
208B VAL 3.4 22.2 - - - -
209B LEU* 4.1 5.4 - - + -
242B ILE* 3.9 15.3 - - + -
250B VAL* 3.9 22.0 - - + -
251B LEU* 4.3 13.0 - - + -
254B TYR* 3.6 44.9 - + + +
502B LEU 3.7 23.1 - - - -
503B SER* 4.2 10.0 + - - -
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Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.7 26.9 + - - +
155B ASP 5.6 0.3 + - - -
156B LEU* 5.8 0.2 - - - +
162B VAL* 3.7 18.6 - - + -
163B TYR 3.3 13.7 - - - +
165B LEU* 3.8 13.7 - - + -
199B PHE* 1.3 81.6 - - - +
201B MET* 1.3 67.3 - - - +
202B THR* 4.0 18.8 - - + -
206B TYR* 4.7 7.6 + + - -
207B GLY* 3.2 2.4 - - - -
208B VAL* 2.9 71.1 + - + +
218B PHE* 4.0 20.6 - + - -
228B VAL* 3.4 42.2 + - + +
230B PHE* 4.4 3.6 - + - -
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Residues in contact with MET 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL* 3.6 2.1 - - - +
163B TYR* 2.8 41.1 + - + +
199B PHE* 4.3 7.0 - - + -
200B TYR* 1.3 79.8 - - - +
202B THR* 1.3 66.4 + - - +
206B TYR 3.5 15.3 - - - +
207B GLY* 4.0 4.9 - - - -
247B PRO* 3.3 44.0 - - + +
250B VAL* 4.4 10.1 - - + -
251B LEU* 4.2 23.3 - - + -
502B LEU* 3.5 40.4 - - + +
592B MET* 4.2 8.7 - - + -
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.2 0.4 - - + -
160B GLU* 3.0 31.5 + - - +
161B THR 3.0 15.5 - - - +
162B VAL* 4.0 11.0 - - + -
163B TYR* 4.3 0.4 - - - -
200B TYR* 4.0 17.5 - - + -
201B MET* 1.3 87.2 - - - +
203B ASN* 1.3 59.4 + - - +
204B ARG* 2.9 18.9 + - - +
205B GLY* 3.5 10.4 + - - -
206B TYR* 3.3 26.4 + - + +
247B PRO* 4.8 2.8 - - - +
592B MET* 4.1 12.0 - - - +
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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