Contacts of the strand formed by residues 196 - 202 (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 ASN 196 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 5.5 0.3 + - - -
165C LEU 4.5 3.1 - - - -
168C ARG* 2.7 30.5 + - - +
180C GLU 3.3 12.5 - - - +
181C THR* 3.5 18.5 - - - -
182C TRP 3.0 31.1 + - - +
183C ASN* 2.8 36.3 + - - +
193C ALA* 3.2 14.7 + - - +
195C LYS* 1.3 70.1 - - - +
197C ILE* 1.3 74.8 + - - +
198C PRO* 4.3 3.8 - - - +
438C ASN* 4.8 5.3 + - - +
468C ALA 3.8 7.5 + - - +
469C SER* 4.0 6.4 + - - -
470C VAL 4.5 0.3 + - - -
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Residues in contact with ILE 197 (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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165C LEU* 3.1 26.2 + - - +
166C GLY* 3.8 20.6 - - - +
181C THR* 4.0 4.1 - - - +
195C LYS 4.1 3.8 - - - +
196C ASN* 1.3 88.5 - - - +
198C PRO* 1.3 66.9 - - + +
199C PHE* 2.8 24.8 + - + +
254C TYR* 3.5 23.6 - - - +
468C ALA* 4.8 2.0 - - + -
469C SER* 3.6 7.9 - - - +
470C VAL* 3.6 27.4 - - + +
473C GLN* 5.4 0.4 - - - +
503C SER* 4.3 11.2 - - - +
505C PHE* 3.6 31.6 - - + -
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Residues in contact with PRO 198 (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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82C TYR* 3.3 33.0 - - + +
165C LEU* 4.5 0.2 - - + -
181C THR* 3.7 27.6 - - + +
196C ASN 4.4 2.5 - - - +
197C ILE* 1.3 78.6 - - - +
199C PHE* 1.3 56.3 + - - +
208C VAL 3.8 1.2 - - - +
209C LEU* 3.6 4.6 - - + -
210C VAL* 2.9 47.7 + - + +
212C HIS 4.2 2.2 - - - +
216C VAL* 4.3 7.4 - - + -
218C PHE* 3.9 19.6 - - + -
470C VAL* 3.7 11.2 - - + -
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Residues in contact with PHE 199 (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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164C GLY* 4.2 0.2 - - - -
165C LEU* 2.9 26.7 + - - +
166C GLY 4.6 0.2 + - - -
197C ILE* 2.8 22.2 + - + +
198C PRO* 1.3 73.9 - - - +
200C TYR* 1.3 80.3 + - - +
201C MET* 4.2 9.0 - - + -
207C GLY* 4.2 1.6 - - - -
208C VAL 3.3 24.5 - - - -
209C LEU* 4.0 6.5 - - + -
242C ILE* 3.9 13.9 - - + -
250C VAL* 4.0 21.5 - - + -
251C LEU* 4.4 9.0 - - + -
254C TYR* 3.5 47.3 - + + +
502C LEU 3.7 22.7 - - - -
503C SER* 4.3 10.1 + - - -
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Residues in contact with TYR 200 (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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154C LEU* 3.7 20.6 + - - +
156C LEU* 5.4 0.4 - - + +
162C VAL* 3.5 22.0 - - + -
163C TYR 3.3 14.4 - - - +
165C LEU* 3.8 11.9 - - + -
199C PHE* 1.3 82.9 - - - +
201C MET* 1.3 68.3 + - - +
202C THR* 3.9 18.4 - - + -
206C TYR* 4.7 7.3 + + - -
207C GLY* 3.2 2.3 - - - -
208C VAL* 3.0 72.2 + - + +
218C PHE* 4.0 19.5 - + - -
228C VAL* 3.6 40.8 - - + +
230C PHE* 4.3 6.9 - + - -
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Residues in contact with MET 201 (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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162C VAL* 3.4 3.8 - - - +
163C TYR* 2.8 36.0 + - + +
199C PHE* 4.2 10.3 - - + -
200C TYR* 1.3 77.5 - - - +
202C THR* 1.3 72.0 + - - +
206C TYR 3.4 14.6 - - - +
207C GLY* 3.8 6.1 - - - -
247C PRO* 3.2 47.3 - - + +
250C VAL* 4.4 8.7 - - + -
251C LEU* 4.1 26.7 - - + -
502C LEU* 4.1 35.7 - - + +
592C MET* 4.8 3.6 - - + -
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Residues in contact with THR 202 (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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156C LEU* 4.4 2.2 - - + -
160C GLU* 3.0 30.3 + - - +
161C THR 3.0 15.0 - - - +
162C VAL* 4.2 9.2 - - + -
163C TYR* 4.4 4.9 - - - -
200C TYR* 3.9 24.2 - - + -
201C MET* 1.3 85.8 - - - +
203C ASN* 1.3 59.5 + - - +
204C ARG 2.9 14.6 + - - -
205C GLY* 3.3 11.3 + - - -
206C TYR* 3.1 27.6 + - + +
247C PRO* 4.7 8.8 - - - +
592C MET* 5.1 0.9 - - - -
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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