Contacts of the strand formed by residues 198 - 205 (chain C) in PDB entry 4LXZ
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 VAL 198 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 3.6 37.0 - - + -
169C LEU* 3.7 13.9 - - + -
175C VAL* 3.3 12.8 - - + +
177C TYR* 4.6 1.8 - - + -
192C PHE* 3.6 44.4 - - + -
195C THR* 3.3 7.7 - - + +
196C ASP 4.5 1.1 - - - -
197C ARG* 1.3 84.8 - - - +
199C MET* 1.4 63.7 - - - +
200C THR* 4.0 7.8 + - + -
227C TYR* 3.7 1.4 - - - +
257C TYR* 3.2 2.4 + - - -
403C NA 2.4 31.0 - - - -
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Residues in contact with MET 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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175C VAL 3.1 6.9 + - - -
176C LEU* 3.6 6.5 - - + +
177C TYR* 2.8 29.5 + - - +
198C VAL* 1.4 73.0 - - - +
200C THR* 1.3 66.0 + - - +
201C VAL* 4.3 6.7 - - + -
226C TYR 3.4 25.1 - - - +
227C TYR* 3.2 20.6 - - + +
229C VAL* 4.1 4.0 - - + -
253C VAL* 3.7 30.1 - - - -
257C TYR* 3.5 31.9 + - + -
375C LEU* 3.8 21.5 - - + -
378C LEU* 3.9 20.9 - - + -
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Residues in contact with THR 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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177C TYR* 3.6 23.8 - - + -
185C GLY 5.8 0.2 - - - -
188C VAL* 4.0 13.7 - - + +
189C GLU* 3.8 37.0 + - - +
192C PHE* 4.5 7.0 - - + -
198C VAL* 4.1 14.1 - - + +
199C MET* 1.3 76.7 - - - +
201C VAL* 1.3 57.3 + - - +
202C SER* 6.4 0.7 - - - -
227C TYR 3.1 7.2 + - - +
228C ALA* 3.7 16.8 - - - +
229C VAL* 2.7 34.1 + - - +
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 3.9 25.6 - - + -
177C TYR* 2.8 13.1 + - - +
178C ILE* 3.4 3.9 - - - +
179C ASP* 2.9 28.3 + - - +
199C MET* 4.3 3.1 - - + -
200C THR* 1.3 76.8 - - - +
202C SER* 1.3 63.1 + - - +
203C PHE* 3.7 30.7 - - + -
229C VAL* 3.5 29.8 - - + -
231C PHE* 6.5 0.2 - - + -
249C ILE* 4.5 4.0 - - + -
250C ILE* 3.9 13.5 - - + -
253C VAL* 4.2 14.8 - - + -
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Residues in contact with SER 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C TYR* 5.9 0.9 - - - -
179C ASP* 3.7 8.0 - - - +
184C HIS* 3.8 12.6 - - - -
185C GLY* 3.3 16.4 + - - -
189C GLU* 5.5 0.4 - - - -
200C THR* 4.2 0.9 - - - -
201C VAL* 1.3 76.6 - - - +
203C PHE* 1.3 60.7 + - - +
204C HIS* 2.8 30.4 + - - -
229C VAL 3.0 7.3 + - - +
230C ASN* 3.6 4.2 - - - -
231C PHE* 2.9 27.4 + - - +
402C CA 2.9 18.2 - - - -
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Residues in contact with PHE 203 (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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178C ILE* 4.2 3.6 - - + -
179C ASP 3.2 14.1 + - - +
180C ILE* 4.4 1.5 - - + +
181C ASP 3.0 8.0 - - - +
201C VAL* 3.7 28.5 - - + -
202C SER* 1.3 70.8 - - - +
204C HIS* 1.3 57.8 + - - +
231C PHE* 3.6 28.5 - + + -
233C MET* 3.9 11.0 - - + -
242C TYR* 3.3 28.1 + + + +
245C ILE* 3.7 29.2 - - + -
246C PHE* 3.6 38.8 - + - -
249C ILE* 3.9 20.2 - - + -
250C ILE* 4.0 6.7 - - + -
279C PHE* 5.1 1.8 - - - -
371C LEU* 5.6 0.2 - - + -
402C CA 2.7 22.9 - - - -
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Residues in contact with HIS 204 (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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182C ILE 3.2 15.5 - - - +
183C HIS 3.6 1.6 - - - -
184C HIS* 3.4 34.0 - + + +
202C SER* 2.8 30.6 + - - -
203C PHE* 1.3 73.1 - - - +
205C LYS* 1.3 68.8 + - - +
206C TYR* 4.1 8.7 - - + -
213C THR 4.4 2.9 - - - -
214C GLY* 2.8 26.1 + - - -
230C ASN* 3.3 28.9 - - + -
231C PHE 3.2 7.4 + - - -
232C PRO* 4.1 5.3 - - + +
233C MET* 2.7 32.0 + - - -
279C PHE* 3.8 10.3 - - - -
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Residues in contact with LYS 205 (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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182C ILE* 2.9 19.4 + - + +
184C HIS* 5.1 1.7 + - - +
204C HIS* 1.3 81.0 - - - +
206C TYR* 1.3 70.2 + - - +
207C GLY 3.5 24.1 + - - -
208C GLU 5.1 0.2 - - - -
209C TYR* 3.4 48.7 - - + +
210C PHE 4.8 2.6 - - - +
211C PRO* 6.0 0.5 - - - +
213C THR 5.6 0.2 - - - +
233C MET 3.4 14.6 - - - +
234C ARG* 4.2 4.2 - - - +
235C ASP* 2.8 41.0 + - - +
278C CYS* 3.7 7.9 - - - -
279C PHE* 3.5 19.9 - - + -
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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