Contacts of the strand formed by residues 198 - 205 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ILE* 3.5 36.6 - - + -
169A LEU* 3.7 17.9 - - + -
175A VAL* 3.3 12.8 - - + +
177A TYR* 4.5 2.7 - - + -
192A PHE* 3.7 36.8 - - + -
195A THR* 3.5 5.4 + - + +
196A ASP 4.4 1.6 - - - -
197A ARG* 1.3 86.4 - - + +
199A MET* 1.3 66.0 + - - +
200A THR* 3.9 10.0 + - + -
227A TYR* 3.7 1.0 - - - +
257A TYR* 3.5 2.0 - - - -
403A NA 2.5 30.1 - - - -
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Residues in contact with MET 199 (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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175A VAL 3.1 6.9 + - - -
176A LEU* 3.6 3.1 - - + +
177A TYR* 2.8 29.3 + - - +
198A VAL* 1.3 73.1 - - - +
200A THR* 1.3 62.2 + - - +
201A VAL* 4.1 12.6 - - + -
226A TYR 3.4 24.9 - - - +
227A TYR* 3.2 21.5 - - + +
229A VAL* 4.5 4.3 - - + -
253A VAL* 3.6 36.8 - - - -
257A TYR* 3.3 29.7 + - + -
375A LEU* 4.2 10.5 - - + -
378A LEU* 3.7 26.9 - - + -
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Residues in contact with THR 200 (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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177A TYR* 3.6 24.9 - - + -
185A GLY 5.8 0.2 - - - -
188A VAL* 4.0 22.2 - - + +
189A GLU* 3.8 27.9 + - - +
192A PHE* 4.6 7.1 - - + +
198A VAL* 4.1 17.7 - - + +
199A MET* 1.3 76.6 - - - +
201A VAL* 1.3 57.9 + - - +
202A SER* 4.2 1.1 - - - -
227A TYR 3.1 6.6 + - - +
228A ALA* 3.5 13.5 - - - +
229A VAL* 2.8 33.5 + - - +
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Residues in contact with VAL 201 (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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176A LEU* 3.8 24.2 - - + -
177A TYR* 2.8 14.0 + - - +
178A ILE* 3.3 9.7 - - + +
179A ASP* 2.8 27.1 + - - +
199A MET* 4.1 8.5 - - + -
200A THR* 1.3 77.7 - - - +
202A SER* 1.3 61.4 + - - +
203A PHE* 3.7 29.7 - - + -
229A VAL* 3.4 28.3 - - + -
231A PHE* 6.5 0.2 - - + -
249A ILE* 4.4 4.3 - - + -
250A ILE* 4.2 9.6 - - + -
253A VAL* 4.3 12.8 - - + -
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Residues in contact with SER 202 (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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177A TYR* 5.9 0.9 - - - -
179A ASP* 3.7 9.0 - - - -
184A HIS* 3.8 16.2 - - - -
185A GLY* 3.3 17.3 + - - -
189A GLU* 5.5 0.4 - - - -
200A THR* 4.2 0.9 - - - -
201A VAL* 1.3 75.8 - - - +
203A PHE* 1.3 55.4 + - - +
204A HIS* 2.8 26.1 + - - -
229A VAL 3.0 7.1 + - - -
230A ASN* 3.5 6.7 - - - -
231A PHE* 2.8 31.5 + - - +
402A CA 3.0 15.8 - - - -
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Residues in contact with PHE 203 (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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178A ILE* 4.0 6.7 - - + -
179A ASP 3.1 13.7 + - - +
180A ILE* 4.3 2.0 - - + -
181A ASP 3.1 7.6 - - - +
201A VAL* 3.7 28.5 - - + -
202A SER* 1.3 73.2 - - - +
204A HIS* 1.3 59.1 + - - +
231A PHE* 3.6 29.8 - + + -
233A MET* 3.9 11.7 - - + -
242A TYR* 3.2 25.1 + + + +
245A ILE* 3.5 31.9 - - + -
246A PHE* 3.5 36.1 - + - -
249A ILE* 3.9 20.9 - - + -
250A ILE* 4.2 3.1 - - + -
279A PHE* 5.3 1.7 - - - -
371A LEU* 5.8 0.4 - - + -
402A CA 2.6 23.4 - - - -
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Residues in contact with HIS 204 (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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182A ILE 3.2 15.7 - - - +
183A HIS 3.6 1.6 - - - -
184A HIS* 3.4 33.0 - + + +
202A SER* 2.8 30.3 + - - -
203A PHE* 1.3 74.3 - - - +
205A LYS* 1.3 66.8 + - - +
206A TYR* 4.1 9.9 - - + -
213A THR 4.2 3.1 - - - -
214A GLY* 2.7 27.8 + - - -
230A ASN* 3.3 28.7 - - + -
231A PHE 3.2 9.1 + - - +
232A PRO* 4.2 3.0 - - + +
233A MET* 2.8 31.3 + - - -
279A PHE* 3.9 9.9 - - - -
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Residues in contact with LYS 205 (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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182A ILE* 2.8 20.9 + - + +
184A HIS* 5.1 1.6 + - - +
204A HIS* 1.3 81.5 - - - +
206A TYR* 1.3 68.6 + - - +
207A GLY 3.8 22.6 + - - -
209A TYR* 3.4 41.0 - - + +
210A PHE 5.0 2.8 - - - +
233A MET 3.4 12.8 - - - +
234A ARG* 4.1 6.6 - - - +
235A ASP* 2.7 42.7 + - - +
278A CYS* 3.7 12.3 - - - -
279A PHE* 3.5 22.1 - - + -
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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