Contacts of the strand formed by residues 198 - 205 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ILE* 3.5 37.7 - - + -
169B LEU* 3.7 18.2 - - + -
175B VAL* 3.3 13.0 - - + +
177B TYR* 4.5 2.9 - - + -
192B PHE* 3.7 35.6 - - + +
195B THR* 3.5 5.8 - - + +
196B ASP 4.5 1.3 - - - -
197B ARG* 1.3 84.2 - - - +
199B MET* 1.3 65.9 + - - +
200B THR* 3.9 9.4 + - + -
227B TYR* 3.5 1.4 - - - +
257B TYR* 3.6 2.0 - - - -
403B NA 2.5 30.5 - - - -
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Residues in contact with MET 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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175B VAL 3.1 6.3 + - - -
176B LEU* 3.6 3.3 - - + +
177B TYR* 2.8 28.6 + - - +
198B VAL* 1.3 71.1 - - - +
200B THR* 1.3 64.2 + - - +
201B VAL* 4.0 10.8 - - + -
226B TYR 3.6 23.1 - - - +
227B TYR* 3.2 23.6 - - + +
229B VAL* 4.1 14.1 - - + -
253B VAL* 3.6 32.3 - - - -
257B TYR* 3.5 28.1 + - + -
375B LEU* 4.3 6.1 - - + -
378B LEU* 3.7 28.3 - - + -
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 3.6 23.3 - - + -
188B VAL* 4.0 13.2 - - + +
189B GLU* 3.9 33.9 + - - +
192B PHE* 4.7 6.3 - - + +
198B VAL* 4.1 15.0 - - + +
199B MET* 1.3 76.7 - - - +
201B VAL* 1.3 58.7 + - - +
202B SER* 5.8 0.9 - - - -
227B TYR 3.1 5.2 + - - +
228B ALA* 3.5 18.9 - - - +
229B VAL* 2.7 34.0 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.8 24.9 - - + -
177B TYR* 2.8 13.8 + - - +
178B ILE* 3.4 3.7 - - - +
179B ASP* 2.8 27.9 + - - +
199B MET* 4.0 9.9 - - + -
200B THR* 1.3 78.4 - - - +
202B SER* 1.4 61.0 + - - +
203B PHE* 3.6 31.4 - - + -
229B VAL* 3.4 24.5 - - + -
231B PHE* 6.4 0.2 - - + -
249B ILE* 4.5 4.3 - - + -
250B ILE* 4.0 13.0 - - + -
253B VAL* 4.2 12.6 - - + -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 5.8 1.3 - - - -
179B ASP* 3.7 8.7 - - - -
184B HIS* 3.8 7.6 - - - -
185B GLY* 3.4 15.9 + - - -
189B GLU* 5.6 0.2 - - - -
200B THR 4.2 0.8 - - - -
201B VAL* 1.4 75.2 - - - +
203B PHE* 1.4 55.4 + - - +
204B HIS* 2.7 26.3 + - - -
229B VAL 2.9 8.7 + - - +
230B ASN* 3.4 13.9 - - - -
231B PHE* 2.8 32.6 + - - +
402B CA 2.9 18.3 - - - -
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Residues in contact with PHE 203 (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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178B ILE* 4.1 6.5 - - + -
179B ASP 3.1 14.6 + - - +
180B ILE* 4.3 3.1 - - + -
181B ASP 3.0 8.0 - - - +
201B VAL* 3.6 28.9 - - + -
202B SER* 1.4 72.1 - - - +
204B HIS* 1.3 57.6 + - - +
231B PHE* 3.6 26.0 - + + -
233B MET* 3.9 12.1 - - + -
242B TYR* 3.3 23.2 + + - +
245B ILE* 3.5 30.5 - - + -
246B PHE* 3.6 37.0 - + - -
249B ILE* 3.9 23.6 - - + -
250B ILE* 4.1 3.6 - - + -
279B PHE* 5.3 1.6 - - - -
402B CA 2.6 24.1 - - - -
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Residues in contact with HIS 204 (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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182B ILE 3.1 16.6 - - - +
183B HIS 3.6 1.1 - - - -
184B HIS* 3.4 31.6 - + + +
202B SER* 2.7 30.5 + - - -
203B PHE* 1.3 73.7 - - - +
205B LYS* 1.3 71.5 + - - +
206B TYR* 4.1 6.5 - - + -
213B THR 4.4 2.9 - - - -
214B GLY* 2.7 28.5 + - - -
230B ASN* 3.3 28.7 - - + -
231B PHE 3.2 7.6 + - - +
232B PRO* 4.4 4.0 - - + +
233B MET* 2.7 32.7 + - - -
279B PHE* 3.8 10.8 - - - -
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Residues in contact with LYS 205 (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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182B ILE* 2.9 11.2 + - + +
184B HIS* 5.1 1.6 + - - +
204B HIS* 1.3 83.1 - - - +
206B TYR* 1.3 66.9 + - - +
207B GLY* 4.2 12.6 + - - -
208B GLU 5.5 0.2 - - - -
209B TYR* 3.6 57.6 - - + +
210B PHE 5.0 2.4 - - - +
211B PRO* 6.1 0.2 - - - +
213B THR 5.5 0.2 - - - +
233B MET 3.2 10.5 - - - +
234B ARG* 4.8 6.5 - - - +
235B ASP* 2.7 30.2 + - - +
278B CYS* 3.0 26.5 - - - -
279B PHE* 3.5 18.8 - - + -
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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