Contacts of the strand formed by residues 198 - 208 (chain B) in PDB entry 1LHR
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 TYR 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LEU 5.0 3.6 - - - +
192B SER* 3.2 30.8 + - - +
194B ARG* 3.0 78.0 + - + -
195B GLY* 3.1 8.3 + - - +
196B SER 4.1 5.0 - - - +
197B ASP* 1.3 85.3 - - + +
199B LEU* 1.3 61.5 + - - +
200B MET 3.9 0.7 + - - -
222B GLU* 4.2 10.5 - - + -
223B MET 3.2 5.6 - - - +
224B HIS* 3.6 46.9 - + + +
225B LYS* 4.1 4.3 - - - +
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Residues in contact with LEU 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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187B SER* 4.5 18.4 - - - -
188B SER 4.2 17.5 - - - +
198B TYR* 1.3 73.4 - - - +
200B MET* 1.3 61.0 + - - +
222B GLU* 3.1 6.2 - - - -
223B MET* 2.6 51.5 + - + +
225B LYS* 3.6 26.2 - - + +
402B ATP 3.9 54.5 - - + +
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLN* 4.3 11.4 - - + +
185B ILE* 5.7 0.3 - - - +
187B SER* 3.7 3.1 - - - -
188B SER* 3.1 38.5 + - - +
190B LEU* 4.1 35.5 + - - +
191B LEU 3.4 15.5 - - - +
192B SER* 3.4 9.2 - - - -
193B PRO* 3.3 33.7 - - + -
198B TYR 3.9 1.6 + - - -
199B LEU* 1.3 74.9 - - - +
201B ALA* 1.3 64.0 + - - +
202B LEU* 4.4 7.0 - - + +
220B ARG* 3.7 34.8 - - + -
221B MET 3.2 3.6 - - - +
222B GLU* 4.4 1.8 - - + +
223B MET* 4.2 2.2 - - - -
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Residues in contact with ALA 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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184B VAL* 5.4 1.3 - - + -
185B ILE* 3.3 14.1 - - - +
186B THR* 3.6 10.8 - - - +
200B MET* 1.3 74.0 - - - +
202B LEU* 1.3 71.3 + - - +
220B ARG* 3.5 2.4 - - - +
221B MET* 2.7 51.5 + - + +
223B MET* 3.6 22.2 - - + +
237B PHE* 6.1 2.0 - - + -
260B VAL* 5.6 1.6 - - + -
402B ATP 6.1 0.2 - - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLN* 4.2 18.6 - - + -
168B ALA* 3.6 30.1 - - + -
169B LEU* 4.7 4.7 - - + -
172B MET* 3.9 17.1 - - + +
184B VAL* 3.3 5.4 - - - +
185B ILE* 2.7 54.3 + - + +
188B SER* 5.1 4.5 - - - +
190B LEU* 4.2 15.9 - - + -
200B MET* 4.4 7.0 - - + +
201B ALA* 1.3 81.0 - - - +
203B GLY* 1.3 59.0 + - - +
219B ILE 3.3 8.3 - - - +
220B ARG* 3.9 24.9 - - + -
221B MET* 4.7 2.7 - - - -
312B LEU* 4.4 6.5 - - + -
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Residues in contact with GLY 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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172B MET* 3.9 5.9 - - - +
183B VAL 3.3 8.5 - - - -
184B VAL* 4.1 6.7 - - - -
202B LEU* 1.3 76.0 - - - +
204B SER* 1.3 62.6 + - - -
218B ARG* 3.3 3.1 - - - -
219B ILE* 2.9 44.1 + - - +
221B MET* 5.2 0.7 - - - -
252B LEU* 3.7 12.6 - - - -
256B CYS* 5.3 0.2 - - - -
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Residues in contact with SER 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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172B MET* 3.8 23.8 - - - -
173B ASP* 5.0 0.3 + - - -
176B HIS* 2.6 30.7 + - - -
182B THR* 3.5 1.2 - - - -
183B VAL* 2.8 36.1 + - - +
203B GLY* 1.3 76.2 - - - -
205B GLN* 1.3 62.3 + - - +
216B THR* 3.4 18.7 - - - +
217B GLN 3.2 7.0 - - - -
218B ARG* 4.1 6.9 + - - +
252B LEU* 3.4 6.0 - - - +
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Residues in contact with GLN 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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176B HIS* 4.4 0.4 - - - -
181B ASP* 3.2 5.5 - - + +
182B THR* 3.4 22.8 + - - +
204B SER* 1.3 77.1 + - - +
206B ARG* 1.3 66.9 + - - +
207B THR* 4.0 12.8 + - - +
215B VAL 3.7 1.4 - - - +
216B THR* 3.6 1.8 - - - -
217B GLN* 2.9 37.5 + - + +
249B PRO 3.2 24.9 + - - +
250B ASN* 4.3 9.3 + - - +
251B ASN 4.3 1.7 + - - -
252B LEU* 3.4 42.0 + - + +
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Residues in contact with ARG 206 (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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173B ASP* 3.8 16.2 + - - +
176B HIS* 3.5 55.4 + - + +
177B SER* 3.6 23.2 + - - +
181B ASP* 2.7 41.5 + - - +
205B GLN* 1.3 74.8 + - - +
207B THR* 1.3 70.7 + - - +
208B ARG* 4.0 29.7 - - + +
214B VAL* 3.4 29.8 - - + +
215B VAL 3.6 2.2 - - - -
216B THR* 4.0 10.2 + - - +
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Residues in contact with THR 207 (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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181B ASP* 5.9 0.2 - - - -
205B GLN* 4.3 15.2 + - - +
206B ARG* 1.3 78.8 + - - +
208B ARG* 1.3 73.4 + - - +
209B ALA* 3.6 2.7 + - - +
214B VAL* 3.6 2.2 - - - -
215B VAL* 2.9 51.1 + - + +
250B ASN* 5.5 6.2 + - - +
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 5.5 6.3 + - - +
206B ARG* 4.0 27.8 - - - +
207B THR* 1.3 78.9 - - - +
209B ALA* 1.3 66.7 + - - +
210B PRO* 4.6 0.5 - - - +
212B GLY* 5.6 5.6 - - - -
213B SER 3.6 5.4 - - - +
214B VAL* 4.3 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