Contacts of the strand formed by residues 198 - 208 (chain F) in PDB entry 1RFU
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188F SER 5.2 1.6 - - - +
190F LEU 5.3 1.6 - - - +
192F SER* 3.5 18.1 + - - +
194F ARG* 2.9 63.9 + - + +
195F GLY* 3.6 5.5 - - - +
196F SER 3.0 9.3 + - - +
197F ASP* 1.3 111.0 - - - +
199F LEU* 1.3 65.9 + - - +
200F MET 4.0 0.5 + - - -
222F GLU* 4.4 16.8 - - + -
223F MET 3.1 21.8 - - - +
224F HIS* 3.3 31.8 - + + -
225F LYS* 3.9 5.9 - - - +
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F SER* 4.1 17.5 - - - +
188F SER 4.1 17.7 - - - +
192F SER* 4.4 0.9 - - - -
198F TYR* 1.3 74.6 - - - +
200F MET* 1.3 58.5 + - - +
221F MET 3.5 0.7 - - - +
222F GLU* 3.4 1.4 - - - -
223F MET* 2.6 66.2 + - + +
225F LYS* 4.1 28.3 - - + +
5402F ADP 3.7 45.1 - - + +
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Residues in contact with MET 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F GLN* 4.0 5.6 - - - +
187F SER* 2.9 23.6 - - - -
188F SER* 3.1 23.1 + - - +
190F LEU* 3.9 35.2 - - + +
191F LEU 4.9 1.8 - - - +
192F SER* 3.7 19.7 - - - +
193F PRO* 3.6 21.3 - - + -
198F TYR 4.0 1.6 + - - -
199F LEU* 1.3 74.1 - - - +
201F ALA* 1.3 64.6 + - - +
202F LEU* 4.4 7.6 - - + -
220F ARG* 3.0 53.4 - - + +
221F MET 3.0 13.9 - - - +
222F GLU* 4.5 1.6 - - + +
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Residues in contact with ALA 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F VAL* 5.4 2.5 - - + -
185F ILE 3.3 15.7 - - - +
186F THR* 3.4 17.7 - - - +
200F MET* 1.3 75.6 - - - +
202F LEU* 1.3 63.9 + - - +
220F ARG* 3.4 2.6 - - - -
221F MET* 2.7 55.9 + - + +
223F MET* 4.0 15.3 - - + -
237F PHE* 6.2 1.6 - - + -
260F VAL* 5.8 2.0 - - + -
5402F ADP 5.2 0.4 - - - +
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F GLN* 4.3 10.8 - - + +
168F ALA* 3.4 33.2 - - + -
169F LEU* 4.7 3.6 - - + +
172F MET* 3.2 24.9 - - + +
184F VAL* 3.4 4.0 - - - +
185F ILE* 2.7 43.4 + - + +
188F SER* 5.8 0.9 - - - +
190F LEU* 4.1 15.5 - - + -
200F MET* 4.4 7.4 - - - -
201F ALA* 1.3 74.8 - - - +
203F GLY* 1.3 59.0 + - - +
219F ILE 3.3 2.9 - - - +
220F ARG* 3.2 42.6 - - + +
221F MET* 5.2 1.3 - - - -
312F LEU* 4.2 11.4 - - + -
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Residues in contact with GLY 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F MET* 4.3 1.1 - - - -
183F VAL 3.4 6.3 - - - -
184F VAL* 4.1 9.6 - - - -
202F LEU* 1.3 75.4 - - - +
204F SER* 1.3 59.2 + - - -
218F ARG* 3.6 1.9 - - - -
219F ILE* 2.7 47.6 + - - +
221F MET* 4.9 1.4 - - - +
252F LEU* 3.1 21.5 - - - +
256F CYS* 5.1 0.9 - - - -
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Residues in contact with SER 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F MET* 3.8 23.4 - - - -
173F ASP* 4.7 0.3 + - - -
176F HIS* 2.8 28.6 + - - -
182F THR* 3.4 1.9 - - - -
183F VAL* 2.7 40.1 + - - +
203F GLY* 1.3 74.5 - - - -
205F GLN* 1.3 64.1 + - - +
216F THR* 5.0 2.8 - - - +
217F GLN 3.4 4.9 + - - -
218F ARG* 3.5 28.4 + - - +
252F LEU* 3.5 4.0 - - - +
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Residues in contact with GLN 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F HIS* 4.1 2.2 - - - -
181F ASP 3.3 9.0 - - - +
182F THR* 3.7 21.4 + - + +
204F SER* 1.3 76.9 + - - +
206F ARG* 1.3 69.1 + - - +
207F THR* 4.6 10.1 + - - +
215F VAL 4.1 0.6 - - - +
216F THR* 3.5 5.2 - - - +
217F GLN* 2.6 69.4 + - + +
245F THR* 6.2 1.8 - - - +
249F PRO 2.8 27.0 + - - +
251F ASN 4.2 0.2 + - - -
252F LEU* 3.4 29.7 + - + +
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Residues in contact with ARG 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ASP* 5.8 4.9 + - - +
176F HIS* 4.1 29.5 - - + +
181F ASP* 2.8 49.5 + - - +
205F GLN* 1.3 76.8 - - - +
207F THR* 1.3 68.9 + - - +
208F ARG* 6.1 4.0 - - + +
214F VAL* 3.5 36.2 - - + +
215F VAL 3.7 4.5 - - - -
216F THR* 3.9 16.5 + - + +
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Residues in contact with THR 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F GLN* 4.4 13.5 + - - +
206F ARG* 1.3 77.7 + - - +
208F ARG* 1.3 73.2 + - - +
209F ALA* 4.4 2.2 - - - +
214F VAL* 3.0 7.5 - - - -
215F VAL* 2.7 61.5 + - + +
217F GLN* 5.3 2.0 + - - -
250F ASN* 4.0 19.8 + - - +
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Residues in contact with ARG 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F ARG* 5.4 4.4 - - + +
207F THR* 1.3 78.4 - - - +
209F ALA* 1.3 69.5 + - - +
210F PRO* 4.5 1.0 - - - +
212F GLY* 3.3 30.4 + - - -
213F SER 3.5 1.6 - - - -
214F VAL* 3.5 24.1 - - + +
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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