Contacts of the strand formed by residues 198 - 208 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188H SER 5.1 1.6 - - - +
190H LEU 5.3 1.2 - - - +
192H SER* 3.4 20.7 + - - +
194H ARG* 2.8 69.7 + - + +
195H GLY* 3.8 4.1 - - - +
196H SER 3.1 8.6 + - - +
197H ASP* 1.3 107.2 - - - +
199H LEU* 1.3 64.8 + - - +
200H MET 3.9 0.3 + - - -
222H GLU* 4.3 16.8 - - + -
223H MET 3.1 21.5 - - - +
224H HIS* 3.4 30.8 + + + -
225H LYS* 3.9 5.4 - - - +
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Residues in contact with LEU 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H SER* 4.2 15.9 - - - +
188H SER 4.1 17.5 - - - +
192H SER* 4.4 1.6 - - - -
198H TYR* 1.3 74.1 - - - +
200H MET* 1.3 60.0 + - - +
222H GLU* 3.4 1.2 - - - -
223H MET* 2.5 67.6 + - + +
225H LYS* 4.1 29.7 - - + +
7402H ADP 3.7 45.1 - - + +
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Residues in contact with MET 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H GLN* 4.2 4.5 - - + +
187H SER* 2.9 23.5 - - - -
188H SER* 3.1 23.6 + - - +
190H LEU* 3.7 36.3 - - + +
191H LEU 4.9 1.8 - - - +
192H SER* 3.7 17.5 + - - +
193H PRO* 3.5 22.4 - - + -
198H TYR 3.9 1.4 + - - -
199H LEU* 1.3 74.6 - - - +
201H ALA* 1.3 64.2 + - - +
202H LEU* 4.5 7.4 - - + -
220H ARG* 3.0 52.5 - - + +
221H MET 3.1 13.9 - - - +
222H GLU* 4.6 1.6 - - + +
223H MET* 4.1 0.2 - - - -
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Residues in contact with ALA 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H VAL* 5.4 2.7 - - + -
185H ILE* 3.2 17.0 - - - +
186H THR* 3.4 17.9 - - - +
187H SER 5.1 0.2 - - - -
200H MET* 1.3 75.8 - - - +
202H LEU* 1.3 62.7 + - - +
220H ARG* 3.4 2.1 - - - -
221H MET* 2.7 49.7 + - + +
223H MET* 3.9 14.6 - - + -
237H PHE* 6.3 1.3 - - + -
260H VAL* 5.9 2.0 - - + -
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Residues in contact with LEU 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H GLN* 4.2 11.7 - - + +
168H ALA* 3.4 33.0 - - + -
169H LEU* 4.6 2.9 - - + +
172H MET* 3.2 25.2 - - + +
184H VAL* 3.4 4.6 - - - +
185H ILE* 2.7 43.3 + - + +
188H SER* 5.7 1.3 - - - +
190H LEU* 4.1 15.5 - - + -
200H MET* 4.5 6.7 - - + -
201H ALA* 1.3 75.3 - - - +
203H GLY* 1.3 58.7 + - - +
219H ILE 3.4 2.7 - - - +
220H ARG* 3.2 42.4 - - + -
221H MET* 5.1 0.9 - - - -
312H LEU* 4.1 11.9 - - + -
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Residues in contact with GLY 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H MET* 4.2 1.8 - - - -
183H VAL 3.3 7.4 - - - -
184H VAL* 4.0 9.4 - - - -
201H ALA 4.3 0.2 - - - -
202H LEU* 1.3 75.4 - - - +
204H SER* 1.3 57.4 + - - -
218H ARG* 3.7 1.9 - - - -
219H ILE* 2.8 46.8 + - - +
221H MET* 4.8 1.2 - - - +
252H LEU* 3.2 21.6 - - - +
256H CYS* 5.2 0.7 - - - -
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Residues in contact with SER 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H MET* 3.8 25.8 - - - -
173H ASP* 4.8 0.5 + - - -
176H HIS* 2.7 30.2 + - - -
182H THR* 3.4 1.7 - - - -
183H VAL* 2.7 39.8 + - - +
203H GLY* 1.3 74.8 - - - -
205H GLN* 1.3 63.4 + - - +
216H THR* 5.0 2.9 - - - +
217H GLN 3.3 4.5 + - - -
218H ARG* 3.7 25.5 + - - +
252H LEU* 3.5 3.0 - - - +
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Residues in contact with GLN 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176H HIS* 4.1 1.8 - - - -
181H ASP* 3.2 5.4 - - + +
182H THR* 3.5 25.8 + - + +
204H SER* 1.3 76.9 + - - +
206H ARG* 1.3 67.9 + - - +
207H THR* 4.6 9.4 + - - +
215H VAL 4.0 0.6 - - - +
216H THR* 3.4 4.5 - - - +
217H GLN* 2.7 72.0 + - + +
245H THR* 6.2 3.2 - - - +
249H PRO 2.9 26.2 + - - +
250H ASN* 4.8 0.4 - - - -
251H ASN 4.2 0.2 + - - -
252H LEU* 3.3 30.9 + - + +
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Residues in contact with ARG 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H ASP* 5.9 4.0 + - - +
176H HIS* 4.1 31.6 - - + +
181H ASP* 2.8 42.3 + - - +
205H GLN* 1.3 76.2 - - - +
207H THR* 1.3 69.4 + - - +
208H ARG* 6.1 4.5 - - + +
214H VAL* 3.5 35.6 - - + +
215H VAL 3.6 4.0 - - - -
216H THR* 4.0 17.3 + - + +
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Residues in contact with THR 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H GLN* 4.6 12.7 + - - +
206H ARG* 1.3 77.8 + - - +
208H ARG* 1.3 73.3 + - - +
209H ALA* 4.3 2.5 - - - +
214H VAL* 3.0 6.9 - - - -
215H VAL* 2.7 61.9 + - + +
217H GLN* 5.3 1.8 + - - -
250H ASN* 4.0 18.9 + - - +
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Residues in contact with ARG 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H ARG* 6.1 4.8 - - + +
207H THR* 1.3 78.8 - - - +
209H ALA* 1.3 70.2 + - - +
210H PRO* 4.4 1.0 - - - +
212H GLY* 3.3 29.6 + - - -
213H SER 3.5 1.6 - - - -
214H VAL* 3.6 21.3 - - + +
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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