Contacts of the strand formed by residues 198 - 208 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C SER 5.2 1.6 - - - +
190C LEU 5.2 1.7 - - - +
192C SER* 3.5 19.8 + - - +
194C ARG* 2.9 66.5 + - + +
195C GLY* 3.6 5.7 - - - +
196C SER 3.1 8.6 + - - +
197C ASP* 1.3 109.1 - - - +
199C LEU* 1.3 64.9 + - - +
200C MET 3.9 0.5 + - - -
222C GLU* 4.3 16.6 - - + -
223C MET 3.1 19.3 - - - +
224C HIS* 3.3 31.8 + + + -
225C LYS* 3.9 5.3 - - - +
64F GLU* 4.8 9.1 + - - -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLN* 6.1 0.4 - - - +
187C SER* 4.2 18.2 - - - +
188C SER 4.2 15.3 - - - +
192C SER* 4.4 1.1 - - - -
198C TYR* 1.3 72.4 - - - +
200C MET* 1.3 59.8 + - - +
221C MET 3.4 0.9 - - - +
222C GLU* 3.4 1.6 - - - -
223C MET* 2.6 65.9 + - + +
225C LYS* 4.1 28.7 - - + +
2402C ADP 3.7 47.1 - - + +
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Residues in contact with MET 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C GLN* 4.3 4.9 - - + +
187C SER* 2.9 23.9 - - - -
188C SER* 3.1 22.1 + - - +
190C LEU* 3.6 40.2 - - + +
191C LEU 4.9 1.3 - - - +
192C SER* 3.8 15.7 - - - +
193C PRO* 3.5 21.8 - - + -
198C TYR 3.9 1.2 + - - -
199C LEU* 1.3 76.0 - - - +
201C ALA* 1.3 65.1 + - - +
202C LEU* 4.7 4.9 - - + -
220C ARG* 3.0 52.9 - - + +
221C MET 3.1 10.5 - - - +
222C GLU* 4.9 0.7 - - + -
223C MET* 4.1 0.4 - - - -
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Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C VAL* 5.5 2.7 - - + -
185C ILE 3.3 9.2 - - - +
186C THR* 3.4 22.9 - - - +
187C SER 5.1 0.2 - - - -
200C MET* 1.3 75.2 - - - +
202C LEU* 1.3 64.1 + - - +
219C ILE 3.9 0.5 - - - +
220C ARG* 3.4 2.4 - - - -
221C MET* 2.8 50.7 + - + +
223C MET* 3.9 16.4 - - + -
237C PHE* 6.3 1.6 - - + -
260C VAL* 5.8 1.6 - - + -
2402C ADP 5.2 0.2 - - - +
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C GLN* 4.2 12.6 - - + +
168C ALA* 3.4 32.5 - - + -
169C LEU* 4.6 2.5 - - + +
172C MET* 3.2 25.7 - - + +
184C VAL* 3.4 3.5 - - - -
185C ILE* 2.8 43.2 + - + +
188C SER* 5.8 0.7 - - - +
190C LEU* 4.0 16.2 - - + -
200C MET* 4.7 5.6 - - + -
201C ALA* 1.3 75.4 - - - +
203C GLY* 1.3 58.3 + - - +
219C ILE 3.4 2.7 - - - +
220C ARG* 3.2 42.2 - - + +
221C MET* 5.2 0.7 - - - -
312C LEU* 4.3 10.8 - - + -
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Residues in contact with GLY 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C MET* 4.2 1.3 - - - -
183C VAL 3.3 7.9 - - - -
184C VAL* 4.1 12.3 - - - -
201C ALA 4.3 0.2 + - - -
202C LEU* 1.3 75.2 - - - +
204C SER* 1.3 59.2 + - - -
218C ARG* 3.6 1.3 - - - -
219C ILE* 2.8 50.0 + - - +
221C MET* 5.0 1.7 - - - +
252C LEU* 3.3 14.6 - - - +
256C CYS* 5.1 0.9 - - - -
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C MET* 3.8 25.1 - - - +
173C ASP* 4.7 0.7 + - - -
176C HIS* 2.7 28.6 + - - -
182C THR* 3.4 1.7 - - - -
183C VAL 2.7 40.5 + - - +
203C GLY* 1.3 74.4 - - - -
205C GLN* 1.3 62.3 + - - +
216C THR* 5.1 2.6 - - - +
217C GLN 3.4 5.1 + - - -
218C ARG* 3.7 24.6 + - - +
252C LEU* 3.5 3.9 - - - +
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Residues in contact with GLN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C HIS* 4.2 1.8 - - - -
181C ASP 3.2 6.3 - - - +
182C THR* 3.6 24.1 + - + +
204C SER* 1.3 76.5 + - - +
206C ARG* 1.3 65.3 + - - +
207C THR* 4.4 13.6 + - - +
215C VAL 4.1 0.8 - - - +
216C THR* 3.5 5.1 - - - +
217C GLN* 2.5 72.5 + - + +
245C THR* 6.3 1.8 - - - +
249C PRO 2.8 27.6 + - - +
250C ASN* 4.2 0.4 - - - -
252C LEU* 3.5 29.6 + - + +
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Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASP* 5.7 5.9 + - - +
176C HIS* 4.2 30.7 - - + +
181C ASP* 2.8 46.3 + - - +
205C GLN* 1.3 77.3 - - - +
207C THR* 1.3 68.6 + - - +
208C ARG* 6.0 4.0 - - + +
214C VAL* 3.7 33.9 - - + +
215C VAL 3.7 4.0 - - - -
216C THR* 4.1 17.0 + - + +
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Residues in contact with THR 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLN* 4.5 13.3 + - - +
206C ARG* 1.3 78.4 + - - +
208C ARG* 1.3 71.1 + - - +
209C ALA* 4.4 2.5 - - - +
214C VAL* 3.1 7.6 - - - +
215C VAL* 2.8 57.3 + - + +
217C GLN* 5.2 2.3 + - - -
250C ASN* 3.8 21.5 + - - +
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Residues in contact with ARG 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ARG* 6.0 4.6 - - + +
207C THR* 1.3 79.6 - - - +
209C ALA* 1.3 68.0 + - - +
210C PRO* 4.5 1.7 - - - +
212C GLY* 3.4 30.0 + - - -
213C SER 3.6 1.3 - - - -
214C VAL* 3.4 22.5 - - + +
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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