Contacts of the strand formed by residues 214 - 224 (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 VAL 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C ARG* 3.7 28.5 - - + +
207C THR 3.1 8.7 - - - +
208C ARG* 3.4 46.0 - - + +
212C GLY 3.8 2.2 - - - +
213C SER* 1.3 71.2 - - - +
215C VAL* 1.3 64.6 + - - +
216C THR* 3.5 7.4 + - - +
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Residues in contact with VAL 215 (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 4.1 0.7 - - - +
206C ARG* 3.7 1.4 - - - -
207C THR* 2.8 65.2 + - + +
209C ALA* 5.1 8.3 - - + +
213C SER* 3.9 3.4 - - - +
214C VAL* 1.3 71.4 - - - +
216C THR* 1.3 68.1 + - - +
217C GLN* 4.2 10.2 + - + +
250C ASN* 5.9 0.2 - - - +
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Residues in contact with THR 216 (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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204C SER* 5.1 2.5 - - - +
205C GLN 3.5 9.3 + - - +
206C ARG* 4.1 27.0 + - + +
214C VAL* 3.5 9.6 + - - +
215C VAL* 1.3 79.1 + - - +
217C GLN* 1.3 67.2 + - - +
218C ARG* 4.2 28.2 + - + +
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Residues in contact with GLN 217 (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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203C GLY 4.5 0.9 - - - -
204C SER* 3.4 4.0 + - - -
205C GLN* 2.5 74.0 + - + +
207C THR* 5.2 1.9 + - - -
215C VAL* 4.2 8.9 + - + +
216C THR* 1.3 75.6 - - - +
218C ARG* 1.3 64.6 + - - +
219C ILE* 5.6 3.3 - - + +
250C ASN* 3.5 24.8 + - - +
251C ASN* 3.5 4.8 + - - +
252C LEU* 3.1 32.3 - - + +
253C LYS* 4.2 5.3 - - - +
311C VAL* 6.3 0.4 - - - -
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Residues in contact with ARG 218 (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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169C LEU* 3.4 47.4 + - + +
173C ASP* 2.9 35.2 + - - -
203C GLY 3.6 3.4 - - - -
204C SER* 3.7 26.4 + - - -
216C THR* 4.2 17.1 + - + +
217C GLN* 1.3 76.6 - - - +
219C ILE* 1.3 68.0 + - - +
311C VAL* 3.6 8.9 - - - +
312C LEU* 2.9 50.4 + - + +
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Residues in contact with ILE 219 (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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169C LEU* 6.0 0.2 - - - +
201C ALA 3.9 0.3 - - - +
202C LEU* 3.4 3.8 - - - +
203C GLY 2.8 53.7 + - - +
217C GLN* 5.2 2.7 - - + +
218C ARG* 1.3 83.4 - - - +
220C ARG* 1.3 61.5 + - - +
221C MET* 4.0 8.3 - - + -
252C LEU* 3.5 20.2 - - + +
253C LYS* 3.6 28.9 - - + +
256C CYS* 3.3 39.7 - - + -
309C ALA* 4.4 8.3 - - + -
310C THR 3.3 10.1 - - - +
311C VAL* 4.6 9.2 - - + -
312C LEU* 4.3 4.7 - - - +
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Residues in contact with ARG 220 (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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129B PRO* 6.1 0.2 - - - +
131B ASP* 3.9 11.7 + - - -
165C GLN* 2.6 31.6 + - - +
193C PRO* 3.1 29.5 - - - +
200C MET* 3.0 35.4 - - + +
201C ALA 3.4 3.6 - - - -
202C LEU* 3.2 22.9 - - + -
219C ILE* 1.3 74.8 - - - +
221C MET* 1.3 68.9 + - - +
222C GLU* 3.7 16.7 + - - -
309C ALA* 3.6 0.2 - - - -
310C THR* 2.8 53.5 + - - +
312C LEU* 3.8 17.1 - - + +
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Residues in contact with MET 221 (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* 5.7 4.0 - - + -
199C LEU 3.4 1.0 - - - +
200C MET* 3.1 8.3 - - - +
201C ALA* 2.8 64.7 + - + +
202C LEU 5.2 0.7 - - - -
203C GLY* 5.0 3.1 - - - +
219C ILE* 4.0 14.8 - - + -
220C ARG* 1.3 82.9 - - - +
222C GLU* 1.3 64.7 + - - +
223C MET* 4.3 8.5 - - + +
237C PHE* 6.2 0.9 - - + -
256C CYS* 3.8 35.2 - - + +
257C GLU* 4.7 2.2 - - - -
260C VAL* 4.1 21.8 - - + -
307C VAL* 5.0 9.2 - - + -
308C GLN 4.8 3.4 - - - +
309C ALA* 3.5 30.7 - - + +
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Residues in contact with GLU 222 (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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192C SER* 4.1 14.8 - - - +
193C PRO* 3.8 20.1 - - + +
194C ARG* 2.9 55.8 + - - +
198C TYR* 4.3 13.6 - - + -
199C LEU 3.4 3.8 - - - +
200C MET* 4.9 1.1 - - + -
220C ARG* 3.7 26.1 + - - -
221C MET* 1.3 76.0 - - - +
223C MET* 1.3 64.5 + - - +
307C VAL* 4.3 15.4 - - - +
308C GLN 5.4 2.6 + - - -
310C THR* 5.4 6.2 + - - +
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Residues in contact with MET 223 (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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186C THR 3.4 21.5 - - - +
187C SER* 4.1 4.0 - - - -
198C TYR* 3.1 10.6 - - - +
199C LEU* 2.6 69.9 + - + +
201C ALA* 3.9 17.9 - - + -
221C MET* 4.3 9.4 - - + +
222C GLU* 1.3 77.9 - - - +
224C HIS* 1.3 64.7 + - - +
260C VAL* 3.5 26.0 - - + -
307C VAL* 4.9 6.5 - - + -
2402C ADP 3.2 38.1 - - - +
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Residues in contact with HIS 224 (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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197C ASP* 3.5 17.7 + - + +
198C TYR* 3.3 41.5 + + + -
222C GLU 4.3 0.4 + - - -
223C MET* 1.3 71.3 - - - +
225C LYS* 1.3 69.6 + - - +
226C VAL* 3.6 4.9 + - - +
264C HIS* 4.7 27.3 - - + +
268C GLN* 5.1 7.9 - - - +
2402C ADP 3.2 17.0 - - - -
64F GLU* 5.1 6.3 - - - -
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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