Contacts of the strand formed by residues 203 - 210 (chain C) in PDB entry 1I9R
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 ARG 203 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 6.1 1.4 - - - +
144B GLY* 4.1 5.1 - - - -
145B TYR* 3.1 63.7 - - + +
251B THR* 4.7 12.5 + - - -
194C CYS* 3.6 6.4 - - - +
195C LEU* 3.1 34.9 + - + +
201C PHE 4.3 2.5 - - - +
202C GLU* 1.3 84.3 - - - +
204C ILE* 1.3 89.1 + - - +
205C LEU* 4.4 4.6 + - + +
97M GLU* 4.1 24.8 + - - +
98M ILE 5.9 0.2 + - - -
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Residues in contact with ILE 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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251B THR* 4.1 20.2 + - + +
252B GLY* 4.4 2.5 + - - -
192C SER* 4.3 8.5 - - - -
193C LEU 4.1 3.6 - - - +
194C CYS* 3.8 16.2 - - - -
203C ARG* 1.3 104.0 + - - +
205C LEU* 1.3 67.3 + - - +
206C LEU 3.6 22.9 - - - +
207C ARG* 3.8 36.6 - - + +
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Residues in contact with LEU 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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125B HIS* 5.0 2.4 + - - -
145B TYR* 3.7 41.5 - - + -
252B GLY* 3.6 12.3 - - - +
171C ILE* 4.8 3.1 - - + -
193C LEU* 3.0 25.1 + - + +
195C LEU* 3.7 35.4 - - + +
203C ARG* 4.4 2.4 + - + +
204C ILE* 1.3 82.1 - - - +
206C LEU* 1.3 71.7 + - + +
229C PHE* 3.7 45.8 - - + -
231C LEU* 5.1 1.1 - - + -
237C VAL* 4.7 7.2 - - + -
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Residues in contact with LEU 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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125B HIS* 4.0 12.6 - - + +
174B GLN* 5.1 4.9 - - + +
252B GLY* 3.2 10.3 - - - +
255B SER* 4.5 8.3 - - - +
192C SER* 3.4 0.2 - - - -
193C LEU* 3.1 53.2 + - + -
204C ILE* 3.6 3.9 - - - +
205C LEU* 1.3 88.6 - - - +
207C ARG* 1.3 74.9 + - - +
225C LEU* 3.9 27.1 - - + -
226C GLY* 2.7 31.0 - - - +
229C PHE* 3.1 27.8 - - + -
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Residues in contact with ARG 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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174B GLN* 3.5 8.3 + - - +
251B THR* 3.8 20.8 + - - +
252B GLY 2.7 20.9 + - - +
253B PHE* 3.3 45.9 - - + +
190C ILE* 2.9 34.9 - - + +
191C ALA 3.1 5.6 - - - +
192C SER* 3.1 22.8 + - - +
204C ILE* 3.8 25.6 - - + +
206C LEU* 1.3 86.0 - - - +
208C ALA* 1.3 62.1 + - - +
225C LEU* 3.8 4.3 - - - -
59K ASN* 5.7 1.8 + - - -
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Residues in contact with ALA 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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174B GLN* 3.6 6.3 - - - +
222B SER* 3.1 19.7 - - - +
253B PHE* 4.3 1.1 - - - -
190C ILE* 3.3 1.6 - - - +
191C ALA 2.8 29.9 + - - +
207C ARG* 1.3 74.1 - - - +
209C ALA* 1.3 65.1 + - - +
223C ILE* 3.8 22.7 - - + +
224C HIS 4.9 2.9 - - - +
225C LEU* 3.2 23.2 - - + +
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Residues in contact with ALA 209 (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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176B THR* 4.9 0.2 + - - -
220B GLN* 3.4 15.1 - - + +
221B GLN* 3.1 29.8 + - - -
222B SER* 3.0 9.1 + - - -
253B PHE* 3.8 15.8 - - + -
188C PRO* 4.7 2.9 - - + -
189C PHE 3.3 6.5 - - - +
190C ILE* 3.5 28.3 - - + -
208C ALA* 1.3 78.8 - - - +
210C ASN* 1.3 64.7 + - - +
223C ILE* 4.3 0.7 - - - -
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Residues in contact with ASN 210 (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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210A ASN* 5.1 4.8 - - - +
210B ASN* 5.0 5.5 - - - +
220B GLN 3.7 5.8 - - - -
221B GLN* 4.3 11.8 + - - +
222B SER* 3.7 16.5 + - - +
177C PHE* 4.1 10.5 - - + -
188C PRO* 3.0 21.1 - - - +
189C PHE* 3.0 16.1 + - - +
209C ALA* 1.3 80.3 + - - +
211C THR* 1.3 63.0 + - - +
212C HIS 4.0 0.6 + - - -
221C GLN* 3.1 35.2 + - - +
222C SER 4.3 13.7 + - - +
223C ILE* 3.7 19.6 - - - +
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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