Contacts of the strand formed by residues 189 - 196 (chain A) 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 PHE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A VAL* 4.3 8.3 - - + -
177A PHE* 3.3 70.2 - + + -
188A PRO* 1.3 72.2 - - - +
190A ILE* 1.3 59.8 + - - +
191A ALA* 4.1 21.8 - - + -
208A ALA 3.9 0.2 - - - +
209A ALA* 3.3 17.1 - - - -
210A ASN 3.1 7.8 + - - +
212A HIS* 3.6 10.9 + - + +
223A ILE* 4.1 5.8 - - + +
241A VAL* 3.6 28.7 - - + -
242A THR* 3.6 12.1 - - + -
243A ASP 4.0 22.2 - - - -
246A GLN* 4.4 13.0 - - + -
247A VAL* 5.0 3.8 - - + -
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 4.3 16.8 - - + +
189A PHE* 1.3 77.6 - - - +
191A ALA* 1.3 68.9 + - - +
192A SER* 2.9 18.4 - - - +
207A ARG* 2.8 50.3 - - + +
208A ALA 3.2 4.7 - - - +
209A ALA* 3.6 18.8 - - + -
241A VAL* 3.6 2.6 - - - +
242A THR* 2.7 44.3 + - + +
220C GLN* 5.1 1.3 - - - +
253C PHE* 4.9 7.2 - - + -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 4.9 5.4 - - + -
189A PHE* 4.0 11.8 + - + -
190A ILE* 1.3 79.4 - - - +
192A SER* 1.3 63.6 + - - +
207A ARG* 3.1 0.7 - - - -
208A ALA 2.8 30.3 + - - +
223A ILE* 4.2 23.8 - - + -
225A LEU* 4.9 4.9 - - + -
239A VAL* 5.0 4.7 - - + -
240A ASN 3.5 5.2 - - - -
241A VAL* 3.9 18.8 - - + -
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 2.9 23.6 - - - +
191A ALA* 1.3 72.2 - - - +
193A LEU* 1.3 61.2 + - - +
194A CYS* 3.6 17.0 + - - -
204A ILE* 4.2 7.4 - - - +
206A LEU 3.3 5.2 - - - -
207A ARG* 3.1 21.4 + - - +
225A LEU* 4.9 2.2 - - - -
239A VAL* 3.3 6.8 - - - +
240A ASN* 2.7 47.8 + - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.1 35.7 - - + +
172A TYR 5.0 0.4 - - - +
173A ALA* 5.1 5.2 - - + -
192A SER* 1.3 69.8 - - - +
194A CYS* 1.3 75.6 + - - +
204A ILE* 3.9 1.6 - - - -
205A LEU* 3.0 40.9 + - + +
206A LEU* 2.8 45.5 + - + +
225A LEU* 3.8 15.5 - - + +
229A PHE* 4.6 0.7 - - + -
237A VAL* 3.9 17.7 - - + -
238A PHE 3.8 6.5 - - - +
239A VAL* 4.6 2.7 - - + +
256A PHE* 4.3 12.3 - - + -
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Residues in contact with CYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A SER* 4.1 17.7 - - - -
193A LEU* 1.3 78.8 - - - +
195A LEU* 1.3 61.1 + - - +
202A GLU* 6.4 0.2 - - - -
203A ARG 3.5 7.9 - - - +
204A ILE* 4.1 24.2 - - - -
205A LEU* 5.0 0.2 - - - -
237A VAL* 3.0 6.9 - - - +
238A PHE* 2.6 78.8 + - + +
240A ASN* 4.3 10.5 - - - -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU 4.3 0.2 + - - -
194A CYS* 1.3 75.6 - - - +
196A LYS* 1.3 78.4 + - - +
197A SER* 3.9 11.6 + - - +
201A PHE 4.6 0.2 - - - +
202A GLU* 3.7 4.0 - - - +
203A ARG* 3.0 36.0 + - + +
205A LEU* 3.6 30.7 - - + +
231A LEU* 4.3 7.9 - - + -
235A ALA* 4.2 12.1 - - + -
236A SER 3.5 17.5 - - - +
237A VAL* 3.8 11.0 - - + -
238A PHE* 4.3 1.7 - - - -
145C TYR* 3.4 40.4 - - + +
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Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 1.3 77.5 - - - +
197A SER* 1.3 81.6 + - - +
198A PRO* 4.0 5.0 - - - +
199A GLY 4.5 1.8 - - - +
200A ARG 2.6 27.0 + - - +
201A PHE* 4.2 1.1 - - - +
202A GLU* 3.5 31.4 - - + +
234A GLY 4.4 0.7 - - - +
235A ALA* 3.9 1.0 - - - -
236A SER* 2.6 40.4 + - - +
238A PHE* 4.1 15.5 - - + -
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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