Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 1IRS
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 THR 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A THR* 2.5 56.6 + - - +
190A LYS* 1.3 98.6 - - + +
192A ILE* 1.3 62.4 + - - +
205A VAL* 4.7 10.6 - - + +
206A LEU 3.4 11.2 - - - -
207A GLN* 4.1 20.0 - - + +
208A LEU* 4.9 0.4 - - - -
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Residues in contact with ILE 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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185A LEU* 3.8 27.4 - - + -
186A CYS 3.5 4.9 - - - +
187A LEU* 4.0 12.3 - - + -
188A THR 4.6 0.2 - - - +
191A THR* 1.3 71.0 - - - +
193A SER* 1.3 72.7 + - - +
194A PHE* 3.9 20.4 - - + -
205A VAL* 3.5 6.1 - - - +
206A LEU* 2.9 39.8 + - + +
207A GLN* 4.2 1.0 - - - +
208A LEU* 3.5 22.2 - - + +
211A ILE* 3.1 33.9 - - + -
223A ILE* 4.0 18.2 - - + -
253A ILE* 5.0 2.7 - - + -
257A MET* 6.0 0.2 - - + -
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Residues in contact with SER 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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160A PHE* 3.1 22.1 - - - -
184A ARG 2.7 23.8 - - - +
186A CYS* 3.0 26.2 + - - -
188A THR* 3.1 16.6 + - - -
191A THR* 5.1 0.2 + - - -
192A ILE* 1.3 79.9 + - - +
194A PHE* 1.3 55.7 + - - +
195A VAL* 3.0 15.5 + - - +
202A ALA* 4.5 10.1 - - - -
204A VAL 3.9 3.4 - - - -
205A VAL* 4.4 8.1 - - - +
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Residues in contact with PHE 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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166A VAL* 4.6 1.8 - - + -
168A LEU* 4.4 12.1 - - + -
183A TYR* 3.5 29.5 - - + -
184A ARG 3.3 6.5 - - - -
185A LEU* 3.4 31.0 - - + -
192A ILE* 3.9 20.6 - - + -
193A SER* 1.3 69.7 - - - +
195A VAL* 1.3 59.7 + - - +
203A ALA* 2.7 32.4 + - - +
204A VAL* 3.2 24.6 + - + +
206A LEU* 4.0 24.5 - - + -
223A ILE* 5.0 5.4 - - + -
236A PHE* 4.7 19.3 - + + -
238A MET* 3.8 27.6 - - + -
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Residues in contact with VAL 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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160A PHE* 5.3 5.8 - - + -
183A TYR* 3.2 3.1 - - - -
184A ARG* 2.8 43.4 + - + +
186A CYS* 3.9 15.0 - - - -
193A SER* 3.0 19.3 + - - +
194A PHE* 1.3 76.0 - - - +
196A LYS* 1.3 72.8 + - - +
199A SER* 5.1 1.1 - - - -
200A GLU 4.4 9.6 - - - +
201A ALA 3.8 20.6 - - - +
202A ALA* 3.8 17.7 - - + +
203A ALA 4.0 3.1 - - - +
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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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180A ILE 4.5 6.6 + - - -
181A GLY* 5.4 1.4 - - - -
182A ILE* 3.5 20.4 - - + +
183A TYR* 3.4 41.0 - - + +
184A ARG* 5.5 0.4 - - - -
194A PHE 3.9 2.4 + - - -
195A VAL* 1.3 82.2 - - - +
197A LEU* 1.3 64.7 + - - +
198A ASN* 4.1 20.2 - - + +
199A SER* 3.0 34.9 + - - +
201A ALA 5.0 0.2 + - - -
203A ALA* 4.3 6.1 - - + +
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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