Contacts of the strand formed by residues 188 - 193 (chain F) in PDB entry 1II4
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 188 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F MET 4.9 4.3 - - - +
187F PRO* 1.3 74.8 - - - +
189F MET* 1.3 63.5 + - - +
190F ARG* 5.7 4.3 - - - -
214F TRP* 4.6 0.2 - - - -
232F VAL 3.6 0.8 - - - +
233F VAL* 3.1 11.2 - - - +
234F GLU* 2.7 45.5 + - - +
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Residues in contact with MET 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F CYS* 3.6 24.5 - - + +
188F THR* 1.3 80.5 - - - +
190F ARG* 1.3 71.2 + - - +
191F TRP* 3.3 34.1 - - + +
209F VAL* 5.2 6.3 - - + -
211F ASN* 5.2 12.5 - - - +
214F TRP* 3.5 63.0 - - + +
215F SER 4.5 1.6 - - - +
231F CYS* 4.1 5.6 - - + -
232F VAL 3.4 5.2 - - - +
233F VAL* 4.2 7.2 - - + -
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Residues in contact with ARG 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D GLU* 6.2 6.5 - - + -
188F THR* 5.7 4.7 - - - +
189F MET* 1.3 80.8 - - - +
191F TRP* 1.3 68.0 + - - +
192F LEU* 4.8 18.4 - - + +
231F CYS* 3.4 4.3 - - - -
232F VAL* 2.8 57.4 + - + +
234F GLU* 3.3 36.9 + - - -
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Residues in contact with TRP 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F PHE* 3.5 44.9 - + + -
179F CYS* 3.8 10.8 - - - -
189F MET* 3.3 32.4 - - + -
190F ARG* 1.3 78.0 - - - +
192F LEU* 1.3 66.6 + - - +
197F GLU* 4.4 0.2 - - - -
198F PHE* 3.4 32.0 + - + +
207F TYR* 5.5 3.8 - - + +
209F VAL* 4.5 17.4 - - + +
214F TRP 3.9 4.0 - - - -
215F SER 4.1 5.7 + - - -
216F LEU* 3.5 38.9 - - + +
229F TYR* 4.5 6.1 - - + -
230F THR 3.1 22.2 - - - -
231F CYS* 3.6 29.4 - - + -
244F TYR* 4.4 9.0 - + - -
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ARG* 4.8 20.4 - - + +
191F TRP* 1.3 85.8 - - - +
193F LYS* 1.3 59.8 + - - +
194F ASN 3.9 0.4 - - - -
195F GLY* 3.9 23.3 - - - +
196F LYS* 3.2 25.6 - - - +
197F GLU* 3.9 7.6 - - + +
198F PHE* 4.3 2.5 - - - -
228F ASN 3.4 0.2 - - - +
229F TYR* 3.1 9.7 - - - +
230F THR* 2.6 52.1 + - + +
232F VAL* 4.0 23.3 - - + -
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Residues in contact with LYS 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LEU* 1.3 73.2 - - - +
194F ASN* 1.3 91.8 + - - +
196F LYS* 2.8 22.1 + - - +
197F GLU 5.0 1.1 - - - +
198F PHE* 3.7 40.3 - - + +
202F HIS* 4.0 23.6 + - + +
203F ARG* 5.6 0.4 - - - +
224F SER 3.8 16.9 + - - -
225F ASP* 4.7 5.7 + - - +
226F LYS 4.3 10.5 - - - -
228F ASN 3.2 5.2 - - - +
229F TYR* 3.6 29.4 + - + +
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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