Contacts of the helix formed by residues 192 - 198 (chain F) in PDB entry 1Q57
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 ASN 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F ASP* 3.1 24.7 + - - +
141F LEU* 3.4 25.0 - - - +
144F LYS* 2.9 26.0 + - - -
188F THR* 3.3 14.5 + - - +
189F CYS 2.6 19.5 + - - +
191F ALA* 1.3 79.9 - - - +
193F TYR* 1.3 64.3 + - - +
194F GLU* 3.1 8.9 - - - +
195F TYR* 2.9 21.7 + - + +
196F PHE* 2.9 25.3 + - + +
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Residues in contact with TYR 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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189F CYS 3.4 5.6 + - - -
190F ALA* 3.5 13.0 + - - +
192F ASN* 1.3 75.5 - - - +
194F GLU* 1.3 76.6 + - + +
196F PHE* 3.2 3.4 + - - +
197F ASP* 2.8 35.9 + - + +
222F VAL 3.6 19.1 - - - -
223F LEU 3.9 2.9 - - - -
224F PRO* 3.1 51.5 - - + +
225F ALA* 4.1 6.8 + - - +
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Residues in contact with GLU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F ALA 4.3 2.1 - - - +
191F ALA 3.6 13.3 - - - +
192F ASN* 3.1 12.9 - - - +
193F TYR* 1.3 90.8 + - + +
195F TYR* 1.3 80.0 + - - +
197F ASP* 3.1 16.7 + - - +
198F GLN* 3.3 12.5 + - - +
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Residues in contact with TYR 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLN* 3.0 37.7 - - - +
141F LEU* 4.2 14.1 - - + -
144F LYS* 3.1 39.2 + - + -
147F TRP* 3.3 40.6 + - - -
153F ILE* 4.1 2.5 - - + -
176F VAL* 3.7 3.0 - - + +
192F ASN* 2.9 21.1 + - + +
194F GLU* 1.3 81.3 + - - +
196F PHE* 1.3 86.7 + + - +
198F GLN* 2.9 37.3 - - - +
199F PHE* 3.7 18.1 - + - -
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Residues in contact with PHE 196 (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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141F LEU* 3.1 35.7 - - + -
153F ILE* 3.8 24.0 - - + -
155F VAL* 3.3 34.8 - - + -
178F LEU* 5.7 0.2 - - + -
189F CYS* 4.0 24.2 - - - -
192F ASN* 2.9 33.1 + - + -
193F TYR* 3.8 5.8 - - - +
195F TYR* 1.3 80.0 - + - +
197F ASP* 1.3 58.1 + - - +
198F GLN 2.9 5.2 - - - -
199F PHE* 2.9 31.7 + - - +
202F ILE* 3.6 23.7 - - + +
223F LEU* 3.6 19.7 - - + -
224F PRO* 4.7 1.3 - - + -
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Residues in contact with ASP 197 (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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193F TYR* 2.8 29.7 + - + +
194F GLU* 3.1 8.5 + - - +
196F PHE* 1.3 71.7 - - - +
198F GLN* 1.3 60.4 + - - +
199F PHE 2.9 13.4 + - - +
224F PRO* 4.1 18.6 - - + +
227F LYS* 2.7 40.2 + - - +
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Residues in contact with GLN 198 (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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114F GLN* 3.3 12.4 + - - -
148F ASN* 3.0 48.1 + - - +
149F GLY* 3.5 27.2 - - - +
150F GLY 3.5 5.2 + - - +
194F GLU 3.3 8.4 + - - +
195F TYR* 2.9 26.2 + - - +
196F PHE 2.9 0.4 - - - -
197F ASP* 1.3 78.6 - - - +
199F PHE* 1.3 60.4 + - + +
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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