Contacts of the strand formed by residues 190 - 195 (chain C) in PDB entry 2QC8
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 ILE 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B THR* 2.6 28.6 + - - +
179C HIS* 4.2 10.5 - - + +
180C TYR* 3.7 45.1 - - + -
183C CYS* 4.0 19.1 - - + -
184C LEU* 3.7 28.4 - - + +
188C VAL 2.9 12.4 + - - +
189C LYS* 1.3 72.7 - - - +
191C ALA* 1.3 56.1 + - - +
192C GLY 3.9 9.9 - - - +
193C THR* 4.2 3.1 - - + -
204C PHE* 4.1 21.5 - - + -
205C GLN 3.5 11.0 - - - +
206C ILE* 3.6 8.7 - - + -
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Residues in contact with ALA 191 (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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45B ARG* 3.3 7.1 - - - +
46B THR* 2.7 31.2 + - - +
189C LYS 3.5 1.0 + - - -
190C ILE* 1.3 71.4 - - - +
192C GLY* 1.3 57.4 + - - +
205C GLN* 2.8 25.8 + - + +
207C GLY 3.6 21.1 - - - +
501C ADP 3.7 20.2 - - - +
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Residues in contact with GLY 192 (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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44B THR 3.0 14.8 - - - -
45B ARG* 4.0 0.2 - - - -
180C TYR* 3.4 12.0 + - - -
190C ILE* 3.5 4.1 - - - +
191C ALA* 1.3 81.2 - - - +
193C THR* 1.3 69.4 + - - +
204C PHE* 3.5 1.4 - - - +
205C GLN* 2.9 35.9 + - - +
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Residues in contact with THR 193 (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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43B LYS* 3.7 2.6 - - - +
44B THR* 2.9 30.2 + - - +
90B ARG* 4.6 0.9 + - - -
701B CL 3.2 16.6 - - - +
176C VAL* 4.1 22.4 - - + +
179C HIS* 5.8 1.3 - - - +
180C TYR* 3.2 39.7 - - + -
190C ILE* 4.2 3.6 - - + -
192C GLY* 1.3 76.9 - - - +
194C ASN* 1.3 66.6 + - - +
203C GLU 3.3 15.7 - - - +
204C PHE* 3.9 11.0 - - + -
205C GLN* 3.6 4.4 + - - +
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Residues in contact with ASN 194 (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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43B LYS* 3.7 25.0 - - + +
701B CL 4.2 6.5 - - - -
162C TYR* 4.0 10.2 - - - -
163C CYS* 3.9 6.5 - - - -
193C THR* 1.3 77.5 - - - +
195C ALA* 1.3 81.7 + - - +
196C GLU* 3.4 23.8 + - - +
202C TRP* 3.7 6.3 - - - -
203C GLU* 2.9 42.2 + - - +
205C GLN* 3.1 21.3 + - - -
403C MN 4.2 2.4 + - - -
601C P3S 5.0 0.6 + - - -
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Residues in contact with ALA 195 (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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42B CYS 5.2 1.0 + - - -
161C TYR 3.6 10.8 - - - +
162C TYR* 3.9 1.4 - - - -
163C CYS* 3.0 38.2 + - - +
164C GLY 3.8 7.6 - - - +
169C ARG 5.8 0.2 - - - +
170C ALA* 5.4 2.9 - - + -
173C ARG* 5.7 0.2 - - - +
194C ASN* 1.3 84.5 + - - +
196C GLU* 1.3 59.6 + - - +
201C GLN 4.7 0.4 - - - +
202C TRP* 3.3 41.5 - - + -
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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