Contacts of the strand formed by residues 190 - 195 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C THR* 2.7 27.7 + - - +
179D HIS* 4.0 22.2 - - + +
180D TYR* 3.6 32.8 - - + -
183D CYS* 4.0 18.2 - - + -
184D LEU* 3.6 30.3 - - + +
188D VAL 3.0 9.7 + - - +
189D LYS* 1.3 72.0 - - - +
191D ALA* 1.3 55.5 + - - +
192D GLY 4.0 10.8 - - - +
193D THR* 4.2 4.0 - - + -
204D PHE* 3.8 26.2 - - + -
205D GLN 3.5 11.2 - - - +
206D ILE* 3.6 8.2 - - + +
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Residues in contact with ALA 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ARG* 3.3 8.5 - - - +
46C THR* 2.8 32.1 + - - +
60C TRP* 5.8 0.2 - - - -
189D LYS 3.5 1.6 + - - -
190D ILE* 1.3 69.3 - - - +
192D GLY* 1.3 58.2 + - - +
205D GLN* 2.9 24.9 + - + +
207D GLY 3.6 20.2 - - - +
501D ADP 3.7 18.2 - - - +
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Residues in contact with GLY 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR 3.1 14.1 - - - -
45C ARG* 4.1 0.2 - - - -
180D TYR* 3.4 12.9 + - - -
190D ILE* 3.5 4.4 - - - +
191D ALA* 1.3 81.9 - - - +
193D THR* 1.3 63.7 + - - +
204D PHE* 3.2 5.0 - - - +
205D GLN* 2.8 37.3 + - - +
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Residues in contact with THR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS* 3.7 1.9 - - - +
44C THR* 3.0 30.1 + - - +
60C TRP* 5.4 0.2 - - - -
90C ARG* 4.6 0.9 + - - -
702C CL 3.2 18.2 - - - +
176D VAL* 4.1 22.0 - - + +
179D HIS* 5.6 1.6 - - - +
180D TYR* 3.1 38.5 - - + -
190D ILE* 4.2 3.6 - - + -
192D GLY* 1.3 77.8 - - - +
194D ASN* 1.3 68.8 + - - +
203D GLU 3.2 15.5 - - - +
204D PHE* 3.8 12.6 - - + +
205D GLN* 3.7 2.8 + - - +
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Residues in contact with ASN 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS* 3.7 27.8 - - + +
702C CL 4.4 5.4 - - - -
162D TYR* 4.2 9.6 - - - -
163D CYS* 4.0 5.8 - - - -
193D THR* 1.3 77.7 - - - +
195D ALA* 1.3 82.6 + - - +
196D GLU* 3.5 12.5 + - - +
202D TRP* 3.6 6.9 - - - -
203D GLU* 3.0 50.4 + - - -
205D GLN* 3.0 28.8 + - - -
403D MN 4.2 1.9 + - - -
601D P3S 4.9 1.4 + - - -
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Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C CYS 5.2 1.0 + - - -
161D TYR 3.5 11.4 - - - +
162D TYR* 3.9 2.3 - - - -
163D CYS* 3.0 35.1 + - - +
164D GLY* 3.7 11.7 - - - +
170D ALA* 5.3 3.1 - - + -
173D ARG* 5.6 0.4 - - - +
194D ASN* 1.3 85.6 + - - +
196D GLU* 1.3 60.7 + - - +
201D GLN 4.9 0.7 - - - +
202D TRP* 3.3 40.0 - - + -
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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