Contacts of the strand formed by residues 203 - 209 (chain A) in PDB entry 2QLU
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 CYS 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ILE* 4.0 34.3 - - - -
197A ALA 3.8 10.3 - - - -
198A ARG* 4.6 10.1 - - + -
199A GLY 4.2 0.9 - - - +
202A GLY* 1.3 76.2 - - - +
204A VAL* 1.3 64.7 + - - +
205A TRP* 3.7 14.1 - - - +
216A VAL 3.4 2.9 - - - +
217A LYS* 3.3 3.4 - - - +
218A ILE* 2.9 33.0 + - + +
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Residues in contact with VAL 204 (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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195A ILE* 3.7 4.2 - - - +
196A LYS* 2.8 27.4 + - + -
197A ALA* 2.8 31.6 + - + +
199A GLY* 5.3 2.7 - - - +
203A CYS* 1.3 73.7 - - - +
205A TRP* 1.3 65.6 - - - +
215A ALA* 3.7 30.3 - - + -
216A VAL 3.5 5.8 - - - +
217A LYS* 3.8 31.6 - - + +
267A PHE* 6.0 0.4 - - + -
339A ASP* 5.9 1.3 - - - +
488A ADE 3.9 25.6 - - + +
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Residues in contact with TRP 205 (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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192A LEU* 3.9 40.4 - - + -
193A LEU 4.1 6.1 - - - -
194A GLU* 3.3 40.2 - - - -
195A ILE* 3.7 29.6 - - + +
196A LYS* 4.8 0.2 - - - -
203A CYS* 3.7 19.5 - - - +
204A VAL* 1.3 79.4 - - - +
206A LYS* 1.3 64.6 + - - +
215A ALA* 3.5 5.8 - - - -
216A VAL* 2.9 34.5 + - + +
218A ILE* 3.4 32.3 - - + +
267A PHE* 5.4 0.2 - - - -
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Residues in contact with LYS 206 (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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193A LEU* 2.9 32.5 + - + +
194A GLU* 2.8 36.3 + - + +
196A LYS* 3.8 31.0 - - + +
204A VAL 4.2 0.8 + - - -
205A TRP* 1.3 74.7 - - - +
207A ALA* 1.3 66.3 + - - +
213A PHE* 3.9 37.9 - - - -
214A VAL 4.1 2.5 - - - -
267A PHE* 3.6 42.8 - - + -
269A ASP* 4.7 5.6 + - - -
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Residues in contact with ALA 207 (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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190A LEU* 4.2 4.0 - - + -
191A GLN 3.2 13.9 - - - +
192A LEU* 4.0 12.3 - - + -
193A LEU* 4.0 6.7 - - - +
205A TRP 4.3 0.2 - - - +
206A LYS* 1.3 76.3 - - - +
208A GLN* 1.3 59.8 + - - +
213A PHE* 3.3 9.7 - - - +
214A VAL* 2.9 37.0 + - + +
216A VAL* 3.7 29.8 - - + -
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Residues in contact with GLN 208 (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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189A SER 2.9 21.9 - - - +
190A LEU* 3.3 4.5 - - - +
191A GLN* 2.7 46.1 + - + +
193A LEU* 4.0 10.5 - - + +
207A ALA* 1.3 72.9 - - - +
209A LEU* 1.3 64.0 + - - +
210A MET 3.5 20.0 + - - +
211A ASN* 3.8 5.1 + - - +
212A ASP* 3.4 28.4 + - - +
213A PHE* 4.0 18.8 - - + -
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Residues in contact with LEU 209 (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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189A SER* 3.3 21.5 - - - +
190A LEU* 3.9 34.1 - - + +
207A ALA 4.3 0.6 + - - -
208A GLN* 1.3 75.8 - - - +
210A MET* 1.3 80.8 + - + +
211A ASN 3.1 2.1 + - - -
212A ASP* 2.7 24.6 + - - +
214A VAL* 4.1 27.4 - - + -
248A ILE* 5.0 10.1 - - + -
264A ILE* 4.8 6.5 - - + -
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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