Contacts of the strand formed by residues 212 - 219 (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 ASP 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A GLN* 3.4 8.9 + - - +
209A LEU* 2.7 35.8 + - - +
210A MET* 3.3 1.0 + - + -
211A ASN* 1.3 95.8 + - - +
213A PHE* 1.3 67.9 + - - +
214A VAL* 6.1 1.1 - - + -
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.6 26.2 - - + -
206A LYS* 3.9 28.7 - - + -
207A ALA 3.3 14.4 - - - +
208A GLN* 4.0 20.2 - - - -
212A ASP* 1.3 86.2 + - - +
214A VAL* 1.3 68.1 + - - +
266A ALA* 5.3 0.3 - - - -
267A PHE* 3.9 31.8 + + + +
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Residues in contact with VAL 214 (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* 3.4 33.0 - - + -
206A LYS* 4.1 0.7 - - - -
207A ALA* 2.9 31.8 + - + +
209A LEU* 4.1 22.7 - - + -
212A ASP* 5.7 0.9 - - + -
213A PHE* 1.3 77.7 - - - +
215A ALA* 1.4 56.7 + - - +
216A VAL* 3.9 7.6 - - + -
248A ILE* 3.5 31.4 - - + -
264A ILE* 3.5 18.8 - - + -
265A THR 3.6 3.8 - - - +
266A ALA* 5.3 0.7 - - - -
267A PHE* 3.4 11.9 - - - +
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Residues in contact with ALA 215 (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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204A VAL* 3.7 15.5 - - + -
205A TRP 3.5 4.9 - - - +
214A VAL* 1.4 71.6 - - - +
216A VAL* 1.3 61.1 - - - +
217A LYS 4.0 0.2 - - - -
263A LEU 3.6 1.4 - - - +
264A ILE* 3.3 5.0 - - - +
265A THR* 2.9 34.9 + - - +
266A ALA 3.7 2.2 - - - +
267A PHE* 3.6 8.4 - - + +
488A ADE 3.2 42.4 - - + +
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Residues in contact with VAL 216 (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* 4.0 9.6 - - + -
192A LEU* 4.0 14.1 - - + -
203A CYS 3.4 3.3 - - - +
204A VAL* 4.3 1.8 - - - -
205A TRP* 2.9 34.8 + - - +
207A ALA* 3.7 22.4 - - + -
214A VAL* 3.9 7.4 - - + -
215A ALA* 1.3 74.8 - - - +
217A LYS* 1.3 60.3 + - - +
218A ILE* 3.8 17.6 + - + -
262A TRP* 3.8 33.4 - - + -
263A LEU 3.7 2.5 - - - +
264A ILE* 3.6 21.8 - - + -
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY* 4.7 8.2 - - - -
200A ARG 5.1 1.0 - - - +
201A PHE* 5.1 1.3 - - - +
202A GLY* 3.8 26.7 - - - +
203A CYS 3.3 13.5 - - - +
204A VAL* 3.8 23.6 - - + +
215A ALA 4.0 0.6 - - - -
216A VAL* 1.3 72.3 - - - +
218A ILE* 1.3 64.4 + - - +
219A PHE* 3.6 30.5 - - + -
230A GLU* 3.5 17.1 + - - +
261A LEU 3.4 1.7 - - - +
262A TRP* 3.4 3.5 - - - -
263A LEU* 2.9 44.0 + - + +
339A ASP* 3.2 33.9 + - - +
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Residues in contact with ILE 218 (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* 4.0 20.4 - - + -
202A GLY* 3.2 4.2 - - - -
203A CYS* 2.9 32.6 + - + +
205A TRP* 3.4 34.8 - - + +
216A VAL* 3.8 13.0 - - + -
217A LYS* 1.3 77.9 - - - +
219A PHE* 1.3 67.6 + - - +
220A PRO* 3.9 3.8 - - - +
260A GLU* 3.7 26.0 - - + +
261A LEU 3.4 2.7 - - - +
262A TRP* 3.5 35.0 - - + +
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Residues in contact with PHE 219 (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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201A PHE* 3.3 23.6 - + + +
202A GLY* 4.2 0.2 - - - -
217A LYS* 3.6 46.9 - - + -
218A ILE* 1.3 79.1 - - - +
220A PRO* 1.3 74.8 - - - +
221A LEU 3.6 0.5 + - - -
223A ASP 3.9 17.9 - - - +
226A SER* 4.0 12.3 - - - -
227A TRP* 3.7 32.5 - + + -
230A GLU* 3.8 15.0 - - - -
260A GLU* 4.1 4.2 - - - +
261A LEU* 2.8 45.7 + - + +
263A LEU* 3.9 18.2 - - + -
341A GLY* 6.3 0.2 - - - -
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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