Contacts of the strand formed by residues 198 - 209 (chain A) in PDB entry 1QU2
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A TYR* 3.7 28.9 - - + -
193A LEU* 3.7 33.7 - - + -
194A ALA 3.5 13.9 - - - +
195A GLU* 3.1 31.0 + - - +
196A ALA 3.3 2.3 - - - +
197A GLU* 1.3 79.8 - - - +
199A GLU* 1.3 66.3 + - - +
200A TYR* 4.2 10.0 - - + +
395A PRO* 4.0 24.7 - - + -
396A HIS 3.5 8.1 - - - +
398A TRP* 4.7 1.1 - - - -
404A VAL* 3.8 18.4 - - + -
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Residues in contact with GLU 199 (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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197A GLU 4.1 0.2 + - - -
198A ILE* 1.3 76.0 - - - +
200A TYR* 1.3 65.3 + - - +
201A HIS* 2.5 33.6 + - + +
396A HIS* 3.0 37.0 + - - +
397A ASP 4.8 1.1 - - - +
398A TRP* 3.7 29.4 - - + +
401A LYS* 2.7 33.2 + - - +
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Residues in contact with TYR 200 (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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184A TYR* 3.4 13.7 + - - -
195A GLU* 3.3 26.6 + - - -
198A ILE* 4.2 9.4 - - + +
199A GLU* 1.3 77.0 - - - +
201A HIS* 1.3 71.1 + - - +
393A SER* 3.0 25.8 - - - +
394A TYR* 3.5 19.5 - - - -
395A PRO* 3.3 27.4 - - + +
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Residues in contact with HIS 201 (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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199A GLU* 2.5 34.2 + - + +
200A TYR* 1.3 81.5 + - - +
202A ASP* 1.3 70.8 + - - +
203A LYS 3.6 0.2 + - - -
393A SER* 4.4 1.3 - - - -
394A TYR 3.1 26.2 + - - +
396A HIS* 3.5 40.3 + + + +
401A LYS* 4.1 17.4 - - + +
1992A ZN 2.0 37.0 - - - -
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Residues in contact with ASP 202 (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 HIS* 1.3 80.8 - - - +
203A LYS* 1.3 58.6 + - - +
391A THR* 3.2 28.1 - - + +
392A HIS* 3.4 10.4 - - - -
393A SER* 4.0 13.9 + - - -
396A HIS* 4.4 2.9 + - - -
1992A ZN 4.5 4.2 - - - -
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Residues in contact with LYS 203 (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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202A ASP* 1.3 75.6 - - - +
204A ARG* 1.3 81.4 + - - +
205A SER* 3.4 20.1 + - - +
232A THR 5.8 1.4 + - - -
233A THR* 6.0 3.6 - - - +
235A TRP* 5.7 3.8 - - - +
367A TYR* 4.8 16.3 - - - -
368A ASP* 4.9 5.7 + - - -
372A LYS* 4.4 12.4 - - - +
391A THR* 3.4 23.5 - - - -
392A HIS* 3.1 13.0 + - - +
394A TYR* 4.1 48.1 + - + -
396A HIS* 4.2 9.6 - - + +
403A PRO* 4.7 16.9 - - + +
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Residues in contact with ARG 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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203A LYS* 1.3 82.2 - - - +
205A SER* 1.3 61.2 + - - +
372A LYS* 3.2 27.8 + - - +
389A PHE* 5.5 14.8 - - + -
390A ILE 3.8 5.4 - - - -
391A THR* 4.7 8.7 - - - +
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Residues in contact with SER 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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203A LYS* 3.4 22.5 + - - +
204A ARG* 1.3 75.2 - - - +
206A ALA* 1.3 59.7 + - - +
207A SER* 3.3 5.4 + - - -
232A THR* 3.3 29.8 + - - -
372A LYS* 5.1 2.0 - - - +
389A PHE* 4.6 3.3 - - - +
390A ILE* 3.0 33.5 + - - +
392A HIS* 2.9 27.3 - - - -
394A TYR* 5.2 1.2 - - - -
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Residues in contact with ALA 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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204A ARG 4.3 0.8 + - - -
205A SER* 1.3 70.9 - - - +
207A SER* 1.3 61.5 + - - +
208A ILE* 3.8 4.5 + - - +
231A THR 4.3 0.9 - - - +
232A THR 4.3 4.5 + - - +
234A PRO* 3.9 28.1 - - + +
372A LYS* 4.6 26.0 - - + +
387A LEU* 3.8 21.1 - - + -
388A ASP 3.0 13.0 - - - +
389A PHE* 4.3 17.6 - - + +
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Residues in contact with SER 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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205A SER 3.3 4.8 + - - -
206A ALA* 1.3 72.9 - - - +
208A ILE* 1.3 59.4 + - - +
209A TYR* 5.3 2.7 - - - -
230A TRP* 3.2 32.0 + - - -
231A THR 4.0 5.4 - - - -
232A THR* 4.1 11.2 - - - +
386A LYS 3.2 3.3 - - - +
388A ASP* 2.9 34.3 + - - +
390A ILE* 3.7 23.4 - - - +
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Residues in contact with ILE 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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206A ALA 4.3 4.3 - - - +
207A SER* 1.3 73.5 - - - +
209A TYR* 1.3 65.5 + - - +
210A VAL* 4.0 9.5 + - + +
229A ILE 3.8 0.2 - - - +
230A TRP* 3.0 25.1 - - - -
231A THR* 3.5 18.8 + - - +
234A PRO* 4.8 20.9 - - + -
237A ILE* 5.7 4.9 - - + -
375A THR* 6.4 0.2 - - + -
376A ASP* 4.3 13.7 - - - +
378A LEU 5.5 2.0 - - - +
379A THR* 4.4 7.2 - - - +
385A LEU* 3.4 22.0 - - + -
386A LYS 3.7 4.9 - - - +
387A LEU* 3.3 49.6 - - + +
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Residues in contact with TYR 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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207A SER* 5.3 2.2 - - - -
208A ILE* 1.3 79.1 - - - +
210A VAL* 1.3 54.3 + - - +
211A ALA 3.7 0.9 - - - -
228A ILE* 4.2 13.9 - - + -
229A ILE 3.1 7.4 - - - +
230A TRP* 3.6 32.1 + + + -
271A VAL 5.3 1.5 + - - -
274A ALA* 5.1 13.8 - - + +
275A LEU* 3.8 31.6 - - + -
321A THR* 3.2 38.1 - - + +
323A CYS* 5.1 0.2 - - - -
384A LEU 2.6 30.7 - - - +
385A LEU* 2.8 14.4 - - - +
386A LYS* 4.1 28.3 - - + +
388A ASP* 5.2 5.2 - - - -
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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