Contacts of the helix formed by residues 230 - 240 (chain A) in PDB entry 1QWN
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 HIS 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A TYR* 4.0 15.5 - - - +
54A PHE* 3.7 14.0 - + + -
229A THR* 1.3 74.6 - - - +
231A TYR* 1.3 90.6 + + - +
232A SER* 2.9 45.1 + - - -
233A VAL* 2.9 30.6 + - + +
234A LYS* 3.1 10.2 + - - +
404A PHE* 5.5 1.6 + - - +
406A THR 3.9 10.5 - - - +
407A TYR* 3.7 5.0 - - - +
408A ALA* 3.5 20.5 - - + +
414A TYR* 2.9 44.8 + + - -
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Residues in contact with TYR 231 (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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54A PHE 4.8 3.9 + - - -
55A LYS 4.8 1.6 - - - -
56A ASP* 3.6 33.9 - - + +
64A GLN* 3.4 51.8 - - + +
229A THR 3.3 3.9 + - - -
230A HIS* 1.3 89.8 + + - +
232A SER* 1.3 75.4 + - - +
234A LYS* 3.5 13.4 + - + +
235A LYS* 3.1 21.8 + - - +
408A ALA* 3.3 21.8 + - + -
409A ASP* 4.4 2.9 - - - +
410A ARG* 3.5 17.3 - - - -
411A SER* 2.6 39.7 + - - -
414A TYR* 5.4 0.7 + - - -
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Residues in contact with SER 232 (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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52A MET* 3.5 21.0 - - - +
54A PHE* 3.6 24.9 - - - -
55A LYS 4.6 2.3 + - - -
230A HIS* 2.9 26.8 + - - -
231A TYR* 1.3 92.3 - - - +
233A VAL* 1.3 58.7 + - - +
235A LYS* 3.4 7.2 + - - +
236A GLU* 3.0 28.8 + - - +
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Residues in contact with VAL 233 (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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45A MET* 4.0 20.2 - - + -
48A LEU* 5.1 1.3 - - + -
49A TYR* 3.8 30.1 - - + +
52A MET* 4.0 13.0 - - + -
229A THR* 4.5 1.6 - - - +
230A HIS* 2.9 24.3 + - + +
232A SER* 1.3 74.5 - - - +
234A LYS* 1.3 66.4 + - - +
236A GLU* 3.3 3.4 + - - +
237A LEU* 2.9 46.7 + - + +
263A MET* 4.3 5.6 - - + -
404A PHE* 4.1 13.7 - - + -
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Residues in contact with LYS 234 (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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62A TRP* 5.3 2.5 - - + -
227A GLN* 2.8 35.2 + - - +
228A ARG* 4.9 0.4 - - - +
229A THR* 3.3 34.7 + - - +
230A HIS 3.1 7.6 + - - +
231A TYR* 3.7 13.9 - - + +
233A VAL* 1.3 75.3 - - - +
235A LYS* 1.3 58.6 + - - +
238A ALA* 2.8 32.8 + - - +
243A LEU* 4.0 10.3 - - - +
263A MET* 4.2 3.8 - - - -
264A MET 2.8 29.6 + - - +
265A PRO* 3.6 22.8 - - + +
266A PHE 2.8 27.8 + - - +
267A TYR* 5.3 2.5 - - - +
407A TYR* 5.5 1.3 - - - -
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Residues in contact with LYS 235 (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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55A LYS 5.1 6.6 + - - +
57A ILE* 3.8 32.7 + - - +
62A TRP* 5.0 4.0 - - - -
64A GLN 3.4 22.8 + - - +
65A GLY* 3.7 20.6 + - - -
66A TRP* 3.9 12.5 - - + -
231A TYR 3.1 14.4 + - - +
232A SER* 3.7 7.2 - - - +
233A VAL 3.2 0.2 - - - -
234A LYS* 1.3 80.2 - - - +
236A GLU* 1.3 62.5 + - - +
238A ALA* 3.7 4.4 - - - +
239A GLN* 3.0 55.4 + - - +
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Residues in contact with GLU 236 (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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48A LEU* 3.8 27.0 - - + +
51A ARG* 3.6 23.2 + - - -
52A MET* 4.3 18.9 - - + +
232A SER 3.0 17.5 + - - +
233A VAL* 3.3 6.7 + - - +
235A LYS* 1.3 78.5 - - - +
237A LEU* 1.3 62.6 + - + +
239A GLN* 3.4 23.3 + - - +
240A GLN* 3.5 28.0 + - + +
242A GLN* 6.0 0.4 - - - +
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Residues in contact with LEU 237 (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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43A VAL* 4.2 13.7 - - + -
45A MET* 5.3 0.9 - - - -
48A LEU* 4.2 20.4 - - + -
233A VAL* 2.9 28.9 + - + +
236A GLU* 1.3 73.8 - - + +
238A ALA* 1.3 66.9 + - - +
240A GLN 3.2 1.9 + - - -
241A ARG 3.0 3.8 + - - -
242A GLN* 2.8 70.8 + - + +
243A LEU* 3.9 10.5 - - + -
245A PHE* 4.6 5.2 - - + -
263A MET* 3.6 33.4 - - + -
400A LEU* 4.7 4.0 - - + -
404A PHE* 4.6 4.5 - - + -
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Residues in contact with ALA 238 (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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62A TRP* 4.1 12.1 - - + -
66A TRP* 3.8 20.9 - - + -
234A LYS 2.8 21.4 + - - +
235A LYS 3.7 3.8 - - - +
237A LEU* 1.3 78.1 - - - +
239A GLN* 1.3 63.0 + - - +
241A ARG* 3.1 18.6 + - - +
243A LEU* 3.8 23.9 - - + +
265A PRO* 5.4 0.9 - - + -
327A GLU 5.2 0.2 - - - +
328A LEU* 4.2 14.6 - - + +
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Residues in contact with GLN 239 (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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66A TRP* 3.4 30.7 - - + +
235A LYS* 3.0 48.1 + - - +
236A GLU* 3.7 22.7 - - - +
237A LEU 3.2 0.4 - - - -
238A ALA* 1.3 75.3 - - - +
240A GLN* 1.3 72.5 + - - +
241A ARG* 5.0 2.9 - - - +
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Residues in contact with GLN 240 (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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236A GLU* 3.5 23.3 + - + +
237A LEU 3.2 3.8 + - - +
238A ALA 3.1 0.6 - - - -
239A GLN* 1.3 92.2 + - - +
241A ARG* 1.3 71.5 + - - +
242A GLN* 3.4 32.2 + - + +
330A ARG* 3.3 13.7 + - - -
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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