Contacts of the helix formed by residues 347 - 360 (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 ASP 347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ILE* 4.4 8.3 - - - +
37D GLY* 4.5 11.7 - - - +
111D THR 4.7 3.3 - - - +
113D LEU* 3.2 36.9 - - + +
219D TRP* 3.1 32.6 + - + -
289D ASP 5.7 1.0 - - - -
290D PRO* 5.2 5.0 - - + +
345D ASN 3.8 0.4 + - - -
346D CYS* 1.3 72.5 - - - +
348D PRO* 1.3 61.5 - - - +
349D PHE* 2.9 32.6 + - - -
350D SER* 2.9 26.1 + - - -
351D VAL* 3.1 10.7 + - - +
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Residues in contact with PRO 348 (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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133D MET* 3.6 33.2 - - + -
215D GLY* 3.7 20.4 - - - +
218D LEU* 3.7 15.7 - - + -
219D TRP* 3.3 38.4 - - + +
222D ARG* 3.7 7.6 - - - +
346D CYS 3.7 8.2 - - - +
347D ASP* 1.3 82.6 - - - +
349D PHE* 1.3 56.9 + - - +
351D VAL* 4.2 2.5 - - + -
352D THR* 2.7 35.3 + - + +
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Residues in contact with PHE 349 (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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33D ILE* 4.6 9.4 - - + -
98D LEU* 4.7 4.7 - - + -
113D LEU* 3.6 22.0 - - + +
114D ARG* 3.5 35.7 - - + -
117D CYS* 3.5 9.1 - - + +
212D ILE* 3.7 32.8 - - + -
215D GLY* 3.5 29.4 - - - -
216D ASP* 3.4 22.2 - - - -
219D TRP* 3.6 18.6 - + - -
347D ASP* 2.9 22.9 + - - +
348D PRO* 1.3 78.0 - - - +
350D SER* 1.3 59.1 + - - +
352D THR* 3.8 2.9 - - - -
353D GLU* 3.1 30.0 + - - +
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Residues in contact with SER 350 (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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113D LEU* 4.0 23.3 - - - +
287D ALA* 2.7 36.0 + - - +
347D ASP* 2.9 15.5 + - - -
349D PHE* 1.3 76.9 - - - +
351D VAL* 1.3 66.1 + - - +
353D GLU* 4.0 5.1 - - - +
354D ALA* 3.1 24.3 + - - +
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Residues in contact with VAL 351 (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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133D MET* 4.5 3.1 - - + -
254D THR* 3.6 34.1 - - + +
287D ALA 4.1 3.6 - - - +
288D TYR* 3.8 34.9 - - + -
342D PRO* 4.0 8.1 - - + -
346D CYS* 3.6 37.9 - - + -
347D ASP 3.1 6.1 + - - +
348D PRO* 3.9 8.3 - - + +
349D PHE 3.4 0.2 - - - -
350D SER* 1.3 74.5 - - - +
352D THR* 1.3 66.3 + - + +
354D ALA* 3.1 12.8 + - - +
355D LEU* 3.2 17.3 + - + +
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Residues in contact with THR 352 (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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117D CYS* 3.6 10.2 - - - -
121D MET* 3.5 20.8 - - - +
131D PHE* 3.7 39.2 - - + -
133D MET* 4.4 8.1 - - - -
211D GLY 5.2 0.7 + - - -
214D MET* 3.8 21.5 - - + +
215D GLY 5.3 1.8 + - - +
348D PRO 2.7 29.9 + - - +
349D PHE* 3.8 1.9 - - - -
351D VAL* 1.3 75.2 - - + +
353D GLU* 1.3 64.6 + - - +
355D LEU* 3.4 4.4 + - - +
356D ILE* 3.2 24.6 + - - +
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Residues in contact with GLU 353 (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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113D LEU 4.1 4.0 - - - +
116D THR* 3.3 17.0 - - - +
117D CYS* 3.1 33.1 + - - +
120D ILE* 4.3 12.1 - - + -
121D MET* 4.2 8.1 - - - -
349D PHE 3.1 16.8 + - - +
350D SER* 4.0 4.2 - - - +
352D THR* 1.3 82.2 + - - +
354D ALA* 1.3 62.5 + - - +
356D ILE* 3.2 4.3 + - - +
357D ARG* 2.8 61.9 + - - +
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Residues in contact with ALA 354 (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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283D TYR* 4.1 18.6 - - + +
284D HIS* 3.5 22.7 - - + +
287D ALA* 4.0 20.2 - - + -
288D TYR* 4.5 2.0 - - + -
350D SER 3.1 18.3 + - - +
351D VAL 3.1 5.1 + - - +
353D GLU* 1.3 77.1 - - - +
355D LEU* 1.3 63.0 + - - +
356D ILE 3.2 0.2 + - - -
357D ARG* 3.3 3.8 + - - +
358D THR* 3.0 29.6 + - - -
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Residues in contact with LEU 355 (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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131D PHE* 4.0 18.8 - - + -
254D THR* 3.6 35.2 - - + +
256D PHE* 4.3 17.8 - - + -
277D LEU* 4.0 26.5 - - + -
284D HIS* 3.7 3.3 - - - -
288D TYR* 3.6 20.9 - - - +
337D PHE* 4.6 11.2 - - + -
339D ASP* 3.9 10.3 - - + +
351D VAL* 3.2 15.5 + - + +
352D THR 3.8 7.0 - - - +
354D ALA* 1.3 79.5 - - - +
356D ILE* 1.3 56.3 + - - +
359D CYS* 3.0 36.8 + - - +
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Residues in contact with ILE 356 (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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120D ILE* 3.5 23.8 - - + -
121D MET* 3.6 20.4 - - + -
124D VAL* 3.7 30.1 - - + -
129D PRO* 3.7 24.2 - - + -
131D PHE* 4.0 7.6 - - + -
256D PHE* 4.3 5.4 - - + -
352D THR 3.2 16.3 + - - +
353D GLU 3.7 4.9 - - - +
354D ALA 3.2 0.8 - - - -
355D LEU* 1.3 73.6 - - - +
357D ARG* 1.3 62.5 + - - +
360D LEU* 2.8 50.7 + - + +
361D LEU* 3.0 9.8 + - + -
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Residues in contact with ARG 357 (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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116D THR* 3.5 18.0 - - - +
120D ILE* 3.7 18.8 - - + +
280D ARG* 4.4 5.2 - - - +
283D TYR* 3.4 22.2 + - - +
353D GLU* 2.8 53.2 + - + +
354D ALA 3.3 4.5 + - - +
356D ILE* 1.3 77.9 - - - +
358D THR* 1.3 56.8 - - - +
361D LEU* 3.4 17.2 - - + -
362D ASN 3.1 10.2 + - - -
363D GLU* 2.6 74.8 + - - +
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Residues in contact with THR 358 (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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276D LYS* 3.8 37.5 - - + +
277D LEU* 4.2 8.5 - - + -
280D ARG* 2.9 44.2 + - + +
283D TYR* 4.1 0.3 - - - -
284D HIS* 2.9 32.1 + - - +
354D ALA 3.0 7.8 + - - -
355D LEU 4.4 0.9 - - - -
357D ARG* 1.3 79.0 - - - +
359D CYS* 1.3 60.7 + - - +
362D ASN* 3.8 14.0 - - - -
363D GLU 4.3 3.5 + - - +
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Residues in contact with CYS 359 (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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256D PHE* 4.1 21.5 - - + -
261D MET* 5.5 1.5 - - + +
273D ALA* 3.9 28.1 - - + +
276D LYS* 3.6 24.4 + - - +
277D LEU* 3.7 37.0 - - - -
337D PHE* 4.6 0.9 - - - -
355D LEU* 3.0 21.3 + - - +
358D THR* 1.3 81.2 - - - +
360D LEU* 1.3 68.4 + - + +
362D ASN* 4.4 1.3 - - - -
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Residues in contact with LEU 360 (chain D).
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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124D VAL* 3.9 24.2 - - + +
127D GLN* 3.0 35.1 + - + +
129D PRO* 4.5 3.1 - - + -
256D PHE* 4.6 5.2 - - + -
258D THR* 3.4 32.8 - - + -
261D MET* 5.6 2.7 - - + -
356D ILE* 2.8 42.9 + - + +
359D CYS* 1.3 86.9 - - + +
361D LEU* 1.3 60.6 + - - +
362D ASN* 3.2 15.9 + - - -
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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