Contacts of the helix formed by residues 347 - 360 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H ILE* 4.7 4.2 - - - +
37H GLY* 4.6 9.2 - - - +
111H THR 4.6 5.9 - - - +
113H LEU* 3.7 26.2 + - + +
219H TRP* 3.2 31.9 + - + -
288H TYR 5.6 0.4 - - - -
289H ASP* 5.6 1.6 - - - +
290H PRO* 5.5 6.3 - - + +
345H ASN 3.9 0.4 + - - -
346H CYS* 1.3 73.6 - - - +
348H PRO* 1.3 68.5 - - - +
349H PHE* 2.6 40.7 + - - +
350H SER* 2.9 25.4 + - - -
351H VAL* 3.0 11.6 + - - +
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Residues in contact with PRO 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H MET* 3.8 22.4 - - + -
214H MET* 5.2 0.2 - - + -
215H GLY* 3.7 19.7 - - - +
218H LEU* 3.6 28.7 - - + -
219H TRP* 3.4 31.6 - - + +
222H ARG* 3.6 9.4 - - - +
346H CYS* 3.5 10.5 - - - +
347H ASP* 1.3 85.0 - - - +
349H PHE* 1.3 50.1 + - - +
351H VAL* 4.4 1.3 - - + +
352H THR* 2.6 41.9 + - - +
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Residues in contact with PHE 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ILE* 4.5 11.2 - - + -
98H LEU* 4.6 4.3 - - + -
113H LEU* 3.6 21.1 - - + +
114H ARG* 3.7 38.8 - - + -
117H CYS* 3.3 8.8 - - + +
212H ILE* 3.8 27.1 - - + -
215H GLY* 3.4 30.7 - - - -
216H ASP* 3.5 21.8 - - - -
219H TRP* 3.4 21.3 - + - -
347H ASP* 2.6 29.6 + - - +
348H PRO* 1.3 73.6 - - - +
350H SER* 1.3 54.9 + - - +
352H THR* 3.8 2.9 - - - -
353H GLU* 3.1 29.2 + - - +
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Residues in contact with SER 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H LEU* 4.2 25.4 - - - +
287H ALA* 2.6 36.9 + - - +
347H ASP* 2.9 13.7 + - - -
349H PHE* 1.3 77.0 - - - +
351H VAL* 1.3 64.4 + - - +
353H GLU* 3.5 6.5 + - - +
354H ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H MET* 4.5 1.8 - - + -
254H THR* 3.4 35.2 - - + +
287H ALA 4.4 2.7 - - - +
288H TYR* 3.7 35.6 - - + -
342H PRO* 4.1 7.0 - - + -
346H CYS* 3.5 37.5 - - + -
347H ASP 3.0 10.6 + - - +
348H PRO* 4.0 7.4 - - + +
350H SER* 1.3 75.5 + - - +
352H THR* 1.3 64.6 + - - +
354H ALA* 3.1 14.0 + - - +
355H LEU* 3.2 16.3 + - + +
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Residues in contact with THR 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H CYS* 3.6 4.7 - - - -
121H MET* 3.6 20.7 - - - +
131H PHE* 3.5 40.3 - - + -
133H MET* 4.5 8.1 - - - -
211H GLY 5.5 0.3 + - - -
214H MET* 3.8 20.9 - - + -
215H GLY 5.3 1.9 + - - -
254H THR* 4.9 2.2 - - + -
348H PRO 2.6 28.4 + - - +
349H PHE* 3.5 5.7 + - - -
351H VAL* 1.3 75.9 - - - +
353H GLU* 1.3 62.7 + - - +
355H LEU* 3.5 3.5 + - - +
356H ILE* 3.3 27.4 + - - +
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Residues in contact with GLU 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H LEU* 3.8 8.8 - - - +
116H THR* 3.2 17.8 - - - +
117H CYS* 3.2 34.5 + - - +
120H ILE* 3.9 14.1 - - + -
121H MET* 4.5 2.9 - - - -
349H PHE 3.1 18.5 + - - +
350H SER* 3.8 6.8 - - - +
351H VAL 3.1 0.6 - - - -
352H THR* 1.3 76.6 + - - +
354H ALA* 1.3 66.8 + - - +
356H ILE* 3.3 4.8 + - - +
357H ARG* 3.0 63.9 + - - +
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Residues in contact with ALA 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H TYR* 4.1 16.2 - - + -
284H HIS* 3.7 24.2 - - + +
287H ALA* 4.0 19.7 - - + -
288H TYR* 4.5 2.2 - - + -
350H SER 3.1 12.4 + - - +
351H VAL 3.1 9.7 + - - +
353H GLU* 1.3 74.8 - - - +
355H LEU* 1.3 63.6 + - - +
357H ARG* 3.1 6.3 + - - +
358H THR* 2.9 27.0 + - - -
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Residues in contact with LEU 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H PHE* 4.1 17.5 - - + -
254H THR* 3.7 32.5 - - + +
256H PHE* 4.5 21.8 - - + -
277H LEU* 3.9 30.3 - - + -
284H HIS* 4.0 3.4 - - - -
288H TYR* 3.8 19.5 - - - +
337H PHE* 4.8 4.0 - - + -
339H ASP* 4.2 6.5 - - + +
351H VAL* 3.2 18.9 + - + +
352H THR 3.8 6.7 - - - +
353H GLU 3.2 0.4 - - - -
354H ALA* 1.3 76.9 - - - +
356H ILE* 1.3 58.7 + - - +
359H CYS* 2.9 41.4 + - - +
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Residues in contact with ILE 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H ILE* 3.5 26.5 - - + -
121H MET* 4.0 19.5 - - + -
124H VAL* 3.6 31.9 - - + -
129H PRO* 3.8 13.5 - - + -
131H PHE* 3.8 17.9 - - + -
256H PHE* 3.8 9.4 - - + -
352H THR 3.3 14.4 + - - +
353H GLU 3.9 2.0 - - - +
354H ALA 3.3 0.6 - - - -
355H LEU* 1.3 74.4 - - - +
357H ARG* 1.3 59.7 + - - +
360H LEU* 2.9 50.5 + - + -
361H LEU* 3.0 11.3 + - + -
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Residues in contact with ARG 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H THR* 3.4 18.4 - - - +
120H ILE* 3.6 21.8 - - + +
280H ARG* 4.3 6.1 - - - +
283H TYR* 3.6 19.2 + - - -
353H GLU* 3.0 51.4 + - - +
354H ALA* 3.5 4.5 - - - +
356H ILE* 1.3 77.6 - - - +
358H THR* 1.3 59.4 + - - +
361H LEU* 3.5 17.6 - - + +
362H ASN 3.1 9.5 + - - -
363H GLU* 3.0 64.4 + - - +
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Residues in contact with THR 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H LYS* 3.2 45.3 - - + +
277H LEU* 3.8 17.5 - - + -
280H ARG* 2.9 33.2 + - + +
284H HIS* 2.7 29.3 + - - +
354H ALA 2.9 10.4 + - - -
355H LEU 4.2 0.2 - - - -
357H ARG* 1.3 75.3 - - - +
359H CYS* 1.3 63.5 + - - +
362H ASN* 3.6 13.9 - - - -
363H GLU 4.1 4.3 + - - +
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Residues in contact with CYS 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H PHE* 4.2 15.3 - - + -
273H ALA* 4.0 25.2 - - + +
276H LYS* 3.1 32.6 + - - +
277H LEU* 3.7 39.5 - - - -
355H LEU* 2.9 22.8 + - - +
358H THR* 1.3 79.6 - - - +
360H LEU* 1.3 75.8 + - + +
362H ASN* 3.6 0.4 - - - +
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Residues in contact with LEU 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H VAL* 4.1 29.4 - - + -
127H GLN* 3.8 29.1 + - + +
129H PRO* 4.6 2.5 - - + -
256H PHE* 4.3 1.8 - - + -
258H THR* 3.8 33.0 - - + -
261H MET* 4.8 5.8 - - + -
276H LYS* 5.4 0.2 + - - -
356H ILE* 2.9 38.7 + - + +
359H CYS* 1.3 94.5 - - + +
361H LEU* 1.3 65.0 + - - +
362H ASN* 3.2 15.8 + - - -
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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