Contacts of the helix formed by residues 347 - 360 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33J ILE* 4.7 3.5 - - - +
37J GLY* 4.5 12.2 - - - +
111J THR 4.4 6.6 - - - +
113J LEU* 3.4 37.3 - - + +
219J TRP* 3.0 37.2 + - + -
289J ASP* 5.7 0.8 - - - +
290J PRO* 5.2 6.8 - - + +
346J CYS* 1.3 74.5 - - - +
348J PRO* 1.3 60.0 - - - +
349J PHE* 3.1 18.5 + - - -
350J SER* 2.8 27.2 + - - -
351J VAL* 3.1 10.9 + - - +
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Residues in contact with PRO 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J MET* 4.0 31.9 - - + -
215J GLY* 3.8 22.0 - - - +
218J LEU* 3.9 17.9 - - + -
219J TRP* 3.5 28.7 - - + +
222J ARG* 3.5 12.1 - - - +
346J CYS* 3.5 9.6 - - - +
347J ASP* 1.3 86.9 - - - +
349J PHE* 1.3 49.3 + - - +
351J VAL* 4.4 1.8 - - + +
352J THR* 2.7 43.4 + - + +
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Residues in contact with PHE 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ILE* 4.5 9.0 - - + -
98J LEU* 4.7 4.5 - - + -
113J LEU* 3.8 22.7 - - + +
114J ARG* 3.6 39.5 - - + -
117J CYS* 3.4 7.2 - - + +
212J ILE* 3.9 21.3 - - + -
215J GLY* 3.4 31.0 - - - -
216J ASP* 3.4 25.8 - - - -
219J TRP* 3.4 21.3 - + - -
347J ASP* 3.1 21.4 + - - +
348J PRO* 1.3 75.5 - - - +
350J SER* 1.3 61.5 + - - +
352J THR* 3.3 4.9 + - - -
353J GLU* 3.0 28.8 + - - +
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Residues in contact with SER 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU* 4.0 25.0 - - - +
287J ALA* 2.5 36.9 + - - +
347J ASP* 2.8 16.3 + - - -
349J PHE* 1.3 79.0 - - - +
351J VAL* 1.3 55.4 + - - +
353J GLU* 3.7 5.5 - - - +
354J ALA* 3.1 28.9 + - - +
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Residues in contact with VAL 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J MET* 4.2 7.9 - - + -
254J THR* 3.4 36.1 - - + +
287J ALA 4.1 3.1 - - - +
288J TYR* 3.4 38.1 - - + -
342J PRO* 4.0 9.2 - - + -
346J CYS* 4.0 31.2 - - + -
347J ASP 3.1 7.3 + - - +
348J PRO 3.8 4.5 - - - +
350J SER* 1.3 73.3 - - - +
352J THR* 1.3 67.7 + - - +
354J ALA* 3.4 2.9 + - - +
355J LEU* 3.2 25.4 + - + +
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Residues in contact with THR 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J CYS* 3.4 12.8 - - - -
121J MET* 3.5 15.2 - - - +
131J PHE* 3.9 28.4 - - + -
133J MET* 4.6 6.7 - - - -
211J GLY 5.1 0.7 - - - +
214J MET* 3.8 32.5 - - + -
215J GLY 5.0 1.4 + - - +
254J THR* 5.1 0.2 - - + -
348J PRO* 2.7 31.1 + - + +
349J PHE* 3.3 7.3 + - - -
351J VAL* 1.3 73.7 - - + +
353J GLU* 1.3 63.4 + - - +
355J LEU* 3.2 12.0 + - - +
356J ILE* 3.3 18.2 + - - +
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Residues in contact with GLU 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU* 4.0 4.2 - - - +
116J THR* 3.2 19.0 - - - +
117J CYS* 3.0 32.7 + - - +
120J ILE* 4.1 15.2 - - + +
121J MET* 4.2 8.1 - - - -
283J TYR* 5.5 0.2 + - - -
349J PHE 3.0 21.1 + - - +
350J SER* 3.7 5.3 - - - +
352J THR* 1.3 77.7 + - - +
354J ALA* 1.3 62.2 + - - +
355J LEU 3.3 0.2 + - - -
356J ILE* 3.4 2.6 + - - +
357J ARG* 3.1 56.4 + - - +
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Residues in contact with ALA 354 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283J TYR* 4.1 18.2 - - + -
284J HIS* 3.9 18.2 - - + +
287J ALA* 3.9 21.8 - - + -
288J TYR* 4.6 2.2 - - + -
350J SER 3.1 17.2 + - - +
351J VAL 3.9 4.5 - - - +
353J GLU* 1.3 77.8 - - - +
355J LEU* 1.3 63.6 + - - +
357J ARG* 3.4 5.1 + - - +
358J THR* 3.1 27.7 + - - -
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Residues in contact with LEU 355 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J PHE* 3.9 19.7 - - + -
254J THR* 3.8 33.9 - - + +
256J PHE* 4.1 22.2 - - + -
277J LEU* 4.1 19.1 - - + -
284J HIS* 3.9 10.3 - - + -
288J TYR* 3.7 19.1 - - - +
337J PHE* 4.7 2.9 - - + -
339J ASP* 3.9 11.4 - - + +
351J VAL* 3.2 15.4 + - + +
352J THR 3.2 9.4 + - - +
354J ALA* 1.3 78.6 - - - +
356J ILE* 1.3 53.7 + - - +
358J THR 3.5 0.2 + - - -
359J CYS* 2.8 45.6 + - - +
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Residues in contact with ILE 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J ILE* 3.6 25.1 - - + -
121J MET* 3.8 19.3 - - + -
124J VAL* 3.9 27.6 - - + -
129J PRO* 3.6 27.6 - - + -
131J PHE* 4.0 8.7 - - + -
256J PHE* 4.1 6.1 - - + -
352J THR 3.3 13.7 + - - +
353J GLU 3.9 2.2 - - - +
355J LEU* 1.3 73.6 - - - +
357J ARG* 1.3 61.6 + - - +
360J LEU* 2.8 51.9 + - + -
361J LEU* 2.9 12.0 + - + -
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Residues in contact with ARG 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J THR* 3.4 18.0 - - - +
120J ILE* 3.9 19.3 - - + +
280J ARG* 4.3 5.4 - - - +
283J TYR* 3.5 21.2 + - - -
353J GLU* 3.1 53.2 + - + +
354J ALA* 3.6 5.6 - - - +
356J ILE* 1.3 76.1 - - - +
358J THR* 1.3 58.2 + - - +
361J LEU* 3.6 17.8 - - + +
362J ASN 3.2 9.2 + - - -
363J GLU* 2.9 68.5 + - - +
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Residues in contact with THR 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J LYS* 3.7 39.2 - - + +
277J LEU* 3.7 21.5 - - + +
280J ARG* 2.9 37.7 + - + +
283J TYR* 4.4 0.3 - - - -
284J HIS* 3.0 23.9 + - - +
354J ALA 3.1 8.6 + - - -
355J LEU 4.1 0.2 - - - -
357J ARG* 1.3 79.3 - - - +
359J CYS* 1.3 61.3 + - - +
360J LEU 3.6 0.2 - - - -
362J ASN* 3.7 14.0 - - - -
363J GLU 4.3 3.2 - - - +
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Residues in contact with CYS 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256J PHE* 4.0 23.3 - - + -
261J MET* 5.8 0.3 - - - +
273J ALA* 3.9 25.1 - - + +
276J LYS* 3.5 28.2 + - - +
277J LEU* 3.7 39.0 - - - -
337J PHE* 4.5 0.2 - - - -
355J LEU* 2.8 27.8 + - - +
358J THR* 1.3 74.7 - - - +
360J LEU* 1.3 68.0 + - + +
362J ASN* 4.3 0.7 - - - -
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Residues in contact with LEU 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J VAL* 4.0 22.7 - - + -
127J GLN* 3.8 30.1 + - + +
129J PRO* 4.6 2.0 - - + -
256J PHE* 4.3 4.9 - - + -
258J THR* 3.6 35.0 - - + +
261J MET* 4.9 6.3 - - + -
356J ILE* 2.8 45.0 + - + +
359J CYS* 1.3 92.6 - - + +
361J LEU* 1.3 62.7 + - - +
362J ASN* 3.3 14.7 + - - -
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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