Contacts of the helix formed by residues 347 - 360 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.4 6.8 - - - +
37A GLY* 4.8 9.2 - - - +
111A THR 4.6 3.3 - - - +
113A LEU* 3.4 38.4 + - + +
219A TRP* 2.9 36.5 + - + -
287A ALA 5.3 1.4 + - - -
289A ASP* 5.6 0.8 - - - +
290A PRO* 5.4 5.3 - - + +
345A ASN 3.9 0.2 + - - -
346A CYS* 1.3 74.2 - - - +
348A PRO* 1.3 60.1 - - - +
349A PHE* 2.9 21.7 + - - -
350A SER* 2.8 26.7 + - - -
351A VAL* 3.1 9.7 + - - +
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Residues in contact with PRO 348 (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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133A MET* 3.9 33.0 - - + -
215A GLY* 3.7 20.6 - - - +
218A LEU* 4.1 15.0 - - + -
219A TRP* 3.3 30.1 - - + +
222A ARG* 3.6 11.7 - - - +
346A CYS* 3.5 10.0 - - - +
347A ASP* 1.3 86.9 - - - +
349A PHE* 1.3 49.3 + - - +
350A SER 3.2 0.2 - - - -
351A VAL* 3.8 3.1 - - + +
352A THR* 2.6 41.5 + - - +
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Residues in contact with PHE 349 (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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33A ILE* 4.7 9.2 - - + -
98A LEU* 4.5 5.2 - - + -
113A LEU* 3.7 22.9 - - + +
114A ARG* 3.6 33.9 - - + -
117A CYS* 3.3 8.7 - - + +
212A ILE* 3.7 30.3 - - + -
215A GLY* 3.4 31.4 - - - -
216A ASP* 3.3 25.1 - - - -
219A TRP* 3.5 17.9 - + - -
347A ASP* 2.9 23.2 + - - +
348A PRO* 1.3 77.2 - - - +
350A SER* 1.3 57.4 + - - +
352A THR* 3.7 3.6 - - - -
353A GLU* 3.0 30.4 + - - +
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Residues in contact with SER 350 (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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113A LEU* 4.1 24.6 - - - +
287A ALA* 2.9 33.4 + - - +
347A ASP* 2.8 13.8 + - - -
349A PHE* 1.3 78.4 - - - +
351A VAL* 1.3 64.1 + - - +
353A GLU* 3.6 6.0 + - - +
354A ALA* 3.1 24.8 + - - +
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Residues in contact with VAL 351 (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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133A MET* 4.7 2.5 - - + -
254A THR* 3.5 37.5 - - + +
287A ALA 4.0 2.9 - - - +
288A TYR* 3.8 37.4 - - + -
342A PRO* 3.9 7.9 - - + -
346A CYS* 3.7 38.1 - - + -
347A ASP 3.1 5.5 + - - +
348A PRO* 3.5 7.4 + - + +
350A SER* 1.3 75.3 - - - +
352A THR* 1.3 61.3 + - - +
354A ALA* 3.3 4.3 + - - +
355A LEU* 3.2 24.2 + - + +
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Residues in contact with THR 352 (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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117A CYS* 3.6 9.4 - - - -
121A MET* 3.4 21.7 - - - +
131A PHE* 3.6 40.2 - - + -
133A MET* 4.4 8.1 - - - -
211A GLY 5.3 0.5 + - - -
214A MET* 3.9 19.2 - - + +
215A GLY 5.4 1.2 + - - -
254A THR* 4.8 2.2 - - + -
348A PRO* 2.6 25.5 + - + +
349A PHE* 3.7 1.4 - - - -
351A VAL* 1.3 74.3 - - - +
353A GLU* 1.3 67.5 + - - +
355A LEU* 3.3 3.2 + - - +
356A ILE* 3.1 26.3 + - - +
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Residues in contact with GLU 353 (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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113A LEU* 4.0 4.7 - - - +
116A THR* 3.6 17.7 - - - +
117A CYS* 3.2 28.4 + - - +
120A ILE* 4.0 14.6 - - + -
121A MET* 3.9 7.4 - - - +
349A PHE 3.0 17.4 + - - +
350A SER* 3.8 5.6 - - - +
352A THR* 1.3 81.3 + - - +
354A ALA* 1.3 62.6 + - - +
356A ILE* 3.1 5.5 + - - +
357A ARG* 3.0 63.0 + - - +
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Residues in contact with ALA 354 (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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283A TYR* 4.4 16.2 - - + +
284A HIS* 3.6 22.0 - - + +
287A ALA* 3.9 20.2 - - + -
288A TYR* 4.4 1.3 - - + -
350A SER 3.1 19.0 + - - +
351A VAL 3.5 5.4 - - - +
352A THR 3.3 0.2 - - - -
353A GLU* 1.3 76.9 - - - +
355A LEU* 1.3 62.3 + - - +
357A ARG* 3.4 2.9 + - - +
358A THR* 3.1 28.8 + - - -
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Residues in contact with LEU 355 (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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131A PHE* 3.8 19.5 - - + -
254A THR* 3.7 34.3 - - + +
256A PHE* 4.1 26.0 - - + -
277A LEU* 4.1 25.1 - - + -
284A HIS* 3.9 3.1 - - - -
288A TYR* 3.6 20.0 - - - +
337A PHE* 4.7 2.7 - - + -
339A ASP* 3.9 12.3 - - + +
351A VAL* 3.2 19.0 + - + +
352A THR 3.8 5.8 - - - +
353A GLU 3.3 0.2 - - - -
354A ALA* 1.3 77.3 - - - +
356A ILE* 1.3 58.3 + - - +
359A CYS* 2.8 37.4 + - - +
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Residues in contact with ILE 356 (chain A).
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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120A ILE* 3.4 24.9 - - + +
121A MET* 3.6 21.1 - - + -
124A VAL* 3.8 23.3 - - + -
129A PRO* 3.7 24.0 - - + -
131A PHE* 4.0 6.5 - - + -
256A PHE* 3.9 10.3 - - + -
352A THR 3.1 12.7 + - - +
353A GLU 3.1 8.1 + - - +
355A LEU* 1.3 74.0 - - - +
357A ARG* 1.3 60.3 + - - +
360A LEU* 2.9 50.7 + - + +
361A LEU* 3.1 15.8 + - + -
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Residues in contact with ARG 357 (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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116A THR* 3.6 19.0 - - - +
120A ILE* 3.6 28.6 - - + +
280A ARG* 4.5 4.5 - - - +
283A TYR* 3.6 18.9 + - - -
353A GLU* 3.0 51.4 + - - +
354A ALA* 3.9 3.8 - - - +
356A ILE* 1.3 76.5 - - - +
358A THR* 1.3 59.8 + - - +
361A LEU* 3.4 12.1 - - + +
362A ASN 3.1 11.4 + - - -
363A GLU* 3.0 65.1 + - + +
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Residues in contact with THR 358 (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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276A LYS* 3.8 34.9 - - + +
277A LEU* 3.6 23.3 - - + +
280A ARG* 2.8 39.5 + - + +
283A TYR* 4.0 1.0 - - - -
284A HIS* 2.9 26.9 + - - +
354A ALA 3.1 6.9 + - - -
357A ARG* 1.3 81.0 - - - +
359A CYS* 1.3 60.3 + - - +
362A ASN* 3.7 13.3 - - - -
363A GLU 4.3 4.1 + - - +
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Residues in contact with CYS 359 (chain A).
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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256A PHE* 4.0 21.5 - - + -
261A MET* 6.0 0.2 - - - +
273A ALA* 4.0 24.7 - - + +
276A LYS* 3.5 26.8 + - - +
277A LEU* 3.5 39.9 - - - -
337A PHE* 4.7 0.4 - - - -
355A LEU* 2.8 25.4 + - - +
358A THR* 1.3 80.3 - - - +
360A LEU* 1.3 65.5 + - + +
362A ASN* 4.2 1.1 - - - -
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Residues in contact with LEU 360 (chain A).
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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124A VAL* 4.2 19.5 - - + -
127A GLN* 3.6 37.3 + - + +
129A PRO* 4.4 3.4 - - + -
256A PHE* 4.2 9.0 - - + -
258A THR* 3.3 36.1 - - + -
261A MET* 4.8 5.8 - - + -
356A ILE* 2.9 38.9 + - + +
359A CYS* 1.3 86.3 - - + +
361A LEU* 1.3 64.2 + - - +
362A ASN* 3.4 12.0 + - - +
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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