Contacts of the helix formed by residues 270 - 280 (chain A) in PDB entry 2QQ6
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 THR 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A TYR* 5.3 1.1 - - - +
72A ARG* 4.5 14.1 - - - +
80A GLY 4.5 5.4 - - - +
81A GLN* 4.2 9.8 + - - +
86A ILE* 3.6 28.5 - - + -
269A TYR* 1.3 84.6 - - - +
271A ARG* 1.3 63.3 + - - +
272A PHE* 3.6 18.2 + - + +
273A ASP* 3.1 35.0 + - - +
274A PHE* 3.2 14.9 + - - -
293A CYS 4.4 3.1 - - - +
298A GLU* 3.8 13.5 - - - +
302A ILE* 4.7 0.4 - - - -
246B GLU* 5.2 3.5 - - + +
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Residues in contact with ARG 271 (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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68A TYR* 4.4 5.7 - - - -
69A GLU* 3.6 34.6 + - - -
72A ARG* 4.4 4.0 - - - +
73A ARG* 5.6 0.4 - - - +
270A THR* 1.3 72.3 - - - +
272A PHE* 1.3 105.3 + - + +
274A PHE* 3.1 3.9 + - - +
275A ARG* 3.0 23.1 + - - +
298A GLU* 3.0 43.8 + - - +
301A ARG* 3.2 53.8 - - + +
302A ILE* 4.1 20.0 - - + +
305A LEU* 4.1 9.9 - - + +
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Residues in contact with PHE 272 (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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72A ARG* 3.6 18.2 - - - -
270A THR* 3.2 13.7 - - - +
271A ARG* 1.3 127.5 - - + +
273A ASP* 1.3 59.8 + - - +
275A ARG* 3.2 18.1 - - + +
276A GLU* 2.8 25.2 - - - +
244B PRO* 6.0 0.9 - - + -
246B GLU* 3.3 48.5 - - + -
247B ASN* 4.4 19.1 - - + -
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Residues in contact with ASP 273 (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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81A GLN 4.6 5.2 - - - +
248A LEU* 4.5 3.8 - - + +
268A VAL* 3.4 22.9 - - + +
269A TYR* 3.9 9.4 + - - +
270A THR* 3.1 30.4 + - - +
271A ARG 3.1 1.0 - - - -
272A PHE* 1.3 78.7 - - - +
274A PHE* 1.3 65.2 + - - +
275A ARG 3.0 1.6 - - - -
276A GLU* 3.1 24.8 + - - +
277A LEU* 3.0 18.7 + - - +
246B GLU 5.5 1.7 - - - +
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Residues in contact with PHE 274 (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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265A GLY* 3.6 13.0 - - - -
268A VAL* 3.3 48.7 - - + -
269A TYR 3.7 5.6 - - - -
270A THR 3.2 19.4 + - - -
271A ARG 3.1 6.7 + - - +
273A ASP* 1.3 74.4 - - - +
275A ARG* 1.3 66.0 + - - +
277A LEU* 3.5 23.1 - - + +
278A PHE* 2.9 44.6 + - + -
286A VAL* 4.4 7.6 - - + -
288A PRO* 3.3 30.1 - - + -
293A CYS* 4.9 0.4 - - + -
302A ILE* 3.3 43.7 - - + -
305A LEU* 4.6 2.0 - - + -
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Residues in contact with ARG 275 (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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271A ARG 3.0 13.1 + - - +
272A PHE* 3.2 20.6 - - + +
274A PHE* 1.3 77.5 - - - +
276A GLU* 1.3 67.2 + - - +
278A PHE* 4.0 3.8 - - - +
279A ALA* 3.2 28.9 + - - +
305A LEU* 4.0 19.5 - - + +
247B ASN* 2.9 40.9 + - - +
249B ASP* 3.4 26.2 + - - +
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Residues in contact with GLU 276 (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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248A LEU* 4.4 9.7 - - + +
272A PHE 2.8 22.0 - - - +
273A ASP* 3.4 25.3 - - - +
275A ARG* 1.3 89.7 + - - +
277A LEU* 1.3 65.3 + - - +
279A ALA* 3.3 6.8 + - - +
280A LYS* 3.2 37.7 + - - +
246B GLU 3.9 17.5 - - - +
247B ASN* 4.9 4.3 - - - -
248B LEU* 5.1 4.5 + - - +
280B LYS* 5.9 3.7 - - - -
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Residues in contact with LEU 277 (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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248A LEU* 3.7 26.8 - - + +
251A LEU* 4.4 8.1 - - + -
264A ALA* 4.5 8.1 - - + +
265A GLY* 5.0 0.2 - - - -
268A VAL* 4.6 9.2 - - + -
273A ASP 3.0 13.6 + - - +
274A PHE* 3.5 37.7 - - + +
276A GLU* 1.3 78.4 - - - +
278A PHE* 1.3 62.5 + - + +
280A LYS* 3.4 4.0 + - - +
282A ALA* 3.3 48.9 + - + +
283A VAL* 3.9 20.1 + - + -
286A VAL* 3.7 22.2 - - + -
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Residues in contact with PHE 278 (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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274A PHE* 2.9 37.7 + + + +
275A ARG* 4.0 3.8 - - - +
277A LEU* 1.3 79.3 - - + +
279A ALA* 1.3 60.3 - - - +
281A ARG* 2.8 25.9 + - - +
282A ALA 5.1 0.2 - - - +
283A VAL* 4.6 6.1 - - + +
286A VAL* 3.2 35.9 - - + -
302A ILE* 3.8 9.0 - - + -
305A LEU* 3.7 24.2 - - + +
306A ALA* 3.2 44.6 - - + -
309A ASP* 4.5 18.6 - - - +
311A ILE* 4.2 15.5 - - + -
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Residues in contact with ALA 279 (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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275A ARG* 3.2 21.4 + - - +
276A GLU* 3.3 10.3 + - - +
278A PHE* 1.3 79.4 - - - +
280A LYS* 1.3 59.3 + - + +
281A ARG* 3.0 13.2 + - - +
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Residues in contact with LYS 280 (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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248A LEU* 3.8 27.6 - - + -
249A ASP* 3.1 31.2 + - - +
252A ALA* 3.6 17.6 - - + +
256A ARG* 4.6 5.4 + - - -
276A GLU* 3.2 23.8 + - - +
277A LEU 3.9 4.3 - - - +
278A PHE 3.2 0.6 - - - -
279A ALA* 1.3 78.0 - - + +
281A ARG* 1.3 72.2 + - - +
282A ALA* 2.9 7.0 + - + +
276B GLU* 3.5 30.0 + - - -
280B LYS* 5.2 7.1 - - - +
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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