Contacts of the helix formed by residues 247 - 256 (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 ASN 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A THR* 5.0 0.5 + - - -
244A PRO 3.8 10.6 + - - +
246A GLU* 1.3 77.4 - - - +
248A LEU* 1.3 64.3 + - - +
249A ASP* 2.7 39.2 + - - +
250A ALA* 3.4 27.4 + - + +
251A LEU* 3.9 4.2 + - - +
272B PHE* 4.5 16.6 - - + +
275B ARG* 3.1 40.5 + - - +
276B GLU* 4.5 1.6 - - - +
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Residues in contact with LEU 248 (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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245A PRO* 3.9 22.0 - - + +
246A GLU 3.9 3.8 + - - +
247A ASN* 1.3 72.3 + - - +
249A ASP* 1.3 65.2 + - - +
250A ALA 3.2 0.4 - - - -
251A LEU* 3.2 13.6 + - + +
252A ALA* 3.1 21.8 + - - +
268A VAL* 5.9 10.3 - - + -
273A ASP* 4.5 5.4 - - + +
276A GLU* 4.4 10.5 - - + +
277A LEU* 3.7 51.6 - - + +
280A LYS* 3.8 19.0 - - + +
282A ALA* 4.0 4.2 - - + +
276B GLU* 5.0 4.5 + - - +
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Residues in contact with ASP 249 (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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247A ASN* 2.7 19.2 + - - +
248A LEU* 1.3 73.9 - - - +
250A ALA* 1.3 53.3 + - - +
252A ALA* 3.4 8.0 + - - +
253A GLU* 3.0 29.3 + - - +
256A ARG* 5.3 0.2 + - - -
280A LYS* 3.1 29.5 + - - +
275B ARG* 3.2 24.1 + - - +
276B GLU* 3.2 20.6 - - - +
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Residues in contact with ALA 250 (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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221A ILE* 3.8 23.4 - - + +
243A THR* 4.2 13.9 - - + +
244A PRO 5.9 0.2 - - - +
247A ASN* 3.4 24.1 + - + +
248A LEU 3.2 0.2 - - - -
249A ASP* 1.3 77.3 - - - +
251A LEU* 1.3 59.9 + - - +
253A GLU* 3.2 6.1 + - - +
254A VAL* 3.0 33.6 + - - +
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Residues in contact with LEU 251 (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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241A GLU* 4.7 5.6 - - - -
242A PRO* 3.6 36.3 - - + -
243A THR* 3.8 15.1 + - - +
247A ASN 3.9 2.6 + - - +
248A LEU* 3.2 19.3 + - + +
250A ALA* 1.3 75.1 - - - +
252A ALA* 1.3 57.0 + - - +
254A VAL* 3.1 4.4 + - - +
255A ARG* 2.7 35.9 + - - +
262A ILE* 4.1 9.8 - - + +
264A ALA* 3.9 16.6 - - + -
277A LEU* 4.4 7.0 - - + -
282A ALA* 3.5 24.2 - - + +
283A VAL* 3.6 17.9 - - + -
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Residues in contact with ALA 252 (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 3.1 11.8 + - - +
249A ASP* 3.4 13.5 - - - +
250A ALA 3.2 0.2 - - - -
251A LEU* 1.3 77.6 - - - +
253A GLU* 1.3 56.3 + - - +
255A ARG* 3.2 2.8 + - - +
256A ARG* 2.8 49.3 + - - +
280A LYS* 3.6 27.4 - - + +
281A ARG 4.5 1.9 - - - +
282A ALA* 4.1 14.3 - - + +
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Residues in contact with GLU 253 (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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221A ILE* 5.0 11.2 - - + -
225A ILE* 5.0 9.3 - - + +
249A ASP 3.0 15.5 + - - +
250A ALA* 3.4 12.3 - - - +
251A LEU 3.2 0.2 - - - -
252A ALA* 1.3 76.2 - - - +
254A VAL* 1.3 61.5 + - - +
256A ARG* 2.4 40.5 + - - +
257A SER* 3.3 21.1 + - - -
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Residues in contact with VAL 254 (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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221A ILE* 4.5 9.2 - - + -
224A SER* 4.0 28.0 - - - -
225A ILE* 4.5 8.5 - - + +
228A ALA* 4.7 14.6 - - + -
242A PRO* 4.0 22.4 - - + -
243A THR* 4.3 10.8 - - + -
250A ALA 3.0 20.4 + - - +
251A LEU* 3.5 8.1 - - - +
253A GLU* 1.3 75.7 - - - +
255A ARG* 1.3 62.0 + - - +
257A SER* 2.8 33.5 + - - +
258A THR* 3.7 5.2 + - - +
262A ILE* 4.5 12.1 - - + +
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Residues in contact with ARG 255 (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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251A LEU 2.7 21.5 + - - +
252A ALA* 3.6 5.2 - - - +
254A VAL* 1.3 72.3 - - - +
256A ARG* 1.3 58.2 + - - +
257A SER 3.2 4.5 + - - -
258A THR* 3.3 19.4 + - - +
260A THR 5.0 0.6 - - - +
262A ILE* 3.5 24.6 - - + +
281A ARG* 3.3 38.2 + - - +
282A ALA 4.0 5.2 - - - +
283A VAL* 3.3 27.1 + - - +
284A ASP* 2.7 47.6 + - - +
311A ILE* 4.9 7.5 - - - +
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Residues in contact with ARG 256 (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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249A ASP 5.4 0.2 + - - -
252A ALA* 2.8 36.5 + - - +
253A GLU* 2.4 47.0 + - - +
255A ARG* 1.3 76.8 - - - +
257A SER* 1.3 57.8 + - - +
258A THR 3.6 1.1 + - - -
280A LYS 4.6 5.9 + - - -
281A ARG* 5.8 1.2 + - - +
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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