Contacts of the helix formed by residues 273 - 279 (chain A) in PDB entry 3CQ6
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 HIS 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER* 4.8 3.1 - - - +
44A ALA* 3.4 24.3 + - + +
45A LEU* 3.8 37.2 - - + -
48A ASP* 2.9 41.5 - - + +
269A VAL* 3.2 18.0 + - - +
270A ALA 2.9 10.7 + - - +
272A ARG* 1.3 86.2 - - + +
274A SER* 1.3 60.6 + - - +
275A ALA 3.4 2.4 + - - -
276A ASP* 3.5 11.5 + - + +
277A THR* 3.1 23.4 + - - +
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 4.3 11.0 - - - +
81A LYS* 5.0 7.6 + - - +
230A PHE* 3.5 33.7 - - - -
270A ALA 3.5 0.4 + - - -
271A LEU 3.2 18.3 + - - -
272A ARG 3.5 1.6 + - - -
273A HIS* 1.3 77.6 - - - +
275A ALA* 1.3 60.7 + - - +
277A THR* 4.5 1.1 - - - -
278A LEU* 2.8 45.0 + - - +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 4.4 18.6 - - - +
273A HIS 3.4 1.0 + - - -
274A SER* 1.3 79.9 + - - +
276A ASP* 1.3 63.6 + - - +
278A LEU* 3.9 3.1 - - - +
279A GLY* 3.2 18.9 + - - -
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 3.7 26.4 + - - +
44A ALA* 5.9 1.6 - - - +
273A HIS* 3.5 14.4 + - + +
274A SER 3.4 0.6 - - - -
275A ALA* 1.3 78.3 - - - +
277A THR* 1.3 64.7 + - - +
279A GLY* 3.1 15.4 + - - -
280A THR* 4.2 2.9 + - - +
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 6.2 0.8 - - + +
42A SER* 5.2 6.9 + - - -
45A LEU* 4.1 18.8 - - + +
229A ALA 4.3 3.1 - - - +
230A PHE* 3.7 19.7 - - + +
231A ASP* 3.4 37.7 - - + +
270A ALA 5.0 1.4 + - - -
273A HIS* 3.1 18.4 + - - +
274A SER* 3.9 5.4 - - - -
276A ASP* 1.3 79.9 + - - +
278A LEU* 1.3 59.7 + - - +
279A GLY 3.1 0.2 - - - -
280A THR* 2.9 35.3 + - + +
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Residues in contact with LEU 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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78A TYR* 3.5 37.9 - - + +
82A GLN* 4.8 5.8 - - - +
202A GLU* 4.3 11.4 - - + -
229A ALA* 3.6 39.5 - - + +
230A PHE* 4.1 15.0 - - + +
274A SER* 2.8 31.9 + - - +
275A ALA* 3.9 3.6 - - - +
277A THR* 1.3 69.4 - - - +
279A GLY* 1.3 63.8 + - - +
280A THR* 3.1 2.8 + - - -
281A VAL* 3.2 27.9 + - + +
282A GLU* 4.6 0.9 + - - +
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Residues in contact with GLY 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 ALA 3.2 9.8 + - - -
276A ASP 3.1 13.6 + - - -
278A LEU* 1.3 77.3 - - - +
280A THR* 1.3 59.5 + - - +
281A VAL 3.3 0.7 + - - -
282A GLU* 3.5 30.5 + - - +
283A LYS* 4.2 8.9 + - - +
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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