Contacts of the helix formed by residues 278 - 286 (chain D) in PDB entry 6B0Z
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 SER 278 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ARG* 3.9 19.1 + - - +
130D ILE* 3.8 16.5 + - - +
132D HIS* 3.9 5.4 + - - -
277D GLN* 1.3 77.7 - - - +
279D ASP* 1.3 59.8 + - - +
280D SER 3.3 0.2 - - - -
281D VAL* 3.6 7.3 + - - +
282D ALA 3.3 14.2 + - - -
291D MET* 3.5 15.0 - - - +
502D C81 3.9 24.5 + - - +
504D C81 2.8 28.2 + - - -
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Residues in contact with ASP 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ARG* 3.9 26.2 + - - +
277D GLN* 3.3 23.2 + - - -
278D SER* 1.3 69.8 + - - +
280D SER* 1.3 60.9 + - - -
281D VAL 3.3 0.2 - - - -
282D ALA* 3.6 8.8 - - - +
283D GLN* 2.8 29.2 + - - +
288D LEU* 3.6 18.1 - - + +
291D MET* 4.2 6.7 - - - -
308D ALA 4.2 14.2 - - - +
501D NDP 6.2 0.3 - - - -
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Residues in contact with SER 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 3.7 32.6 + - - +
255B VAL* 3.9 19.3 - - - +
256B ALA* 4.1 4.0 - - - +
277D GLN* 3.1 30.2 + - - -
279D ASP* 1.3 79.2 + - - +
281D VAL* 1.3 60.4 + - - +
283D GLN* 3.3 11.5 + - - +
284D GLY* 3.0 23.4 + - - -
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 4.1 7.2 - - + -
259B MET* 3.5 18.6 - - + +
120D LEU* 4.1 1.8 - - + -
277D GLN 3.8 0.4 + - - +
278D SER* 3.6 8.4 + - - +
279D ASP 3.3 0.2 - - - -
280D SER* 1.3 77.5 - - - +
282D ALA* 1.3 56.4 + - - +
284D GLY 3.2 1.0 + - - -
285D TYR* 2.8 27.7 + - - +
502D C81 3.8 29.4 - - + -
504D C81 3.5 74.7 - - + +
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D SER 3.3 9.2 + - - +
279D ASP* 3.6 8.3 - - - +
280D SER 3.3 0.4 - - - -
281D VAL* 1.3 79.4 - - - +
283D GLN* 1.3 52.6 + - - +
285D TYR 3.3 0.3 + - - -
286D GLY 2.7 30.0 + - - -
287D SER* 2.8 29.2 + - - +
288D LEU* 4.0 15.5 - - + -
291D MET* 3.9 12.1 - - + -
502D C81 3.6 22.1 - - + +
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Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ASP 5.4 1.9 - - - +
253B ASP* 5.5 7.1 + - - +
256B ALA* 4.0 20.3 - - + +
260B LYS* 3.5 22.1 + - - +
279D ASP 2.8 21.3 + - - +
280D SER* 3.6 10.2 + - - +
282D ALA* 1.3 72.9 - - - +
284D GLY* 1.3 62.0 + - - +
286D GLY* 3.3 10.0 + - - -
288D LEU* 3.8 27.5 - - + +
501D NDP 4.9 14.3 - - - +
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Residues in contact with GLY 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ALA* 3.9 18.3 - - - +
259B MET* 3.7 30.1 - - - +
260B LYS* 3.7 19.0 - - - +
280D SER 3.0 12.2 + - - -
281D VAL 3.2 2.7 + - - -
283D GLN* 1.3 80.6 - - - +
285D TYR* 1.3 58.2 + - - +
286D GLY 3.4 0.3 + - - -
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Residues in contact with TYR 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU 5.6 1.6 - - - -
121B VAL* 5.4 7.0 - - + -
259B MET* 3.8 9.7 - - + +
117D ILE* 5.9 0.2 - - + -
118D PRO* 2.9 42.4 + - - +
119D ARG 3.2 8.5 + - - -
120D LEU* 3.7 34.8 - - + -
281D VAL 2.8 20.4 + - - +
282D ALA* 4.5 0.7 - - - -
284D GLY* 1.3 71.9 - - - -
286D GLY* 1.3 61.1 + - - +
287D SER* 3.7 16.4 - - - +
379D CYS* 4.2 21.1 - - - +
502D C81 3.5 32.1 - - + -
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Residues in contact with GLY 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LYS* 5.6 2.7 - - - -
282D ALA 2.7 11.9 + - - -
283D GLN* 3.3 8.6 + - - -
284D GLY 3.2 5.6 + - - -
285D TYR* 1.3 76.8 - - - +
287D SER* 1.3 55.2 + - - -
288D LEU* 3.6 3.1 - - - -
375D ASP* 4.5 24.9 - - - +
376D LEU* 6.0 1.4 - - - +
379D CYS* 5.3 5.4 - - - +
501D NDP 6.6 0.4 - - - -
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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