Contacts of the helix formed by residues 281 - 286 (chain B) in PDB entry 4U7B
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 ALA 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B THR* 5.9 0.4 - - - -
156B ASP* 5.0 3.8 - - + +
247B LEU* 5.6 2.0 - - + -
273B HIS* 3.7 22.0 - - + +
277B SER 3.9 2.0 - - - +
278B PRO* 2.9 12.2 + - + +
279B ASP 3.5 0.6 - - - -
280B LEU* 1.3 76.7 - - - +
282B PRO* 1.3 70.9 - - - +
283B SER* 3.2 3.1 - - - +
284B ASP* 2.7 35.9 + - + +
285B TYR* 3.1 11.6 + - - -
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Residues in contact with PRO 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B THR* 4.2 9.2 - - + +
197B TRP* 3.4 27.4 - - + -
247B LEU* 4.1 17.3 - - + -
280B LEU 3.1 12.6 - - - +
281B ALA* 1.3 80.3 - - - +
283B SER* 1.3 64.8 + - - +
285B TYR* 3.3 22.0 - - + +
286B HIS* 2.9 28.6 + - + +
287B LEU 3.4 0.7 + - - -
325B GLY 4.4 2.0 - - - +
326B ILE* 4.2 8.3 - - + -
329B LEU* 3.4 30.7 - - + -
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 3.4 14.0 + - - +
155B GLY* 3.7 11.3 + - - -
156B ASP* 3.8 26.0 - - - -
195B VAL 5.3 0.4 - - - -
197B TRP* 3.0 30.1 + - - +
281B ALA* 2.9 3.9 + - - -
282B PRO* 1.3 75.2 - - - +
284B ASP* 1.3 56.8 + - - +
287B LEU* 3.4 4.4 - - - +
288B PHE* 2.7 48.0 + - - -
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.1 23.3 - - - +
157B GLU 5.5 0.2 - - - +
278B PRO* 3.5 24.6 - - - +
281B ALA* 2.7 26.3 + - - +
283B SER* 1.3 73.3 - - - +
285B TYR* 1.3 63.5 + - - +
288B PHE* 3.5 18.5 - - - -
289B ALA 3.2 11.6 + - - -
55D G 3.2 30.0 + - + +
56D A 3.8 25.3 + - - +
57D T 4.3 9.0 + - - +
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B PRO 4.1 5.4 - - - +
279B ASP 3.3 16.2 - - - -
280B LEU 3.7 6.5 - - - -
281B ALA 3.1 25.0 + - - -
282B PRO* 3.3 22.5 - - + +
284B ASP* 1.3 79.2 - - - +
286B HIS* 1.3 75.6 + - + +
289B ALA* 3.1 15.4 - - - +
325B GLY 2.9 22.5 + - - -
328B LYS* 3.9 12.5 - - + +
329B LEU* 3.5 27.0 + - + +
332B ARG* 3.4 46.2 - - - +
4C G 3.6 9.2 + - - -
55D G 3.3 25.1 + - - +
56D A 4.0 3.6 - - + -
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Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TRP* 4.3 12.1 - + - -
282B PRO 2.9 18.6 + - - +
284B ASP 3.3 0.4 - - - -
285B TYR* 1.3 91.2 - - + +
287B LEU* 1.3 67.0 + - - +
288B PHE 3.7 0.2 - - - -
289B ALA* 4.0 1.5 - - - +
290B SER* 3.3 22.2 + - - -
321B PHE* 2.8 64.0 + + - -
324B ARG* 4.2 6.3 - - - -
325B GLY* 3.2 26.9 - - - -
328B LYS* 3.4 22.7 + - - -
4C G 4.0 11.7 - - - +
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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