Contacts of the helix formed by residues 289 - 299 (chain B) in PDB entry 3OAA
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 ASP 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B TYR* 2.6 30.1 + - - -
274B SER* 4.6 0.3 + - - -
279B ARG* 5.6 3.1 - - - -
287B PRO* 3.3 21.5 - - - +
288B GLY* 1.3 74.4 - - - +
290B VAL* 1.3 59.2 + - - +
291B PHE* 3.1 3.6 - - - -
292B TYR* 2.9 33.4 + - + +
293B LEU* 2.9 10.6 + - - +
296B ARG* 5.3 6.4 + - - -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ALA* 4.2 25.1 - - + +
270B TYR* 5.1 2.9 - - + -
286B PHE* 4.3 17.0 - - + -
287B PRO* 3.1 20.2 + - + +
288B GLY 3.3 2.2 - - - +
289B ASP* 1.3 80.5 + - - +
291B PHE* 1.3 64.4 + - + +
293B LEU* 3.2 27.6 - - + +
294B HIS* 3.4 16.8 + - + -
340B PHE* 3.4 35.7 - - + -
341B VAL* 5.0 5.4 - - + -
344B ASN* 3.9 10.0 - - - +
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLY 4.4 5.3 + - - +
289B ASP* 3.1 0.8 - - - +
290B VAL* 1.3 81.0 - - + +
292B TYR* 1.3 56.8 + + + +
293B LEU 3.3 0.3 + - - -
294B HIS* 3.3 4.1 + - - +
295B SER* 2.7 56.2 + - - -
340B PHE* 6.1 1.1 - - + -
344B ASN* 3.8 41.1 - - + +
347B SER* 4.2 17.5 - - - -
348B ILE* 3.9 26.7 - - + +
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Residues in contact with TYR 292 (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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289B ASP* 2.9 24.1 + - + +
291B PHE* 1.3 78.8 - + + +
293B LEU* 1.3 65.3 + - - +
295B SER* 3.9 9.2 - - - -
296B ARG* 3.1 83.9 + - + +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 4.0 16.2 - - + -
240B TYR* 2.5 52.4 + - + +
266B GLN* 3.7 21.6 - - - +
267B ALA* 4.2 17.0 - - - -
270B TYR* 3.7 40.6 - - + -
289B ASP* 2.9 9.8 + - - +
290B VAL* 3.2 22.0 - - + +
292B TYR* 1.3 79.5 - - - +
294B HIS* 1.3 65.5 + - + +
296B ARG* 3.6 17.1 - - - +
297B LEU* 3.7 5.5 - - - +
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Residues in contact with HIS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.3 27.7 + - + +
266B GLN* 3.1 33.3 + - - -
267B ALA* 3.8 12.7 - - + +
290B VAL* 3.4 12.2 + - + +
291B PHE* 3.3 4.5 + - - +
293B LEU* 1.3 81.1 - - + +
295B SER* 1.3 60.1 + - - +
297B LEU* 3.2 6.8 + - + +
298B LEU* 2.9 37.4 + - + +
341B VAL* 3.6 29.2 + - + +
344B ASN* 5.2 4.8 - - + +
345B VAL* 3.4 23.2 + - + +
348B ILE* 3.6 17.9 - - + -
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 2.7 46.8 + - - -
292B TYR* 3.3 12.2 + - - -
294B HIS* 1.3 73.1 - - - +
296B ARG* 1.3 57.2 + - - +
298B LEU* 4.1 0.5 - - - +
299B GLU* 2.9 43.5 + - - +
348B ILE* 3.4 15.0 - - - +
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Residues in contact with ARG 296 (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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130B GLU* 3.0 40.7 + - - -
131B ALA 4.7 8.2 - - - +
133B ALA* 5.2 2.5 + - - +
236B TYR* 4.7 9.1 + - - -
240B TYR* 3.2 28.9 + - + -
270B TYR* 5.6 3.4 - - - -
289B ASP* 5.3 4.4 + - - -
292B TYR* 3.1 74.7 + - + +
293B LEU* 3.6 18.3 - - - +
295B SER* 1.3 79.0 + - - +
297B LEU* 1.3 62.1 + - - +
299B GLU* 4.1 7.3 - - - +
300B ARG* 3.4 26.7 + - - -
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Residues in contact with LEU 297 (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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239B PRO* 3.6 37.7 - - + +
240B TYR* 3.8 25.6 - - + -
243B CYS* 4.0 0.4 - - + -
260B TYR* 3.6 37.9 + - + +
263B LEU* 3.9 24.7 - - + -
266B GLN* 4.3 9.0 - - - +
293B LEU 3.7 10.3 - - - +
294B HIS* 3.2 10.7 + - - +
295B SER 3.1 0.6 - - - -
296B ARG* 1.3 79.8 - - - +
298B LEU* 1.3 61.6 + - + +
300B ARG* 3.0 34.7 - - - +
301B ALA 4.0 1.0 + - - -
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Residues in contact with LEU 298 (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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164B ARG* 2.8 29.2 + - + +
260B TYR* 3.9 27.8 - - + -
263B LEU* 4.4 9.9 - - + -
294B HIS* 2.9 15.4 + - + +
297B LEU* 1.3 73.3 - - + +
299B GLU* 1.3 64.8 + - - +
300B ARG 3.1 2.2 - - - -
301B ALA* 3.2 20.0 + - - +
326B ALA* 4.8 2.7 - - + -
328B PRO* 3.9 23.1 - - + -
345B VAL* 4.1 15.9 - - + -
348B ILE* 3.6 37.5 - - + -
349B THR* 3.6 18.8 - - + -
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Residues in contact with GLU 299 (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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133B ALA* 3.4 23.4 - - + +
139B ARG* 3.3 33.3 + - - -
164B ARG* 3.5 22.6 + - - +
295B SER* 2.9 30.6 + - - +
296B ARG* 4.2 6.3 - - - +
297B LEU 3.2 0.2 - - - -
298B LEU* 1.3 74.9 - - - +
300B ARG* 1.3 65.7 + - - +
301B ALA 3.2 4.0 + - - +
348B ILE* 5.6 3.1 - - + -
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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