Contacts of the strand formed by residues 280 - 284 (chain B) in PDB entry 6DO5
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 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PRO* 3.7 2.6 - - - +
276B VAL* 3.0 41.1 + - + +
277B SER* 2.9 31.2 + - - +
278B SER 3.8 0.2 - - - -
279B ASP* 1.3 98.8 - - + +
281B LEU* 1.3 66.1 + - - +
299B THR* 4.6 15.9 - - + -
300B TYR 3.2 6.3 - - - +
301B CYS* 3.9 29.1 - - + +
302B ILE* 4.5 1.6 - - - +
308B ILE* 5.3 4.5 - - + +
359B VAL* 6.1 1.6 - - + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.8 17.7 - - + -
226B VAL* 3.6 29.4 - - + -
231B PHE* 3.7 40.6 - - + -
245B LEU* 5.3 3.4 - - + -
273B LEU* 3.7 27.0 - - + +
274B THR 3.3 1.3 - - - +
275B PRO* 3.8 7.6 - - + -
276B VAL* 5.0 1.3 - - - -
280B HIS* 1.3 78.7 - - - +
282B PHE* 1.3 61.3 + - - +
283B LEU 3.7 0.5 + - - -
298B TRP 3.7 0.3 - - - +
299B THR* 3.2 6.5 - - - -
300B TYR* 2.8 50.9 + - + +
302B ILE* 4.4 8.3 - - + -
307B TRP* 5.1 0.2 - - - -
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B SER* 3.5 3.2 + - - +
273B LEU* 3.2 6.5 - - - -
274B THR* 2.5 43.9 + - - +
276B VAL* 3.6 18.1 - - + +
280B HIS 4.3 0.2 + - - -
281B LEU* 1.3 72.4 - - - +
283B LEU* 1.3 59.9 + - - +
284B PHE* 3.8 19.3 - - + -
297B ALA* 3.8 16.4 - - + -
298B TRP 3.6 9.9 - - - -
299B THR* 4.4 10.8 - - + -
310B PHE* 3.8 28.0 - + - -
332B VAL* 3.7 23.8 - - + -
334B VAL* 5.4 0.7 - - + -
357B PHE* 3.4 47.3 - + + -
359B VAL* 4.5 10.8 - - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE* 4.1 7.0 - - + -
265B PRO* 3.6 39.0 - - + -
268B ARG* 3.9 16.6 - - - +
271B HIS* 3.5 32.8 - - + -
272B SER 3.3 15.9 - - - +
273B LEU* 4.4 7.0 - - + -
281B LEU 3.7 0.6 + - - -
282B PHE* 1.3 76.5 - - - +
284B PHE* 1.3 66.4 + - - +
297B ALA* 3.2 5.7 - - - +
298B TRP* 2.8 45.8 + - + +
307B TRP* 3.7 21.1 - - + -
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 4.6 0.9 - - - -
271B HIS* 4.6 0.7 - - - -
272B SER* 3.2 37.1 + - - +
282B PHE* 3.8 16.2 - - + -
283B LEU* 1.3 77.7 - - - +
285B GLY* 1.3 69.4 + - - +
295B SER* 3.7 25.6 - - - -
296B ASP 3.6 12.3 - - - -
297B ALA* 4.1 7.0 - - + -
312B HIS* 4.4 3.4 - + - -
314B TYR 5.2 0.2 - - - -
317B LYS 3.9 20.4 - - - -
319B ARG* 3.9 28.9 - - + -
322B HIS* 3.2 24.6 + + - -
334B VAL* 4.0 21.5 - - + -
355B LEU* 4.2 4.7 - - + -
357B PHE* 3.6 29.2 - + - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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