Contacts of the strand formed by residues 280 - 287 (chain B) in PDB entry 1OPO
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 GLY 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B ALA* 1.3 75.0 - - - +
281B LYS* 1.3 66.2 + - - -
282B TRP* 3.2 15.0 + - - -
322B VAL* 3.5 3.4 - - - -
323B THR* 2.7 38.7 + - - +
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Residues in contact with LYS 281 (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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280B GLY* 1.3 73.8 - - - +
282B TRP* 1.3 73.3 + - - +
321B LEU 3.5 4.7 - - - -
322B VAL* 4.4 19.3 - - + -
347B ARG* 4.1 2.6 - - - +
348B MET* 3.2 58.2 + - + +
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Residues in contact with TRP 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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114B VAL* 4.3 15.5 - - + -
262B TYR* 3.6 38.4 - + + -
276B VAL* 3.6 20.2 - - + +
278B ALA* 4.0 13.5 - - + -
279B ALA 3.8 17.0 - - - -
280B GLY* 3.2 19.7 + - - -
281B LYS* 1.3 82.1 - - - +
283B CYS* 1.3 63.3 + - - +
284B ILE* 4.9 7.4 - - + -
319B CYS 4.4 0.2 - - - -
321B LEU* 2.8 44.0 + - + +
323B THR* 2.9 30.2 - - + +
345B VAL* 4.2 18.2 - - + -
346B TYR 3.5 16.2 - - - +
347B ARG* 3.8 23.3 - - + -
348B MET* 3.5 11.4 - - - +
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Residues in contact with CYS 283 (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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282B TRP* 1.3 77.4 - - - +
284B ILE* 1.3 64.4 + - - +
285B ILE* 4.3 20.0 - - - -
318B VAL* 4.8 7.4 - - - -
319B CYS 3.2 10.3 - - - +
320B GLU* 4.4 12.6 - - + -
344B VAL 3.8 0.7 - - - +
345B VAL* 3.3 3.5 - - - -
346B TYR* 2.8 51.6 + - + +
348B MET* 4.1 15.5 - - + -
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Residues in contact with ILE 284 (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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263B VAL* 4.9 7.4 - - + -
274B LEU* 4.3 21.8 - - + -
276B VAL* 4.8 14.8 - - + -
282B TRP* 4.9 4.7 - - + -
283B CYS* 1.3 81.0 - - - +
285B ILE* 1.3 72.3 + - - +
286B VAL* 4.1 8.7 - - + -
317B ALA 3.8 1.6 - - - +
319B CYS* 2.9 40.8 + - + +
321B LEU* 3.9 24.7 - - + -
330B LEU* 4.3 16.8 - - + -
343B TRP* 4.5 3.8 - - + -
344B VAL 3.2 10.3 - - - +
345B VAL* 3.9 23.8 - - + -
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Residues in contact with ILE 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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283B CYS* 4.3 14.8 - - - -
284B ILE* 1.3 78.1 - - - +
286B VAL* 1.3 65.3 - - - +
287B ARG* 4.0 32.9 + - - +
316B ILE* 4.5 8.1 - - + -
317B ALA 3.4 10.5 - - - +
318B VAL* 4.5 15.3 - - + -
342B GLN 3.6 0.3 - - - +
343B TRP* 2.9 26.4 - - - -
344B VAL* 3.0 22.5 + - + +
346B TYR* 4.2 22.7 - - + -
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Residues in contact with VAL 286 (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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272B LEU* 6.1 1.8 - - + -
274B LEU* 5.2 2.2 - - + -
284B ILE* 4.4 16.6 - - + +
285B ILE* 1.3 75.9 - - - +
287B ARG* 1.3 65.6 + - - +
294B PHE* 3.8 24.6 - - + -
297B PRO* 5.8 0.2 - - + -
316B ILE* 3.2 8.5 - - - +
317B ALA* 2.8 44.9 + - + +
319B CYS* 5.3 1.6 - - - -
330B LEU* 4.8 6.5 - - + -
332B ILE* 4.7 24.2 - - + -
341B LEU* 4.2 20.9 - - + -
342B GLN 3.3 9.6 - - - +
343B TRP* 4.4 7.6 - - + -
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Residues in contact with ARG 287 (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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285B ILE* 4.0 24.8 + - - +
286B VAL* 1.3 74.0 - - - +
288B GLY* 1.3 59.4 + - - +
294B PHE* 4.0 4.7 - - - -
314B ARG* 3.9 30.9 - - - +
315B PRO 3.4 4.5 - - - +
316B ILE* 3.6 30.3 - - - +
341B LEU* 3.7 7.3 - - - +
342B GLN* 2.8 59.6 + - + +
343B TRP* 5.5 1.4 - - - +
344B VAL* 4.9 11.3 - - - +
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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