Contacts of the strand formed by residues 304 - 311 (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 ILE 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B VAL* 5.6 4.3 - - + -
299B LEU* 4.0 34.0 - - + +
300B ILE 3.9 9.6 - - - +
301B GLY 3.1 30.4 - - - +
302B PRO 3.7 1.5 - - - +
303B GLY* 1.3 80.3 + - - +
305B SER* 1.3 67.2 + - - +
321B LEU* 4.7 15.0 - - + -
322B VAL 3.4 10.1 - - - +
323B THR* 4.7 4.0 - - - -
328B GLN* 3.7 21.8 - - + -
329B ILE 3.9 22.9 - - - +
330B LEU* 5.6 0.4 - - - -
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Residues in contact with SER 305 (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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299B LEU* 4.0 11.4 - - - -
304B ILE* 1.3 76.4 + - - +
306B GLY* 1.3 59.3 + - - +
321B LEU* 3.5 3.7 - - - +
322B VAL* 2.8 41.5 + - - +
324B GLN* 5.7 1.6 + - - -
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.9 9.7 - - - +
305B SER* 1.3 79.2 - - - +
307B ASP* 1.3 60.7 + - - +
308B VAL 4.2 0.4 + - - -
320B GLU 3.1 13.0 - - - -
321B LEU* 3.9 6.7 - - - -
322B VAL* 4.7 2.7 - - - -
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLY* 1.3 74.7 - - - +
308B VAL* 1.3 71.9 + - - +
309B ASP* 4.1 9.2 + - - +
318B VAL 3.5 2.9 - - - +
319B CYS* 3.3 4.5 - - - +
320B GLU* 2.9 49.5 + - + +
321B LEU* 4.5 0.8 - - - +
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Residues in contact with VAL 308 (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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296B LYS* 4.1 30.6 + - + +
297B PRO* 3.6 39.9 - - + +
299B LEU* 4.2 26.2 - - + -
306B GLY 4.2 0.6 + - - -
307B ASP* 1.3 80.3 + - - +
309B ASP* 1.3 67.1 + - - +
310B TYR* 3.6 2.6 + - + -
317B ALA* 5.0 0.7 - - + -
318B VAL 3.9 1.8 - - - -
319B CYS* 4.0 21.1 - - + -
321B LEU* 5.0 1.6 - - + -
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Residues in contact with ASP 309 (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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307B ASP* 3.9 9.1 + - - +
308B VAL* 1.3 70.9 - - - +
310B TYR* 1.3 67.0 + - - +
311B GLU* 5.7 1.0 - - - +
316B ILE* 3.9 1.4 - - - +
317B ALA* 3.4 3.8 - - - -
318B VAL* 2.9 52.9 + - + +
320B GLU* 6.2 0.2 - - - +
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Residues in contact with TYR 310 (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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291B GLU 5.1 0.5 + - - -
292B GLY 4.6 2.6 + - - -
294B PHE* 2.6 50.6 + + - -
295B THR* 3.9 2.3 - - - -
296B LYS* 3.6 55.8 + - + +
297B PRO* 4.2 2.9 - - + -
308B VAL* 3.6 6.2 + - + -
309B ASP* 1.3 81.2 + - - +
311B GLU* 1.3 74.4 + - - +
312B SER* 3.8 30.8 - - - -
315B PRO* 5.5 1.3 - - + +
316B ILE 3.7 8.5 - - - -
317B ALA* 4.5 1.1 - - + +
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Residues in contact with GLU 311 (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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309B ASP* 5.7 1.3 - - - +
310B TYR* 1.3 83.4 - - - +
312B SER* 1.3 70.0 + - - +
313B ALA* 3.0 43.1 + - - +
314B ARG 3.4 1.4 - - - +
316B ILE* 3.0 48.5 + - + -
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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