Contacts of the strand formed by residues 316 - 323 (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 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ILE* 4.5 8.3 - - + -
286B VAL 3.2 12.3 - - - +
287B ARG* 3.6 26.0 - - - +
294B PHE* 3.6 6.0 - - - -
309B ASP 3.9 1.4 - - - +
310B TYR* 3.7 2.4 - - - -
311B GLU* 3.0 46.1 + - + -
314B ARG* 2.9 20.5 + - + +
315B PRO* 1.3 74.8 - - - +
317B ALA* 1.3 70.3 + - - +
318B VAL* 4.8 10.8 - - + -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE 3.8 0.5 - - - +
285B ILE* 3.4 6.8 - - - +
286B VAL* 2.8 39.8 + - + +
294B PHE* 3.9 15.2 - - + -
297B PRO* 4.0 30.3 - - + -
308B VAL* 5.0 0.7 - - + -
309B ASP 3.4 7.9 - - - +
310B TYR* 4.5 2.5 - - + -
316B ILE* 1.3 75.3 - - - +
318B VAL* 1.3 65.7 + - - +
319B CYS* 4.0 6.1 - - - -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B CYS* 4.8 11.2 - - - -
284B ILE 3.9 2.7 - - - -
285B ILE* 4.5 19.1 - - + -
307B ASP* 3.5 4.3 - - - +
309B ASP* 2.9 46.1 + - + +
316B ILE* 4.8 13.7 - - + -
317B ALA* 1.3 77.4 - - - +
319B CYS* 1.3 60.7 + - - +
320B GLU* 4.0 21.5 + - + +
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Residues in contact with CYS 319 (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* 3.2 5.6 - - - -
284B ILE 2.9 43.8 + - - +
286B VAL* 5.3 2.2 - - - -
297B PRO* 4.3 14.1 - - - -
307B ASP 3.3 7.0 - - - +
308B VAL* 4.0 21.1 - - + -
317B ALA* 4.4 4.7 - - - -
318B VAL* 1.3 80.7 - - - +
320B GLU* 1.3 63.3 + - - +
321B LEU* 3.6 24.1 + - + +
330B LEU* 4.1 21.3 - - + -
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Residues in contact with GLU 320 (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 3.6 5.6 - - - -
283B CYS* 4.4 15.6 - - - -
306B GLY* 3.1 4.0 - - - -
307B ASP* 2.9 48.8 + - + +
309B ASP* 6.2 0.2 - - - +
318B VAL* 4.7 14.5 - - + +
319B CYS* 1.3 73.9 - - - +
321B LEU* 1.3 61.4 + - - +
322B VAL* 5.4 0.7 - - - +
348B MET* 4.3 21.8 - - + +
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Residues in contact with LEU 321 (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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276B VAL* 5.3 7.6 - - + -
281B LYS* 3.5 1.6 - - - -
282B TRP* 2.8 45.3 + - + +
284B ILE* 3.9 27.6 - - + -
299B LEU* 3.8 26.0 - - + -
304B ILE* 4.7 13.7 - - + -
305B SER 3.5 10.5 - - - +
306B GLY* 3.9 7.0 - - - -
307B ASP 4.5 2.2 - - - +
308B VAL* 5.0 0.9 - - + -
319B CYS* 4.0 22.4 - - + +
320B GLU* 1.3 81.6 - - - +
322B VAL* 1.3 71.5 + - - +
323B THR* 4.1 2.0 - - - +
330B LEU* 4.2 14.1 - - + -
348B MET* 4.0 2.9 - - - +
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Residues in contact with VAL 322 (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 3.5 9.2 - - - +
281B LYS* 4.4 17.5 - - + -
303B GLY 4.4 0.3 - - - -
304B ILE* 3.4 3.8 - - - -
305B SER* 2.8 44.6 + - - +
306B GLY* 5.5 1.8 - - - -
320B GLU 5.4 1.6 - - - +
321B LEU* 1.3 82.0 - - - +
323B THR* 1.3 63.5 + - - +
324B GLN* 3.7 24.5 + - - +
348B MET* 5.1 5.4 - - + -
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Residues in contact with THR 323 (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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276B VAL* 3.8 10.7 - - + +
278B ALA 2.9 26.6 + - - +
279B ALA* 3.2 2.9 - - - +
280B GLY* 2.7 37.4 + - - +
282B TRP* 2.9 29.1 - - + +
303B GLY 3.6 4.5 - - - -
304B ILE* 4.4 4.3 - - - +
321B LEU* 4.1 2.0 - - - -
322B VAL* 1.3 76.1 - - - +
324B GLN* 1.3 57.9 + - - +
325B MET 2.8 24.3 + - - -
328B GLN* 3.1 21.7 + - - +
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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
------------------------------------------------------------
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