Contacts of the strand formed by residues 316 - 323 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ILE* 4.8 5.6 - - + -
286A VAL 3.2 11.7 - - - +
287A ARG* 3.6 25.8 - - - +
294A PHE* 3.6 4.6 - - - -
309A ASP 3.7 1.9 - - - +
310A TYR* 3.7 1.6 - - - -
311A GLU* 3.0 46.8 + - + +
313A ALA 5.1 0.2 - - - +
314A ARG* 2.9 22.5 + - + +
315A PRO* 1.3 75.5 - - - +
317A ALA* 1.3 71.3 + - - +
318A VAL* 4.7 13.0 - - + -
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ILE 3.7 0.9 - - - +
285A ILE* 3.4 6.6 - - - +
286A VAL* 2.9 39.2 + - + +
294A PHE* 4.0 10.1 - - + -
297A PRO* 3.9 34.3 - - + -
308A VAL* 4.7 1.8 - - + -
309A ASP 3.3 7.4 - - - +
310A TYR* 4.5 2.2 - - + -
316A ILE* 1.3 76.7 - - - +
318A VAL* 1.3 64.3 + - - +
319A CYS* 3.8 7.5 - - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A CYS* 4.8 11.0 - - - -
284A ILE 3.8 3.1 - - - -
285A ILE* 4.5 15.7 - - + -
307A ASP* 3.4 4.5 - - - +
309A ASP* 3.0 43.5 + - + +
316A ILE* 4.7 17.0 - - + -
317A ALA* 1.3 75.4 - - - +
319A CYS* 1.3 59.0 + - - +
320A GLU* 3.8 22.4 + - + +
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Residues in contact with CYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A CYS* 3.3 3.1 - - - -
284A ILE* 2.8 46.1 + - + +
286A VAL* 5.0 2.9 - - - -
297A PRO* 4.2 7.6 - - - -
307A ASP 3.2 10.5 - - - +
308A VAL* 4.2 17.7 - - + -
317A ALA* 4.1 20.9 - - - -
318A VAL* 1.3 72.6 - - - +
320A GLU* 1.3 61.4 + - - +
321A LEU* 3.6 26.4 + - + +
330A LEU* 4.3 17.5 - - + -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A TRP 3.6 6.3 - - - -
283A CYS* 4.5 5.4 - - - -
306A GLY* 3.1 5.0 - - - -
307A ASP* 3.0 43.2 + - + +
318A VAL* 4.4 22.2 - - + +
319A CYS* 1.3 72.3 - - - +
321A LEU* 1.3 61.4 + - - +
322A VAL* 5.5 0.7 - - - +
348A MET* 3.6 29.0 - - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL* 5.3 6.5 - - + -
281A LYS* 3.5 3.8 - - - +
282A TRP* 2.9 46.0 + - + +
284A ILE* 4.1 26.9 - - + -
299A LEU* 4.1 23.8 - - + -
304A ILE* 4.8 15.7 - - + -
305A SER 3.2 11.7 - - - +
306A GLY* 4.3 3.6 - - - -
307A ASP 4.5 3.4 - - - +
308A VAL* 4.9 1.3 - - + -
319A CYS* 3.9 25.4 - - + +
320A GLU* 1.3 81.5 - - - +
322A VAL* 1.3 70.7 + - - +
323A THR* 4.2 1.3 - - - -
330A LEU* 4.3 13.7 - - + -
348A MET* 4.6 2.5 - - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLY 3.6 6.5 - - - +
281A LYS* 4.2 19.7 - - + -
303A GLY 4.0 1.2 - - - +
304A ILE* 3.4 3.5 - - - -
305A SER* 2.8 41.8 + - - +
306A GLY* 5.8 1.8 - - - -
320A GLU 5.5 1.1 - - - +
321A LEU* 1.3 80.4 - - - +
323A THR* 1.3 65.1 + - - +
324A GLN* 4.1 26.7 + - + +
348A MET* 6.2 1.1 - - - -
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Residues in contact with THR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL* 4.1 8.2 - - + +
278A ALA 2.9 27.8 - - - +
279A ALA* 3.2 4.9 - - - +
280A GLY* 2.8 44.6 + - - +
282A TRP* 3.1 17.5 - - - +
303A GLY 3.6 4.5 + - - -
304A ILE* 4.5 4.3 - - - +
321A LEU* 4.2 1.8 - - - -
322A VAL* 1.3 76.6 - - - +
324A GLN* 1.3 60.6 + - - +
325A MET 3.0 20.9 + - - -
328A GLN* 3.5 20.2 - - - +
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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
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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