Contacts of the helix formed by residues 298 - 312 (chain B) in PDB entry 1OPL
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 GLU 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B LEU* 5.1 1.3 - - - -
296B THR 2.7 11.1 + - - +
297B MET* 1.3 80.7 - - - +
299B VAL* 1.3 74.4 + - + +
300B GLU* 3.3 24.1 - - + +
301B GLU* 3.0 18.0 + - - +
302B PHE* 3.8 1.4 + - - +
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Residues in contact with VAL 299 (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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292B LEU* 4.5 20.5 - - + +
298B GLU* 1.3 80.5 - - + +
300B GLU* 1.3 72.8 + - - +
302B PHE* 2.9 21.2 + - + +
303B LEU* 2.9 40.0 + - + +
330B PHE* 3.8 19.7 - - + -
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Residues in contact with GLU 300 (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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298B GLU* 3.0 25.7 + - + +
299B VAL* 1.3 83.8 - - - +
301B GLU* 1.3 57.9 + - - +
303B LEU* 3.9 13.7 - - - +
304B LYS* 3.0 41.3 + - + +
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Residues in contact with GLU 301 (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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297B MET* 4.4 31.5 - - + +
298B GLU 3.0 11.7 + - - +
300B GLU* 1.3 77.8 - - - +
302B PHE* 1.3 64.0 + - - +
304B LYS* 3.4 19.6 + - - +
305B GLU* 3.1 24.4 + - - +
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Residues in contact with PHE 302 (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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290B LYS* 3.3 47.6 - - + -
292B LEU* 3.6 44.9 - - + -
298B GLU 3.8 1.0 + - - +
299B VAL 2.9 9.4 + - - +
301B GLU* 1.3 79.6 - - - +
303B LEU* 1.3 72.3 + - + +
305B GLU* 3.2 10.5 + - + +
306B ALA* 3.1 18.9 + - + +
325B THR* 5.8 2.9 - - + -
330B PHE* 3.4 42.8 - + + -
331B TYR 4.1 2.0 - - - -
332B ILE* 3.6 27.1 - - + +
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Residues in contact with LEU 303 (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 VAL* 2.9 32.9 + - + +
300B GLU* 4.0 14.4 - - - +
302B PHE* 1.3 81.3 - - + +
304B LYS* 1.3 60.5 + - + +
306B ALA* 3.2 7.8 + - + +
307B ALA* 2.9 29.2 + - - +
325B THR* 5.4 10.8 - - + -
330B PHE* 3.5 36.1 - - + -
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Residues in contact with LYS 304 (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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300B GLU* 3.0 28.4 + - - +
301B GLU* 3.8 19.3 + - - +
302B PHE 3.3 0.2 - - - -
303B LEU* 1.3 76.3 - - - +
305B GLU* 1.3 58.7 + - - +
307B ALA* 3.2 7.3 + - + +
308B VAL* 2.9 37.7 + - + +
405B ARG* 5.6 1.5 + - - +
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Residues in contact with GLU 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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290B LYS* 2.9 33.5 + - - +
301B GLU* 3.1 14.6 + - - +
302B PHE* 3.3 13.4 - - - +
303B LEU 3.1 0.4 - - - -
304B LYS* 1.3 77.3 - - - +
306B ALA* 1.3 61.7 + - - +
308B VAL* 3.4 5.7 + - - +
309B MET* 3.0 34.9 + - + +
332B ILE* 4.0 8.4 - - + +
400B ASP 5.1 0.4 - - - +
401B PHE* 3.4 33.2 - - - +
402B GLY* 3.6 12.6 + - - +
538B P16 3.3 15.8 - - - -
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Residues in contact with ALA 306 (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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302B PHE* 3.1 13.8 + - + +
303B LEU* 3.5 11.4 - - + +
305B GLU* 1.3 76.3 - - - +
307B ALA* 1.3 62.5 + - - +
309B MET* 3.3 6.5 + - - +
310B LYS* 3.2 31.0 + - - +
320B LEU* 4.2 2.4 - - - +
323B VAL* 4.3 16.4 - - + -
325B THR* 5.4 8.1 - - + -
332B ILE* 3.9 24.1 - - + +
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Residues in contact with ALA 307 (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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303B LEU 2.9 14.6 + - - +
304B LYS* 3.5 11.9 - - + +
306B ALA* 1.3 76.2 - - - +
308B VAL* 1.3 64.0 + - - +
310B LYS* 3.2 27.8 + - - +
311B GLU* 3.7 9.5 + - - +
405B ARG* 4.5 14.3 + - - +
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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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304B LYS* 2.9 27.7 + - + +
305B GLU* 3.7 5.8 - - - +
307B ALA* 1.3 71.8 - - - +
309B MET* 1.3 60.2 + - - +
311B GLU* 2.9 22.1 + - - +
312B ILE* 3.3 12.9 + - + +
378B PHE* 4.2 12.3 - - + -
400B ASP 4.6 5.2 - - - +
403B LEU* 3.8 53.6 - - + +
405B ARG* 4.3 29.2 - - + +
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Residues in contact with MET 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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305B GLU* 3.0 25.9 + - + +
306B ALA* 3.8 5.2 - - - +
307B ALA 3.3 0.2 - - - -
308B VAL* 1.3 76.4 - - + +
310B LYS* 1.3 60.7 + - - +
311B GLU 3.1 0.6 + - - -
312B ILE* 3.5 21.0 + - - +
318B VAL 3.8 11.0 - - - +
319B GLN* 4.9 1.4 + - - -
320B LEU* 3.8 30.9 + - + +
332B ILE* 4.3 10.8 - - - -
334B THR* 3.7 20.4 - - + -
400B ASP* 3.3 42.4 - - - +
538B P16 3.3 37.2 - - + -
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Residues in contact with LYS 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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252B ASP* 3.3 25.4 + - - +
254B TRP* 3.6 55.3 + - + +
255B GLU* 5.3 0.6 + - - -
306B ALA* 3.2 18.4 + - - +
307B ALA* 3.2 15.3 + - - +
308B VAL 3.1 1.0 + - - -
309B MET* 1.3 78.5 - - - +
311B GLU* 1.3 67.5 + - + +
312B ILE 3.8 2.1 + - - +
313B LYS* 4.9 7.6 - - - +
319B GLN* 5.8 0.5 + - - -
320B LEU* 3.5 15.3 - - + -
323B VAL* 4.4 18.5 - - - +
325B THR* 6.2 0.4 - - - +
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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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307B ALA 3.9 8.5 - - - +
308B VAL 2.9 7.6 + - - +
310B LYS* 1.3 84.9 - - - +
312B ILE* 1.3 63.5 + - - +
313B LYS* 3.5 10.2 + - - +
372B TYR* 4.0 7.8 + - - -
378B PHE* 4.7 16.3 - - + -
405B ARG* 3.9 23.9 + - - +
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Residues in contact with ILE 312 (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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308B VAL* 3.3 19.0 + - + +
309B MET* 3.5 15.0 + - - +
310B LYS 4.6 0.9 - - - +
311B GLU* 1.3 75.7 - - - +
313B LYS* 1.3 66.1 + - - +
314B HIS 4.6 0.4 - - - +
317B LEU* 3.6 28.3 - - + +
318B VAL 5.3 0.8 - - - +
319B GLN* 3.3 17.4 + - - +
320B LEU 5.6 0.2 + - - -
372B TYR* 4.6 7.2 - - + -
373B LEU* 4.0 12.1 - - + -
378B PHE* 4.1 22.0 - - + -
400B ASP* 3.3 27.1 - - + +
403B LEU* 3.4 31.6 - - + -
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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