Contacts of the helix formed by residues 287 - 296 (chain B) in PDB entry 1OFD
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 SER 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B VAL* 4.1 0.4 - - - -
286B ARG* 1.3 75.8 - - - +
288B PRO* 1.3 73.7 - - - +
289B LEU* 3.1 25.3 + - - +
290B GLU* 3.1 16.9 + - - +
291B ALA* 3.0 20.4 + - - +
336B ASP* 5.0 2.2 - - - -
339B ILE* 5.6 8.3 - - - -
412B LYS* 5.8 0.4 - - - +
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Residues in contact with PRO 288 (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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223B LEU* 4.1 13.2 - - + -
278B LEU* 3.8 5.8 - - + +
282B VAL* 3.5 25.3 - - + -
286B ARG 4.3 0.2 - - - +
287B SER* 1.3 88.8 - - - +
289B LEU* 1.3 56.4 + - - +
291B ALA* 3.6 2.4 - - + +
292B ALA* 3.0 28.6 + - - +
334B PHE* 3.6 28.7 - - + -
336B ASP* 3.5 39.9 - - + +
339B ILE* 4.3 14.4 - - + -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER* 3.1 10.7 - - - +
288B PRO* 1.3 74.0 - - - +
290B GLU* 1.3 64.6 + - - +
292B ALA* 3.3 3.3 + - - +
293B MET* 3.0 27.5 + - - +
334B PHE* 3.6 29.2 - - + -
339B ILE* 4.0 22.0 - - + -
389B MET* 3.8 19.4 - - + +
390B ILE 4.4 4.3 - - - +
391B ALA* 3.6 33.2 - - + -
400B LEU* 4.7 5.8 - - + -
405B ILE* 3.7 32.3 - - + -
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Residues in contact with GLU 290 (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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286B ARG* 2.6 44.6 + - + +
287B SER* 3.1 16.7 + - - +
289B LEU* 1.3 75.5 - - - +
291B ALA* 1.3 66.5 + - - +
293B MET* 3.1 11.7 + - - +
294B ILE* 3.1 26.0 + - + +
315B PHE* 3.9 18.2 - - + -
409B ALA* 3.9 25.0 - - + +
412B LYS* 3.0 35.3 + - - -
415B TYR* 4.1 3.1 + - - -
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Residues in contact with ALA 291 (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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278B LEU* 3.5 26.2 - - + +
281B LEU* 3.6 43.0 - - + +
282B VAL* 4.1 6.3 - - + +
286B ARG* 4.4 4.9 - - + +
287B SER 3.0 12.5 + - - +
288B PRO 3.6 4.9 - - - +
289B LEU 3.3 0.2 - - - -
290B GLU* 1.3 77.6 - - - +
292B ALA* 1.3 56.9 + - - +
294B ILE 3.3 1.7 + - - -
295B LEU* 3.1 25.8 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 3.6 11.4 - - + +
288B PRO 3.0 17.8 + - - +
289B LEU* 3.7 4.7 - - - +
290B GLU 3.3 0.2 - - - -
291B ALA* 1.3 72.6 - - - +
293B MET* 1.3 61.2 + - - +
295B LEU* 4.5 2.9 - - - +
296B VAL* 2.8 38.8 + - + +
332B LEU* 4.4 20.4 - - + -
334B PHE* 4.4 13.9 - - + -
343B GLY* 6.3 1.6 - - - -
389B MET* 4.8 7.6 - - - -
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Residues in contact with MET 293 (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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289B LEU 3.0 19.3 + - - +
290B GLU* 3.3 10.5 - - - +
292B ALA* 1.3 76.0 - - - +
294B ILE* 1.3 59.2 + - - +
296B VAL 4.6 3.4 - - - -
297B PRO* 3.3 27.1 - - - +
298B GLU 5.9 0.2 - - - +
312B ILE* 5.1 2.2 - - + -
315B PHE* 3.6 34.5 - - + -
316B HIS* 3.4 20.2 + - + +
319B TYR* 5.9 0.2 - - - +
389B MET* 3.6 20.4 - - + -
405B ILE* 4.9 1.6 - - - +
406B LYS* 3.8 47.8 - - + +
409B ALA* 3.8 21.8 - - + -
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Residues in contact with ILE 294 (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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281B LEU* 4.4 10.1 - - + -
286B ARG* 3.4 49.4 - - - +
290B GLU* 3.1 15.9 + - + +
291B ALA 3.7 5.4 - - - +
292B ALA 3.2 0.4 - - - -
293B MET* 1.3 77.2 - - - +
295B LEU* 1.3 64.1 + - - +
297B PRO* 3.6 11.3 - - - +
315B PHE* 3.7 17.7 - - + -
319B TYR* 3.9 35.3 - - + +
323B GLN* 3.5 30.7 - - + +
528B LEU* 3.9 13.5 - - + +
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Residues in contact with LEU 295 (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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240B MET* 4.3 8.5 - - + -
274B LEU* 4.2 16.4 - - + -
277B ALA* 3.8 14.6 - - + -
278B LEU* 3.8 34.3 - - + +
281B LEU* 3.8 16.4 - - + -
291B ALA 3.1 16.4 + - - +
292B ALA* 4.6 2.0 - - - +
294B ILE* 1.3 77.5 - - + +
296B VAL* 1.3 67.6 + - + +
297B PRO* 3.4 4.8 - - - +
323B GLN* 3.8 30.5 - - + +
325B PRO* 3.6 1.6 - - - +
326B TRP* 2.9 47.1 + - + +
528B LEU* 5.3 0.7 - - + -
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Residues in contact with VAL 296 (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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230B ILE* 5.8 0.9 - - + -
274B LEU* 4.8 9.9 - - + -
292B ALA* 2.8 23.2 + - + +
293B MET* 4.6 1.6 - - - -
295B LEU* 1.3 85.4 - - + +
297B PRO* 1.3 65.3 - - - +
298B GLU 3.6 1.4 + - - -
325B PRO* 5.3 0.7 - - - -
326B TRP* 4.1 20.6 - - + +
327B ASP* 6.2 0.7 - - - -
328B GLY 5.8 0.2 - - - +
330B ALA* 5.1 6.1 - - + -
332B LEU* 4.0 27.8 - - + -
344B LEU 4.3 8.8 - - - +
345B ASP* 3.8 32.8 - - + +
346B ARG 4.6 3.0 + - - +
387B GLY* 6.1 0.5 - - - -
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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