Contacts of the helix formed by residues 287 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A VAL* 4.0 0.4 - - - -
286A ARG* 1.3 76.1 - - - +
288A PRO* 1.3 72.9 - - - +
289A LEU* 3.1 22.1 + - - +
290A GLU* 3.2 16.0 + - - +
291A ALA* 3.0 19.9 + - - +
336A ASP* 5.0 2.2 - - - -
339A ILE* 5.0 13.2 - - - -
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Residues in contact with PRO 288 (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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223A LEU* 4.2 14.6 - - + -
278A LEU* 3.9 4.2 - - + +
282A VAL* 3.5 21.3 - - + -
286A ARG 4.4 0.2 - - - +
287A SER* 1.3 89.8 - - - +
289A LEU* 1.3 61.2 + - - +
291A ALA* 3.6 2.5 - - + +
292A ALA* 3.1 24.3 + - - +
334A PHE* 3.7 28.4 - - + -
336A ASP* 3.3 42.8 - - + +
339A ILE* 4.5 14.1 - - + -
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Residues in contact with LEU 289 (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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287A SER* 3.1 10.5 - - - +
288A PRO* 1.3 78.4 - - - +
290A GLU* 1.3 62.1 + - - +
292A ALA* 3.3 4.4 + - - +
293A MET* 3.1 28.7 + - - +
334A PHE* 3.6 29.4 - - + -
339A ILE* 4.0 23.1 - - + -
389A MET* 4.0 17.4 - - + +
390A ILE 4.6 3.6 - - - +
391A ALA* 3.7 32.3 - - + -
400A LEU* 5.0 6.1 - - + -
405A ILE* 3.7 33.0 - - + -
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Residues in contact with GLU 290 (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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286A ARG* 2.4 48.1 + - + +
287A SER* 3.2 15.2 + - - +
289A LEU* 1.3 76.2 - - - +
291A ALA* 1.3 65.4 + - - +
293A MET* 3.2 19.1 + - - +
294A ILE* 3.2 15.0 + - + +
315A PHE* 3.9 19.9 - - + -
409A ALA* 3.9 25.9 - - + +
412A LYS* 2.6 35.2 + - - +
415A TYR* 4.1 4.3 + - - -
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Residues in contact with ALA 291 (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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278A LEU* 3.6 29.2 - - + +
281A LEU* 3.7 34.3 - - + +
282A VAL* 4.1 4.7 - - + +
286A ARG* 4.4 4.7 - - + +
287A SER 3.0 13.0 + - - +
288A PRO 3.6 3.8 - - - +
290A GLU* 1.3 76.5 - - - +
292A ALA* 1.3 57.5 + - - +
294A ILE* 3.2 4.9 + - - +
295A LEU* 3.0 32.5 + - - +
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Residues in contact with ALA 292 (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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278A LEU* 4.4 7.2 - - + +
288A PRO 3.1 17.4 + - - +
289A LEU* 3.7 4.3 - - - +
291A ALA* 1.3 72.7 - - - +
293A MET* 1.3 59.4 + - - +
295A LEU* 4.5 4.0 - - - +
296A VAL* 2.7 39.7 + - + +
332A LEU* 4.5 20.9 - - + -
334A PHE* 4.5 15.9 - - + -
343A GLY* 6.3 1.6 - - - -
389A MET* 5.0 7.2 - - + -
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Residues in contact with MET 293 (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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289A LEU 3.1 19.4 + - - +
290A GLU* 3.2 11.0 + - - +
292A ALA* 1.3 77.4 - - - +
294A ILE* 1.3 57.0 + - - +
296A VAL 4.5 3.4 - - - -
297A PRO* 3.2 28.6 - - - +
298A GLU 5.8 0.2 - - - +
312A ILE* 5.2 1.8 - - + -
315A PHE* 3.8 35.7 - - + -
316A HIS* 3.5 19.7 + - + +
389A MET* 4.1 19.2 - - + -
405A ILE* 4.8 2.2 - - - +
406A LYS* 3.7 49.6 - - + +
409A ALA* 3.8 21.8 - - + -
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Residues in contact with ILE 294 (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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281A LEU* 4.3 11.4 - - + -
286A ARG* 3.4 48.2 - - - +
290A GLU* 3.2 11.7 + - + +
291A ALA 3.6 5.4 - - - +
292A ALA 3.2 0.2 - - - -
293A MET* 1.3 77.4 - - - +
295A LEU* 1.3 64.9 + - + +
297A PRO* 3.6 11.6 - - - +
315A PHE* 3.6 21.3 - - + -
319A TYR* 3.8 28.5 - - + +
323A GLN* 3.5 24.3 - - + +
528A LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 295 (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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240A MET* 4.3 8.1 - - + -
274A LEU* 4.1 16.2 - - + -
277A ALA* 3.8 29.4 - - + +
278A LEU* 3.8 20.9 - - + +
281A LEU* 3.9 16.4 - - + -
291A ALA 3.0 16.8 + - - +
292A ALA* 4.4 2.2 - - - +
294A ILE* 1.3 77.5 - - - +
296A VAL* 1.3 67.6 + - + +
297A PRO* 3.4 4.0 - - - +
323A GLN* 3.8 31.0 - - + +
325A PRO* 3.5 1.6 - - - +
326A TRP* 2.9 46.3 + - + +
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Residues in contact with VAL 296 (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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230A ILE* 5.7 1.1 - - + -
274A LEU* 4.8 9.2 - - + -
292A ALA* 2.7 23.5 + - + +
293A MET* 4.5 1.6 - - - -
295A LEU* 1.3 85.9 - - + +
297A PRO* 1.3 65.1 - - - +
298A GLU 3.7 1.0 + - - -
325A PRO* 5.2 0.9 - - + -
326A TRP* 3.7 23.6 - - + +
327A ASP* 6.0 0.4 - - - -
330A ALA* 5.2 5.8 - - + -
332A LEU* 4.2 25.8 - - + -
344A LEU 4.3 9.2 - - - +
345A ASP* 3.8 33.4 - - + +
346A ARG 4.7 2.6 + - - +
387A 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