Contacts of the strand formed by residues 283 - 294 (chain A) in PDB entry 2OM5
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 GLY 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ALA* 4.0 9.4 - - - +
209A PRO* 3.1 18.9 - - - +
279A GLU* 3.3 3.5 - - - +
280A ASN* 3.2 21.8 + - - +
281A SER 3.5 2.4 - - - -
282A LYS* 1.3 79.3 - - - +
284A ARG* 1.3 61.8 + - - -
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Residues in contact with ARG 284 (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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208A ALA* 5.0 1.0 - - - +
209A PRO* 4.0 2.0 - - - +
277A GLU* 2.8 46.7 + - - +
278A ALA 3.1 11.7 - - - +
279A GLU* 3.7 22.3 + - + -
283A GLY* 1.3 76.4 - - - +
285A ASP* 1.3 60.1 + - - +
286A THR* 4.1 6.9 + - + +
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Residues in contact with ASP 285 (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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209A PRO* 3.1 25.2 + - - +
210A SER* 3.4 5.4 + - - -
211A ILE* 2.6 47.6 + - + +
214A ARG* 5.2 6.1 + - - -
278A ALA* 2.7 41.6 + - + +
284A ARG* 1.3 73.2 - - - +
286A THR* 1.3 74.3 + - - +
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Residues in contact with THR 286 (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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211A ILE* 3.8 2.0 - - - -
214A ARG* 4.6 5.4 + - - -
275A GLU* 4.1 19.2 + - - +
276A CYS 3.1 7.4 - - - -
277A GLU* 3.4 38.6 - - + +
284A ARG* 4.1 10.0 + - + +
285A ASP* 1.3 88.5 + - - +
287A VAL* 1.3 64.0 + - - +
288A GLN* 5.9 0.6 - - - +
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Residues in contact with VAL 287 (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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211A ILE* 3.7 13.0 - - + -
214A ARG* 3.6 45.3 - - + +
215A PHE* 3.5 24.5 - - + +
231A CYS* 3.4 33.2 - - - -
275A GLU* 3.5 1.3 - - - -
276A CYS* 2.9 33.3 + - + -
286A THR* 1.3 76.6 - - - +
288A GLN* 1.3 72.3 + - - +
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Residues in contact with GLN 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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215A PHE* 4.1 3.8 - - - +
216A PRO 4.9 0.2 - - - +
217A ALA* 4.7 7.3 - - - +
244A ARG* 4.5 2.4 - - - +
246A VAL* 3.5 17.7 - - - +
273A THR* 3.7 21.0 - - + +
274A TYR 3.3 5.6 - - - +
275A GLU* 2.8 42.5 + - + +
286A THR* 5.8 0.7 - - - +
287A VAL* 1.3 84.7 - - - +
289A GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 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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215A PHE* 3.4 20.3 - - - -
216A PRO 3.7 7.9 - - - -
217A ALA 3.4 11.2 - - - -
229A LEU* 5.7 1.3 - - - -
273A THR* 3.4 5.9 - - - +
274A TYR* 2.8 36.5 + - - +
288A GLN* 1.3 75.0 - - - +
290A ARG* 1.3 58.1 + - - -
291A ILE* 4.3 0.4 - - - -
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Residues in contact with ARG 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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216A PRO 4.5 0.6 + - - -
217A ALA 2.8 14.7 + - - +
218A GLU* 3.3 29.6 + - + +
219A THR* 2.9 26.2 + - - -
229A LEU* 6.4 0.2 - - - -
271A GLU* 5.2 3.8 + - - -
272A GLY* 3.5 18.8 - - - +
273A THR* 3.4 23.6 + - + +
289A GLY* 1.3 72.3 - - - -
291A ILE* 1.3 64.9 + - - +
292A ILE* 3.4 29.6 + - - +
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Residues in contact with ILE 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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219A THR* 3.7 12.6 - - + +
221A ALA* 5.3 3.1 - - + -
227A VAL* 3.7 35.2 - - + -
229A LEU* 3.8 28.9 - - + -
263A ILE* 5.6 2.5 - - + -
266A VAL* 5.1 7.4 - - + -
270A ASP 3.9 16.8 - - - +
271A GLU* 3.1 21.8 - - - +
272A GLY* 3.0 11.0 + - - +
274A TYR* 3.5 29.2 - - + -
290A ARG* 1.3 74.7 - - - +
292A ILE* 1.3 74.1 + - - +
293A VAL* 4.4 8.5 - - + -
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Residues in contact with ILE 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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218A GLU* 4.9 8.3 - - + -
219A THR 3.0 11.3 + - - +
220A TYR* 3.9 30.5 - - + +
221A ALA* 3.3 25.8 + - - +
271A GLU* 3.3 18.6 - - - +
290A ARG* 3.4 49.1 - - + +
291A ILE* 1.3 75.7 - - - +
293A VAL* 1.3 61.7 + - - +
294A GLN* 3.8 20.7 + - - +
323A LYS* 3.8 14.1 - - - +
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Residues in contact with VAL 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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221A ALA* 3.6 6.3 - - + +
223A VAL* 3.8 28.7 - - + +
266A VAL* 3.9 20.0 - - + -
267A SER 3.6 27.4 - - - +
268A PHE* 3.0 31.4 - - + +
270A ASP 4.2 0.9 - - - -
271A GLU* 3.5 35.7 + - + +
291A ILE* 4.4 4.3 - - + -
292A ILE* 1.3 74.5 - - - +
294A GLN* 1.3 63.0 + - - +
323A LYS* 3.2 16.3 + - - +
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Residues in contact with GLN 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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220A TYR* 3.6 12.5 - - + -
221A ALA 2.8 19.7 + - - +
222A LEU* 3.3 4.0 - - + -
223A VAL* 2.9 28.2 + - - +
268A PHE* 4.2 2.0 - - - -
292A ILE* 4.2 14.9 - - + +
293A VAL* 1.3 77.0 + - - +
295A ALA* 1.3 63.7 + - - +
323A LYS* 3.5 44.9 + - - +
324A PRO* 3.9 5.8 - - - +
370A LYS* 3.5 30.4 + - - +
371A HIS* 3.4 27.1 - - + +
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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