Contacts of the helix formed by residues 284 - 295 (chain B) in PDB entry 3OAX
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 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B PRO* 3.5 13.4 - - - +
182B GLY* 5.0 0.9 - - - -
283B PHE* 1.3 80.2 - - - +
285B PRO* 1.3 74.4 - - - +
286B ILE 3.5 2.5 - - - -
287B PHE* 3.1 18.1 - - - +
288B MET* 4.2 2.3 + - - +
6026B ID3 2.9 25.8 - - - -
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Residues in contact with PRO 285 (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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12B PRO* 3.3 22.0 - - + +
13B PHE* 4.9 5.8 - - + -
31B LEU* 3.7 35.9 - - + +
182B GLY* 2.9 32.6 - - - +
183B MET* 4.0 13.7 - - + +
284B GLY* 1.3 84.6 - - - +
286B ILE* 1.3 62.7 + - + +
287B PHE 3.5 0.2 + - - -
288B MET 4.0 0.2 + - - -
289B THR* 2.7 27.9 + - - -
6026B ID3 4.8 3.4 - - + -
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Residues in contact with ILE 286 (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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31B LEU 5.9 0.2 - - - +
32B ALA* 4.6 11.4 - - + -
36B GLN* 4.7 7.0 - - - +
183B MET* 3.3 33.2 - - + -
284B GLY 3.5 1.0 - - - -
285B PRO* 1.3 81.4 - - + +
287B PHE* 1.3 67.6 + - - +
288B MET 3.4 0.4 + - - -
289B THR* 3.4 7.1 + - - -
290B ILE* 3.3 41.0 - - + +
6026B ID3 3.4 30.6 + - + +
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Residues in contact with PHE 287 (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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271B VAL* 3.5 36.6 - - + +
274B TYR* 3.8 26.0 - + - -
275B ILE* 3.9 9.2 - - + -
283B PHE* 3.4 29.4 - + + -
284B GLY 3.1 15.5 - - - +
285B PRO 3.2 0.2 - - - -
286B ILE* 1.3 76.7 - - - +
288B MET* 1.3 57.6 + - + +
291B PRO* 3.2 22.3 - - - +
1506B HTG 3.8 37.0 - - + -
6026B ID3 3.4 49.5 + - + +
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Residues in contact with MET 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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181B GLU* 3.1 42.4 - - + +
182B GLY* 4.0 11.2 - - - +
191B TYR* 4.2 0.9 - - + -
192B TYR* 4.0 10.8 - - + +
268B TYR* 3.2 39.0 - - + +
271B VAL* 4.0 12.6 - - + -
272B ALA* 3.9 31.9 - - + +
275B ILE* 4.5 6.1 - - + -
283B PHE* 6.4 0.7 - - + -
284B GLY 4.2 1.4 + - - +
285B PRO 4.0 2.4 + - - -
287B PHE* 1.3 77.7 - - + +
289B THR* 1.3 59.7 + - - +
290B ILE 3.5 0.7 - - - -
291B PRO* 3.8 9.2 - - - -
292B ALA* 2.9 30.1 + - + +
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Residues in contact with THR 289 (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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40B LEU* 4.0 16.8 - - + -
181B GLU 4.7 0.6 + - - -
182B GLY* 3.3 2.8 - - - -
183B MET* 2.8 48.4 + - + +
186B SER* 5.7 1.1 - - - -
285B PRO 2.7 24.0 + - - -
286B ILE* 3.4 4.7 + - - -
288B MET* 1.3 78.4 - - - +
290B ILE* 1.3 64.4 + - + +
292B ALA* 4.5 3.1 - - - -
293B PHE* 2.8 49.5 + - + +
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Residues in contact with ILE 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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40B LEU* 6.3 1.3 - - + -
183B MET* 5.5 2.2 - - + -
286B ILE* 3.3 36.1 - - + +
289B THR* 1.3 83.3 - - + +
291B PRO* 1.3 66.6 - - + +
293B PHE* 3.9 1.6 - - - +
294B PHE* 2.8 35.9 + - + +
6026B ID3 4.5 7.0 - - - +
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Residues in contact with PRO 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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264B CYS 4.9 0.7 - - - +
267B PRO* 4.0 14.1 - - + +
268B TYR* 3.8 29.9 - - - +
271B VAL* 4.0 11.4 - - + -
287B PHE 3.2 23.8 - - - +
288B MET* 3.4 16.2 - - - +
290B ILE* 1.3 95.9 - - + +
292B ALA* 1.3 63.8 + - - +
294B PHE* 3.7 6.9 - - + +
295B ALA* 3.0 25.8 + - - +
6026B ID3 5.4 1.3 - - - +
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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
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181B GLU* 4.9 2.5 - - + +
186B SER* 3.9 20.4 - - - +
268B TYR* 3.5 28.9 - - + -
288B MET* 2.9 26.7 + - + +
289B THR* 3.9 2.7 - - - +
291B PRO* 1.3 79.3 - - - +
293B PHE* 1.3 61.5 + - + +
295B ALA 3.7 3.3 + - - -
296B LYS* 3.3 5.2 + - - +
1296B RET 3.2 29.7 - - + +
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Residues in contact with PHE 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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40B LEU* 4.0 42.2 - - + -
43B TYR* 2.6 54.3 + + + -
44B MET* 3.7 31.0 - - + -
94B THR* 3.9 11.0 - - - -
98B SER* 4.1 7.2 - - - -
183B MET* 6.4 0.4 - - + -
185B CYS* 4.2 11.0 - - + -
186B SER* 3.7 25.6 - - - -
289B THR* 2.8 35.6 + - + +
290B ILE* 4.1 2.0 - - - +
292B ALA* 1.3 74.0 - - - +
294B PHE* 1.3 58.6 + - - +
296B LYS* 3.3 20.4 + - + +
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Residues in contact with PHE 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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43B TYR* 3.5 9.2 - - - -
263B ILE* 3.5 37.9 - - + -
264B CYS* 4.0 16.8 - - - -
267B PRO* 4.7 8.5 - - + -
290B ILE* 2.8 23.5 + - + +
291B PRO* 3.7 4.9 - - + +
293B PHE* 1.3 78.1 - - - +
295B ALA* 1.3 60.9 + - - +
296B LYS 3.0 1.8 + - - -
297B THR* 2.9 42.5 + - + +
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Residues in contact with ALA 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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264B CYS* 3.4 29.8 - - - +
265B TRP* 3.8 32.8 - - + -
268B TYR* 4.4 4.5 - - + -
291B PRO 3.0 15.9 + - - +
292B ALA 4.0 5.6 - - - +
293B PHE 3.3 0.2 - - - -
294B PHE* 1.3 76.9 - - - +
296B LYS* 1.3 57.0 + - - +
297B THR 3.0 1.1 - - - -
298B SER* 2.8 30.5 + - - -
1296B RET 4.7 2.0 - - + -
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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