Contacts of the helix formed by residues 281 - 289 (chain B) in PDB entry 3BRW
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 GLN 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B GLU* 6.1 0.2 - - - -
211B PHE* 3.9 15.7 - - + -
212B SER* 3.2 32.5 + - - +
273B PRO 3.7 4.2 + - - -
274B TYR* 3.3 20.5 - - - +
275B THR* 2.9 50.8 + - - +
278B ASP* 3.2 20.2 + - - +
279B ALA 5.3 0.7 - - - +
280B GLN* 1.3 79.0 - - - +
282B LEU* 1.3 60.8 + - - +
283B GLN 3.4 2.2 - - - -
284B ARG* 3.1 25.1 + - + +
285B LYS* 2.8 24.4 + - - +
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Residues in contact with LEU 282 (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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275B THR* 4.8 0.2 + - - -
278B ASP* 3.4 26.2 + - - +
280B GLN* 4.3 10.5 - - + +
281B GLN* 1.3 67.8 - - - +
283B GLN* 1.3 57.9 + - - +
284B ARG 2.9 5.5 + - - -
285B LYS* 4.4 1.8 - - - +
286B ARG* 2.8 40.7 + - + +
13D GLY* 4.6 6.3 - - - +
32D TYR* 3.6 43.3 - - + -
117D LYS* 3.5 27.6 - - - +
171D GDP 4.0 16.2 - - - +
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Residues in contact with GLN 283 (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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249B GLN 4.4 7.4 + - - +
250B THR* 5.7 0.2 - - - +
272B LEU* 3.8 9.4 - - - +
273B PRO* 3.5 40.9 - - + +
274B TYR 4.3 1.7 - - - +
275B THR* 2.7 43.7 + - + +
281B GLN* 3.4 0.6 - - - +
282B LEU* 1.3 76.4 - - + +
284B ARG* 1.3 58.5 + - - +
286B ARG* 4.6 11.2 - - - +
287B HIS* 3.2 24.0 + - - -
86D ALA* 5.3 15.3 - - + +
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 2.9 34.2 + - + -
212B SER* 4.0 2.0 - - - +
213B THR* 3.1 33.7 + - - +
214B ASN* 4.7 3.8 + - - -
269B SER* 2.9 21.2 + - - +
270B THR 4.0 7.3 + - - -
272B LEU* 2.7 37.4 + - + +
273B PRO 2.8 16.8 + - - +
274B TYR* 3.4 29.3 - - - +
281B GLN* 3.1 22.8 + - + +
282B LEU 3.0 0.4 - - - -
283B GLN* 1.3 78.8 - - - +
285B LYS* 1.3 62.8 + - - +
286B ARG 3.3 1.6 - - - -
287B HIS* 3.4 5.0 + - - +
288B ILE* 3.3 36.9 + - + +
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Residues in contact with LYS 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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207B GLU* 2.7 34.5 + - - +
211B PHE* 3.7 30.9 - - + -
280B GLN* 3.9 16.6 - - + +
281B GLN 2.8 18.9 + - - +
282B LEU 4.3 0.4 - - - +
284B ARG* 1.3 69.1 - - - +
286B ARG* 1.3 57.4 + - - +
287B HIS 3.0 5.6 + - - -
289B GLY* 2.8 37.3 + - - +
309B ILE* 4.0 7.1 - - - +
310B ALA* 3.4 19.5 + - - +
31D LYS* 5.9 1.0 - - - +
32D TYR* 3.4 49.3 + - + -
34D PRO* 4.0 8.1 - - - -
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Residues in contact with ARG 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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242B GLY 5.2 3.2 + - - -
250B THR* 3.9 7.1 - - - +
282B LEU* 2.8 20.7 + - + +
283B GLN* 4.3 12.7 + - - +
284B ARG 3.3 0.4 - - - -
285B LYS* 1.3 77.2 - - - +
287B HIS* 1.3 95.4 + - + +
290B ASN* 3.2 20.4 + - - +
11D SER* 3.8 25.7 + - - -
12D GLY* 3.5 30.4 - - - +
13D GLY* 4.4 1.6 - - - +
32D TYR* 3.4 20.3 - - + +
86D ALA* 5.4 2.9 - - - +
88D SER* 2.9 32.2 + - - -
89D THR* 4.0 14.1 - - - +
92D ASP* 4.1 8.9 + - - -
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Residues in contact with HIS 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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194B LYS* 5.3 0.2 + - - -
241B GLY 5.0 0.4 + - - -
242B GLY* 3.7 22.3 + - - -
243B LEU* 3.8 12.4 - - + +
250B THR* 3.5 31.4 - - + +
267B HIS* 3.4 26.2 + - + +
272B LEU* 3.7 16.2 - - + -
283B GLN 3.2 25.9 + - - -
284B ARG 3.4 3.8 + - - +
285B LYS 3.0 0.4 - - - -
286B ARG* 1.3 110.0 + - + +
288B ILE* 1.3 64.2 + - - +
289B GLY 3.3 0.9 - - - -
290B ASN* 3.4 9.6 + - - +
291B ASP* 3.0 22.4 + - - +
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Residues in contact with ILE 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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196B GLY* 4.0 17.3 - - - -
197B VAL 4.3 2.2 - - - +
198B ILE* 4.2 11.7 - - + -
211B PHE* 4.2 25.8 - - + -
267B HIS* 3.6 32.1 - - + +
269B SER* 3.9 30.3 - - - -
272B LEU* 4.1 5.8 - - + -
284B ARG 3.3 19.1 + - - +
287B HIS* 1.3 75.8 - - - +
289B GLY* 1.3 60.7 + - - +
290B ASN 3.2 0.4 - - - -
291B ASP* 3.3 12.3 + - - +
294B ALA* 4.7 6.3 - - + -
309B ILE* 6.1 1.3 - - + -
314B LEU* 3.3 27.2 - - + +
317B TYR* 6.5 0.2 - - + -
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Residues in contact with GLY 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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211B PHE* 5.3 0.9 - - - -
285B LYS* 2.8 26.6 + - - +
288B ILE* 1.3 78.0 - - - +
290B ASN* 1.3 55.7 + - - +
291B ASP 3.4 1.6 - - - -
311B SER* 3.5 7.9 + - - -
313B PHE* 3.3 14.6 - - - +
314B LEU* 3.7 13.5 - - - -
34D PRO* 3.3 30.5 - - - +
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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