Contacts of the helix formed by residues 281 - 289 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A PHE* 3.5 24.9 - - + +
212A SER* 3.4 21.8 + - - +
273A PRO 4.5 0.8 + - - -
274A TYR* 3.4 23.6 + - - +
275A THR* 2.8 46.4 + - - +
277A GLY 5.0 0.2 + - - -
278A ASP* 3.0 31.3 + - - +
279A ALA 3.2 4.5 - - - +
280A GLN* 1.3 78.6 - - - +
282A LEU* 1.3 65.6 + - - +
283A GLN 3.2 2.9 - - - +
284A ARG* 3.0 19.0 + - - +
285A LYS* 2.9 17.7 + - - +
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Residues in contact with LEU 282 (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 ASP* 3.6 15.8 + - - +
280A GLN* 3.4 28.7 - - + +
281A GLN* 1.3 75.5 - - - +
283A GLN* 1.3 58.4 + - + +
285A LYS* 3.6 8.1 - - + -
286A ARG* 2.9 46.6 + - + +
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Residues in contact with GLN 283 (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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249A GLN* 3.9 11.7 + - - +
250A THR* 4.4 2.0 - - - +
273A PRO* 3.3 47.0 - - + +
274A TYR 6.0 0.2 - - - -
275A THR* 3.8 19.5 + - - +
281A GLN* 3.1 1.7 + - - +
282A LEU* 1.3 79.5 - - - +
284A ARG* 1.3 59.6 + - - +
286A ARG* 2.9 35.8 + - - +
287A HIS* 3.6 19.4 + - - -
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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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210A LEU 5.7 0.2 + - - -
211A PHE* 3.4 38.8 + - + -
212A SER 4.6 0.4 - - - -
213A THR 3.6 18.0 + - - -
214A ASN* 3.0 26.8 - - - +
269A SER* 2.8 46.4 + - - +
270A THR* 3.7 6.3 + - - +
272A LEU* 3.2 36.4 + - + +
273A PRO 3.2 21.3 + - - +
274A TYR* 3.4 23.3 - - - +
281A GLN* 3.0 18.1 + - - +
283A GLN* 1.3 75.6 - - - +
285A LYS* 1.3 64.0 + - - +
286A ARG 3.3 2.9 + - - -
287A HIS 3.6 2.1 + - - -
288A ILE* 3.5 20.8 + - - +
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Residues in contact with LYS 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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207A GLU* 3.6 24.5 + - - +
211A PHE* 3.7 25.6 - - + -
280A GLN* 3.6 22.8 - - + +
281A GLN 2.9 15.8 + - - +
282A LEU* 3.2 7.6 + - + +
284A ARG* 1.3 75.0 - - - +
286A ARG* 1.3 62.4 + - - +
287A HIS 3.3 0.9 - - - -
289A GLY* 3.2 30.2 + - - +
309A ILE* 4.6 8.1 - - - -
310A ALA* 2.9 30.1 + - - +
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Residues in contact with ARG 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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242A GLY 5.0 3.6 + - - -
249A GLN* 6.1 0.2 - - - +
250A THR* 3.7 12.5 - - - +
282A LEU* 2.9 28.3 + - + +
283A GLN* 2.9 43.8 + - - +
284A ARG 3.3 0.4 - - - -
285A LYS* 1.3 78.9 - - - +
287A HIS* 1.3 92.4 + - - +
290A ASN* 3.7 24.2 + - - +
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Residues in contact with HIS 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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194A LYS* 4.5 0.6 + - - +
241A GLY 5.3 0.2 + - - -
242A GLY* 4.1 18.1 + - - -
243A LEU* 4.2 7.7 - - + +
250A THR* 3.6 20.4 - - + +
267A HIS* 3.6 31.7 + + + +
272A LEU* 3.4 29.6 - - + -
283A GLN 3.6 15.5 + - - -
284A ARG 3.6 3.5 + - - +
285A LYS 3.3 0.2 - - - -
286A ARG* 1.3 122.4 + - - +
288A ILE* 1.3 63.7 + - - +
289A GLY 3.1 1.1 - - - -
290A ASN* 3.1 12.9 + - - +
291A ASP* 2.9 18.7 + - - +
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Residues in contact with ILE 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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196A GLY* 4.5 11.2 - - - -
197A VAL 3.6 15.7 - - - +
198A ILE* 4.2 24.9 - - + -
211A PHE* 4.2 24.5 - - + -
267A HIS* 3.5 34.1 - - + +
269A SER* 3.8 23.1 - - - +
272A LEU* 4.5 1.3 - - + -
284A ARG 3.5 14.3 + - - +
287A HIS* 1.3 74.4 - - - +
289A GLY* 1.3 59.7 + - - +
291A ASP* 3.4 18.9 + - - +
294A ALA* 4.8 3.4 - - + -
314A LEU* 3.4 20.2 - - + +
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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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211A PHE* 6.2 0.2 - - - -
285A LYS* 3.2 31.6 + - - +
286A ARG 4.6 0.2 - - - -
287A HIS 3.1 1.2 - - - -
288A ILE* 1.3 80.1 - - - +
290A ASN* 1.3 58.9 + - - +
291A ASP 3.3 1.1 - - - +
311A SER* 2.8 29.9 + - - -
312A ASN 5.0 0.3 + - - -
313A PHE* 3.4 12.3 - - - +
314A LEU* 4.5 3.4 - - - -
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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