Contacts of the helix formed by residues 219 - 228 (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 ALA 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B SER* 3.1 4.4 + - - +
218B PRO* 1.3 76.2 - - - +
220B PHE* 1.3 65.0 + - - +
222B GLU* 3.6 9.2 + - - +
223B PHE* 3.2 22.2 + - - +
297B PHE* 3.6 3.7 - - - -
299B ASP* 3.4 26.0 - - - +
322B ALA* 4.1 17.0 - - + -
330B PRO* 5.5 7.2 - - + -
332B TYR* 4.3 4.9 + - - +
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Residues in contact with PHE 220 (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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197B VAL* 4.1 18.2 - - + -
198B ILE 4.5 1.1 - - - -
199B TYR* 3.5 25.1 - + + -
216B GLU* 3.7 21.5 - - + -
217B SER* 3.0 21.8 + - - +
219B ALA* 1.3 74.4 - - - +
221B VAL* 1.3 53.6 + - - +
222B GLU 3.0 3.8 - - - -
223B PHE* 2.8 22.9 + - - +
224B LEU* 2.9 49.3 + - + +
268B VAL* 4.7 2.5 - - + -
269B SER* 5.6 0.4 - - - -
270B THR* 3.6 34.8 - - + -
297B PHE* 3.1 54.8 - + + -
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Residues in contact with VAL 221 (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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216B GLU* 3.4 30.3 - - + +
217B SER 2.8 17.4 + - - +
218B PRO* 3.5 21.5 - - + +
220B PHE* 1.3 72.3 - - - +
222B GLU* 1.3 62.1 + - + +
224B LEU* 4.1 7.0 - - + +
225B GLU* 3.6 24.1 + - - +
230B LYS* 5.3 12.8 - - - -
271B LYS* 5.6 0.9 - - - +
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Residues in contact with GLU 222 (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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218B PRO 3.5 15.2 + - - +
219B ALA* 3.7 5.2 - - - +
220B PHE 3.0 0.6 - - - -
221B VAL* 1.3 79.1 - - + +
223B PHE* 1.3 60.9 + - - +
224B LEU 3.3 0.2 - - - -
225B GLU* 3.5 7.0 + - + +
226B PHE* 3.0 26.7 + - - +
329B GLY* 4.9 1.7 - - - -
330B PRO* 3.3 33.7 - - - +
332B TYR* 3.9 6.7 + - - -
357B LYS* 3.3 41.1 + - - +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 4.9 4.3 - - + -
219B ALA 3.2 11.5 + - - +
220B PHE 2.8 7.3 + - - +
222B GLU* 1.3 80.8 - - - +
224B LEU* 1.3 68.2 + - + +
226B PHE* 3.1 36.7 - + - -
227B LEU* 2.7 56.4 + - + +
295B VAL* 4.2 23.1 - - + -
297B PHE* 3.4 40.8 - + + -
320B VAL* 3.8 21.5 - - + -
332B TYR* 4.0 17.9 - + - +
361B PHE* 4.8 2.9 - + - -
365B LEU* 4.4 7.0 - - + -
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Residues in contact with LEU 224 (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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197B VAL* 4.7 4.0 - - + -
216B GLU* 4.5 1.6 - - - +
220B PHE* 2.9 59.2 + - + +
221B VAL* 4.5 6.3 - - + +
222B GLU 3.3 0.2 - - - -
223B PHE* 1.3 91.4 - - + +
225B GLU* 1.3 63.4 + - - +
226B PHE 3.2 1.3 - - - -
227B LEU* 3.6 13.7 + - + +
228B GLY 3.5 15.4 + - - +
230B LYS* 4.4 8.1 - - + +
255B VAL* 4.1 17.4 - - + +
268B VAL* 3.8 28.7 - - + -
271B LYS* 3.4 33.4 - - - +
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Residues in contact with GLU 225 (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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221B VAL* 3.6 19.8 + - - +
222B GLU* 3.5 6.9 + - - +
223B PHE 3.4 0.2 - - - -
224B LEU* 1.3 77.9 - - - +
226B PHE* 1.3 63.0 + - - +
228B GLY 3.4 13.4 - - - +
229B GLN* 5.7 0.2 - - - +
230B LYS* 4.3 24.7 - - + +
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Residues in contact with PHE 226 (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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222B GLU 3.0 18.6 + - - +
223B PHE* 3.1 39.3 - + - +
224B LEU 3.2 0.2 - - - -
225B GLU* 1.3 79.9 - - - +
227B LEU* 1.3 71.1 + - - +
228B GLY* 4.4 0.5 - - - -
332B TYR* 5.2 3.1 - + - +
357B LYS* 3.7 34.8 - - + +
358B GLY* 3.8 20.4 - - - -
361B PHE* 3.2 40.2 - + - -
362B GLN* 3.6 44.2 - - + +
365B LEU* 4.7 5.8 - - + -
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Residues in contact with LEU 227 (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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197B VAL* 4.5 13.5 - - + -
223B PHE* 2.7 46.0 + - + +
224B LEU* 4.0 11.2 - - + +
225B GLU 3.5 0.6 - - - -
226B PHE* 1.3 82.4 - - + +
228B GLY* 1.3 58.4 + - - +
255B VAL* 4.3 7.6 - - + -
257B CYS* 4.4 7.2 - - - -
266B PHE* 3.7 44.9 - - + -
295B VAL* 5.2 3.1 - - + -
362B GLN* 3.6 20.4 - - + +
365B LEU* 3.8 24.5 - - + -
366B LEU* 4.1 10.7 - - + +
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Residues in contact with GLY 228 (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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224B LEU 3.5 8.7 + - - +
225B GLU* 3.4 18.3 - - - +
226B PHE 3.4 1.5 - - - -
227B LEU* 1.3 81.1 - - - +
229B GLN* 1.3 64.7 + - - +
230B LYS 3.6 1.6 + - - -
255B VAL* 3.7 13.6 - - - +
256B TYR 3.7 4.9 - - - -
257B CYS* 4.4 10.8 - - - -
362B GLN* 5.0 2.5 - - - -
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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