Contacts of the helix formed by residues 202 - 211 (chain B) in PDB entry 3BUW
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 TRP 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B VAL 3.6 1.4 + - - -
201B PRO* 1.3 70.5 - - - +
203B LYS* 1.3 78.1 + - + +
205B PHE* 3.0 26.1 + + - +
206B ARG* 2.8 66.5 + - + +
221B ALA* 3.3 25.2 - - + +
222B MET* 5.3 6.6 - - - -
224B LEU* 4.0 19.3 - - + -
225B LYS* 3.6 58.3 - - + +
228B ILE* 4.9 2.0 - - + -
234B ASP* 2.9 27.9 + - + +
235B TYR* 4.1 0.2 - - - +
236B ILE* 3.9 24.0 - - + -
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Residues in contact with LYS 203 (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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201B PRO* 3.7 16.0 - - + +
202B TRP* 1.3 111.0 - - + +
204B SER* 1.3 63.1 + - - +
206B ARG* 3.5 22.2 + - - +
207B GLN* 3.1 36.9 + - - +
234B ASP* 3.3 19.0 + - - +
235B TYR* 6.0 0.2 - - - -
146D GLN* 4.6 21.5 - - + +
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Residues in contact with SER 204 (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 PHE* 3.6 17.8 - - - -
200B VAL* 4.4 4.1 - - - +
201B PRO* 3.0 28.2 + - - +
203B LYS* 1.3 76.3 - - - +
205B PHE* 1.3 67.1 + - - +
207B GLN* 3.5 12.3 + - - +
208B ALA* 3.0 24.6 + - - +
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Residues in contact with PHE 205 (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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189B PHE* 4.4 8.7 - + - -
190B TRP* 4.1 7.6 - + - -
194B PHE* 3.9 22.2 - + - -
200B VAL* 3.9 10.0 - - + +
201B PRO 3.1 10.6 + - - +
202B TRP* 3.0 27.4 + + - +
204B SER* 1.3 78.5 - - - +
206B ARG* 1.3 60.5 + - - +
208B ALA* 3.3 1.9 + - - +
209B LEU* 2.8 61.3 + - + +
228B ILE* 3.8 24.0 - - + -
236B ILE* 3.9 25.8 - - + -
241B PHE* 3.5 37.9 - + - -
244B PHE* 6.1 0.4 - + - -
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Residues in contact with ARG 206 (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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202B TRP* 2.8 52.7 + - + +
203B LYS* 3.7 28.8 + - - +
205B PHE* 1.3 79.4 - - - +
207B GLN* 1.3 77.1 + - - +
209B LEU* 3.9 3.5 - - - +
210B HIS* 2.9 28.4 + - + +
215B ILE* 3.8 23.9 - - + +
221B ALA* 4.6 12.0 - - + +
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Residues in contact with GLN 207 (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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203B LYS* 3.1 26.9 + - - +
204B SER* 3.8 11.9 - - - +
206B ARG* 1.3 92.2 - - - +
208B ALA* 1.3 62.9 + - - +
210B HIS* 3.4 12.8 + - - +
211B GLU* 3.6 18.1 + - - +
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Residues in contact with ALA 208 (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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189B PHE* 3.6 14.0 - - + -
193B ALA* 4.0 15.0 - - + -
194B PHE* 3.4 28.5 - - + -
204B SER 3.0 18.0 + - - +
205B PHE 3.6 0.4 - - - +
207B GLN* 1.3 77.8 - - - +
209B LEU* 1.3 63.2 + - - +
211B GLU* 3.3 21.3 + - - +
212B VAL* 4.1 0.5 + - - +
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Residues in contact with LEU 209 (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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189B PHE* 3.6 16.5 - - + -
205B PHE* 2.8 47.7 + - + +
206B ARG* 3.9 4.0 - - - +
208B ALA* 1.3 73.5 - - - +
210B HIS* 1.3 54.3 + - - +
212B VAL* 3.0 4.0 + - - +
213B HIS* 2.8 52.1 + - + +
215B ILE* 4.8 2.9 - - + -
224B LEU* 3.9 23.6 - - + -
228B ILE* 5.2 2.2 - - + -
241B PHE* 5.2 0.4 - - + -
244B PHE* 5.8 0.2 - - + -
251B TRP* 3.9 28.7 - - + -
254B LEU* 4.4 8.7 - - + -
255B LEU* 4.6 14.6 - - + -
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Residues in contact with HIS 210 (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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206B ARG* 2.9 20.6 + - + +
207B GLN* 3.6 8.5 - - - +
208B ALA 3.3 0.4 - - - -
209B LEU* 1.3 76.7 - - - +
211B GLU* 1.3 70.8 + - - +
212B VAL 3.4 0.7 + - - -
213B HIS 3.6 7.4 - - - -
214B PRO* 3.5 26.8 - - + +
215B ILE* 2.9 54.6 + - + +
343D ARG* 3.7 23.2 + - + -
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Residues in contact with GLU 211 (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 GLN 3.6 14.5 - - - +
208B ALA* 3.3 11.6 + - - +
209B LEU 3.1 1.0 + - - -
210B HIS* 1.3 87.4 + - - +
212B VAL* 1.3 64.9 + - + +
214B PRO* 5.2 1.8 - - - +
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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