Contacts of the helix formed by residues 198 - 212 (chain B) in PDB entry 3BRS
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 ASN 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B GLU* 4.3 4.6 + - - -
139B PHE* 3.6 24.0 - - + +
149B ARG* 3.7 11.7 - - - +
172B SER* 3.4 22.8 + - - -
196B GLY 3.4 1.2 - - - -
197B LEU* 1.3 79.7 - - - +
199B GLN* 1.3 65.8 + - - +
200B TYR* 3.6 19.7 - - - +
201B SER* 3.0 27.5 + - - -
202B ALA* 2.9 20.8 + - - +
223B ILE* 3.2 14.1 + - - -
224B ASP 6.0 0.2 - - - -
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Residues in contact with GLN 199 (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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18B SER 3.6 13.9 + - - -
19B SER* 4.1 6.5 + - - +
20B ASP* 3.3 23.7 + - - +
21B PHE* 3.9 5.3 + - + +
174B TYR* 3.1 24.5 + - - -
198B ASN* 1.3 74.8 - - - +
200B TYR* 1.4 57.9 + - + +
202B ALA* 3.7 3.0 - - - +
203B THR* 2.7 50.1 + - - +
223B ILE 3.7 2.8 + - - -
224B ASP* 3.3 27.7 - - - +
225B SER* 3.3 23.3 - - - +
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Residues in contact with TYR 200 (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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14B VAL* 4.1 7.5 - - + +
16B ASP* 2.6 37.9 + - - +
19B SER* 3.6 19.9 - - - -
22B TRP* 5.0 1.1 - + - -
48B GLU* 3.7 18.8 - - + -
170B CYS* 4.5 0.7 - - - -
172B SER* 3.4 42.8 - - - -
173B ASN 4.2 1.6 - - - +
174B TYR* 3.4 55.9 - + + -
177B ALA* 3.4 10.4 - - - +
198B ASN* 3.6 18.2 - - - +
199B GLN* 1.4 81.0 - - + +
201B SER* 1.3 60.6 + - - +
204B GLY 3.2 17.3 + - - -
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Residues in contact with SER 201 (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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137B ILE* 3.1 41.3 + - - +
138B SER* 3.1 23.4 + - - -
170B CYS* 3.4 4.9 - - - -
177B ALA* 3.9 6.8 - - - +
196B GLY* 3.9 1.5 - - - -
197B LEU 3.8 6.8 + - - -
198B ASN* 3.0 21.5 + - - -
200B TYR* 1.3 74.8 - - - +
202B ALA* 1.3 68.3 + - - +
204B GLY 3.6 0.5 + - - -
205B ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 202 (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 7.7 - - - -
198B ASN 2.9 14.7 + - - +
199B GLN* 3.7 7.2 - - - +
201B SER* 1.3 77.7 - - - +
203B THR* 1.3 57.9 + - - +
205B ALA* 3.3 5.3 + - - +
206B ALA* 2.8 30.0 + - - +
220B LEU* 5.0 1.3 - - - -
222B CYS* 3.5 33.2 - - + -
224B ASP* 4.9 2.2 - - - +
238B PHE* 3.6 21.3 - - + -
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Residues in contact with THR 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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174B TYR* 3.5 23.1 - - + -
199B GLN* 2.7 38.1 + - - +
202B ALA* 1.3 71.7 - - - +
204B GLY* 1.3 64.4 + - - +
206B ALA* 3.2 5.6 + - - +
207B ARG* 3.1 56.1 + - + +
234B GLU 5.3 7.4 + - - +
238B PHE* 5.0 3.9 - - - -
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Residues in contact with GLY 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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174B TYR* 3.8 13.2 - - - -
177B ALA* 3.7 15.9 - - - -
178B TYR* 3.6 16.4 - - - -
200B TYR 3.2 9.5 + - - -
203B THR* 1.3 80.7 - - - +
205B ALA* 1.3 61.2 + - - +
207B ARG* 3.4 8.3 + - - -
208B ALA* 3.0 24.4 + - - +
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Residues in contact with ALA 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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137B ILE* 4.5 7.0 - - + -
177B ALA 4.2 0.8 + - - -
181B THR* 3.3 30.1 + - + +
194B MET* 5.0 4.3 - - + -
196B GLY* 5.6 0.9 - - - -
201B SER 3.1 19.6 + - - +
202B ALA 3.5 3.4 - - - +
204B GLY* 1.3 73.5 - - - +
206B ALA* 1.3 66.3 + - - +
208B ALA* 3.2 1.4 + - - +
209B ILE* 3.0 28.4 + - + +
220B LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 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 ALA 2.8 14.4 + - - +
203B THR* 3.2 4.7 + - - +
205B ALA* 1.3 78.5 - - - +
207B ARG* 1.3 63.1 + - - +
209B ILE* 3.4 5.2 + - - +
210B LYS* 3.2 22.0 + - - +
220B LEU* 3.4 26.4 - - + +
236B GLY 4.8 10.8 - - - +
237B ILE 5.1 1.3 - - - +
238B PHE* 4.2 11.0 - - + -
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Residues in contact with ARG 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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174B TYR* 3.9 33.5 + - - +
175B ASP* 5.3 3.8 + - - -
178B TYR* 3.9 15.5 - - + +
203B THR* 3.1 41.4 + - + +
204B GLY* 3.7 8.3 - - - +
206B ALA* 1.3 77.9 - - + +
208B ALA* 1.3 62.5 + - - +
210B LYS* 3.4 11.6 - - + +
211B ASP* 3.0 28.4 + - - +
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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
----------------------------------------------------------
178B TYR* 3.5 39.9 - - + +
181B THR* 3.6 19.5 - - + -
182B VAL* 4.1 10.0 - - + +
204B GLY 3.0 17.3 + - - +
205B ALA 3.2 0.2 + - - -
207B ARG* 1.3 77.8 - - - +
209B ILE* 1.3 60.0 + - - +
211B ASP* 3.1 3.3 + - - +
212B MET* 3.1 29.8 + - - +
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 4.5 2.2 - - + -
185B LEU* 4.0 22.7 - - + -
194B MET* 4.3 11.2 - - + -
205B ALA* 3.0 20.9 + - + +
206B ALA* 3.8 4.0 - - - +
208B ALA* 1.3 73.9 - - - +
210B LYS* 1.3 60.2 + - - +
212B MET* 3.5 2.4 + - - -
213B SER 3.4 2.8 + - - -
214B LEU* 2.9 55.9 + - + +
215B GLU* 3.9 12.0 + - + +
218B VAL* 3.9 30.1 - - + +
220B LEU* 4.1 29.4 - - + -
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Residues in contact with LYS 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 ALA 3.2 13.1 + - - +
207B ARG* 3.4 13.5 - - + +
209B ILE* 1.3 79.3 - - - +
211B ASP* 1.3 69.0 + - - +
213B SER* 3.4 14.7 + - - -
215B GLU* 3.6 29.9 - - + +
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Residues in contact with ASP 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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178B TYR* 2.4 40.0 + - + +
207B ARG* 3.0 20.2 + - - +
208B ALA 3.1 5.3 + - - +
210B LYS* 1.3 86.4 + - - +
212B MET* 1.3 61.4 + - + +
213B SER* 3.1 9.5 + - - -
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Residues in contact with MET 212 (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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182B VAL* 3.9 34.3 - - + +
185B LEU* 3.7 26.2 - - + +
186B THR* 4.0 17.3 - - - +
208B ALA* 3.1 19.1 + - - +
209B ILE 4.1 1.3 - - - +
210B LYS 3.2 0.4 - - - -
211B ASP* 1.3 79.6 - - + +
213B SER* 1.3 68.7 + - - +
214B LEU* 3.5 39.3 + - + +
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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