Contacts of the helix formed by residues 198 - 212 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU* 4.4 3.8 + - - -
139A PHE* 3.6 21.8 - - + +
149A ARG* 3.6 13.9 - - - +
172A SER* 3.5 14.8 + - - -
196A GLY 3.4 0.4 - - - -
197A LEU* 1.3 80.9 - - - +
199A GLN* 1.3 65.5 + - - +
200A TYR* 3.3 28.8 - - - +
201A SER* 3.0 29.3 + - - -
202A ALA* 3.0 21.5 + - - +
223A ILE 3.2 13.4 - - - +
224A ASP* 5.2 0.4 - - - +
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 3.7 13.5 + - - -
19A SER* 4.0 4.7 + - - -
20A ASP* 3.1 15.5 + - - +
21A PHE 3.9 0.2 + - - -
174A TYR* 3.4 21.6 + - - +
198A ASN* 1.3 76.4 - - - +
200A TYR* 1.4 56.7 + - + +
202A ALA* 3.2 4.4 + - + +
203A THR* 2.8 48.9 + - - +
223A ILE 3.9 1.4 + - - -
224A ASP* 3.4 23.1 + - - +
225A SER* 2.2 36.5 + - - +
229A GLN* 2.9 27.0 - - - +
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Residues in contact with TYR 200 (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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14A VAL* 4.0 9.1 - - + +
16A ASP* 2.7 42.1 + - - +
19A SER* 3.4 17.8 - - - -
22A TRP* 4.9 0.9 - + - -
48A GLU* 3.4 21.5 - - + -
170A CYS* 4.4 0.7 - - - -
172A SER* 3.3 44.2 - - - -
173A ASN* 4.0 2.9 - - - +
174A TYR* 3.6 49.8 - + + -
177A ALA* 3.4 10.5 - - - +
198A ASN* 3.3 19.7 - - - +
199A GLN* 1.4 80.9 - - + +
201A SER* 1.3 61.8 + - - +
204A GLY 3.2 17.2 + - - -
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 3.0 34.1 + - - +
138A SER* 3.1 23.0 + - - -
139A PHE 3.8 0.2 + - - -
170A CYS* 3.5 2.6 - - - -
177A ALA* 3.7 13.7 - - - +
196A GLY* 3.8 2.2 - - - -
197A LEU 3.7 6.4 + - - -
198A ASN* 3.0 23.2 + - - -
200A TYR* 1.3 78.0 - - - +
202A ALA* 1.3 64.4 + - - +
205A ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 202 (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* 4.2 7.2 - - - -
198A ASN 3.0 11.5 + - - +
199A GLN* 3.8 4.7 - - - +
201A SER* 1.3 77.6 - - - +
203A THR* 1.3 60.4 + - - +
205A ALA* 3.3 6.0 + - - +
206A ALA* 2.9 28.9 + - - +
220A LEU* 3.8 4.0 - - + +
222A CYS* 3.5 34.3 - - + -
223A ILE 5.1 0.2 - - - +
224A ASP* 5.5 2.0 - - - +
238A PHE* 3.7 18.6 - - + -
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Residues in contact with THR 203 (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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174A TYR* 3.7 23.2 - - + -
199A GLN* 2.8 37.3 + - - +
202A ALA* 1.3 73.7 - - - +
204A GLY* 1.3 61.7 + - - +
206A ALA* 3.3 5.8 + - - +
207A ARG* 3.2 50.1 + - + +
229A GLN* 5.3 1.2 + - - -
238A PHE* 4.7 5.5 - - - -
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Residues in contact with GLY 204 (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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174A TYR* 4.1 8.0 - - - -
177A ALA* 3.7 16.6 - - - -
178A TYR* 3.6 21.4 - - - -
200A TYR 3.2 10.3 + - - -
203A THR* 1.3 78.4 - - - +
205A ALA* 1.4 61.5 + - - +
207A ARG* 3.4 8.0 + - - -
208A ALA* 3.2 24.4 + - - +
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Residues in contact with ALA 205 (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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137A ILE* 4.6 7.9 - - + -
177A ALA 4.3 0.6 + - - -
181A THR* 3.3 27.6 + - + +
194A MET* 4.8 4.7 - - + -
196A GLY* 5.6 1.6 - - - +
201A SER 3.1 14.3 + - - +
202A ALA* 3.5 8.5 - - - +
204A GLY* 1.4 72.1 - - - +
206A ALA* 1.4 64.9 + - - +
208A ALA* 3.9 0.9 - - - +
209A ILE* 3.0 33.8 + - + +
220A LEU* 3.9 20.4 - - + -
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Residues in contact with ALA 206 (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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202A ALA 2.9 13.4 + - - +
203A THR* 3.3 6.0 + - - +
205A ALA* 1.4 77.1 - - - +
207A ARG* 1.3 63.0 + - + +
209A ILE* 3.8 6.0 - - - +
210A LYS* 3.0 21.8 + - - +
220A LEU* 3.5 24.4 - - + +
237A ILE* 5.4 7.9 - - + +
238A PHE* 4.3 11.7 - - + -
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Residues in contact with ARG 207 (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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174A TYR* 3.6 36.6 + - - +
175A ASP* 5.1 4.9 + - - -
178A TYR* 3.9 17.3 - - + +
203A THR* 3.2 36.8 + - + +
204A GLY* 3.8 8.9 - - - +
205A ALA 3.3 0.2 - - - -
206A ALA* 1.3 78.3 - - + +
208A ALA* 1.3 52.8 + - - +
210A LYS* 3.0 11.9 + - - +
211A ASP* 2.8 39.4 + - - +
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Residues in contact with ALA 208 (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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178A TYR* 3.4 34.5 - - + +
181A THR* 3.6 23.8 - - + -
182A VAL* 3.9 10.3 - - + -
204A GLY 3.2 15.0 + - - +
206A ALA 3.4 0.2 - - - -
207A ARG* 1.3 77.2 - - - +
209A ILE* 1.3 64.1 + - - +
211A ASP* 3.1 2.2 + - - +
212A MET* 2.9 32.0 + - - +
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Residues in contact with ILE 209 (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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181A THR* 4.5 2.5 - - + -
185A LEU* 3.9 23.8 - - + -
194A MET* 4.1 17.5 - - + -
205A ALA* 3.0 25.3 + - + +
206A ALA* 3.8 4.5 - - - +
208A ALA* 1.3 76.4 - - - +
210A LYS* 1.3 58.3 + - - +
212A MET* 3.6 5.3 + - - -
213A SER 3.4 1.6 + - - -
214A LEU* 3.1 35.0 + - + +
215A GLU* 3.9 26.2 + - + -
218A VAL* 3.8 30.3 - - + +
220A LEU* 4.1 22.0 - - + -
237A ILE* 5.1 8.3 - - + -
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Residues in contact with LYS 210 (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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206A ALA 3.0 13.8 + - - +
207A ARG* 3.0 16.1 + - - +
209A ILE* 1.3 78.0 - - - +
211A ASP* 1.4 65.5 + - - +
213A SER* 3.0 21.8 + - - -
215A GLU* 5.0 12.9 - - + +
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Residues in contact with ASP 211 (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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178A TYR* 2.3 41.3 + - - +
182A VAL* 6.4 0.4 - - + -
207A ARG* 2.8 21.7 + - - +
208A ALA 3.1 3.8 + - - +
210A LYS* 1.4 84.0 - - - +
212A MET* 1.3 61.5 + - + +
213A SER* 3.2 2.8 + - - -
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Residues in contact with MET 212 (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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181A THR 4.6 0.4 - - - +
182A VAL* 4.0 34.8 - - + +
185A LEU* 3.9 27.1 - - + +
186A THR* 4.1 18.6 - - - +
208A ALA 2.9 19.4 + - - +
209A ILE 4.0 1.8 - - - +
210A LYS 3.2 0.2 - - - -
211A ASP* 1.3 78.6 - - + +
213A SER* 1.3 70.7 + - - +
214A LEU* 3.4 37.7 + - + +
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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