Contacts of the helix formed by residues 190 - 201 (chain B) in PDB entry 2AVD
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.4 17.0 - - + +
187B ASP* 2.9 23.0 + - - +
188B LYS 3.2 0.2 - - - -
189B GLU* 1.3 81.0 - - - +
191B CYS* 1.3 64.0 + - - +
192B SER 3.2 3.4 - - - -
193B ALA* 3.1 13.9 + - + +
194B TYR* 2.9 52.7 + - + -
601B SAM 4.9 2.8 + - - -
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Residues in contact with CYS 191 (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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184B VAL* 4.6 9.6 - - + +
187B ASP 3.9 9.7 + - - +
188B LYS* 3.1 42.8 + - + +
189B GLU 3.5 0.4 - - - -
190B ASN* 1.3 77.7 - - - +
192B SER* 1.3 60.7 + - - +
194B TYR* 3.5 13.2 - - + +
195B TYR* 2.9 29.3 + - - +
210B VAL* 5.5 0.4 - - + -
231B CYS* 3.8 24.9 - - - -
232B VAL* 4.5 3.1 - - - -
235B LEU* 3.7 25.9 - - + +
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Residues in contact with SER 192 (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 GLU 5.3 0.8 + - - -
190B ASN 3.2 0.8 - - - -
191B CYS* 1.3 81.0 - - - +
193B ALA* 1.3 62.6 + - - +
195B TYR* 3.2 4.0 + - - +
196B GLU* 3.0 31.3 + - - +
231B CYS* 4.7 2.3 + - - +
234B ASN* 4.8 5.2 - - - +
235B LEU* 3.9 32.8 + - - +
238B ARG* 5.7 2.5 - - - +
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Residues in contact with ALA 193 (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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164B LEU* 3.8 18.8 - - + -
190B ASN* 3.1 17.3 + - + +
192B SER* 1.3 76.9 - - - +
194B TYR* 1.3 63.8 + - - +
196B GLU* 3.5 3.2 + - - -
197B ARG* 3.1 53.3 + - - +
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Residues in contact with TYR 194 (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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109B LEU* 3.8 20.4 - - + -
163B ALA* 3.8 8.7 - - + +
164B LEU* 3.7 29.8 + - + +
167B LEU* 3.6 19.5 - - + -
184B VAL* 3.9 15.3 - - + -
186B ALA* 3.8 12.6 - - + -
187B ASP* 2.5 44.9 + - - -
190B ASN* 2.9 35.9 + - + +
191B CYS* 3.5 14.6 - - - +
193B ALA* 1.3 74.8 - - - +
195B TYR* 1.3 61.0 + - - +
197B ARG* 3.3 1.6 + - - +
198B CYS* 2.8 35.9 + - - -
601B SAM 3.3 16.3 + - - -
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 4.8 5.5 - - + +
191B CYS 2.9 16.9 + - - +
192B SER 3.2 3.8 + - - +
194B TYR* 1.3 76.0 - - - +
196B GLU* 1.3 77.3 + - + +
198B CYS* 4.7 0.9 - - - -
199B LEU* 3.0 31.2 + - + +
208B LEU* 3.6 38.9 - - + +
210B VAL* 4.5 2.5 - - + -
235B LEU* 3.7 22.4 - - + -
238B ARG* 3.8 13.9 - - - -
239B ILE* 3.7 29.2 - - + +
242B ASP* 2.7 31.6 + - - +
244B ARG* 3.9 8.5 - - - -
245B VAL* 3.6 24.1 - - - +
259B ALA* 4.5 9.4 - - + -
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Residues in contact with GLU 196 (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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192B SER* 3.0 23.1 + - - +
193B ALA* 3.9 5.2 - - - +
195B TYR* 1.3 81.2 - - - +
197B ARG* 1.3 70.7 + - - +
199B LEU* 3.4 4.8 + - - +
200B GLN* 3.2 22.6 + - - +
238B ARG* 2.8 36.5 + - - +
244B ARG* 2.9 33.4 + - - -
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Residues in contact with ARG 197 (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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164B LEU* 3.5 27.4 - - - +
167B LEU* 3.9 25.6 - - + -
168B ASP* 2.9 27.8 + - - -
171B LEU* 3.9 20.3 - - + +
193B ALA* 3.1 41.7 + - - +
194B TYR 3.9 2.0 - - - +
196B GLU* 1.3 83.3 - - + +
198B CYS* 1.3 59.0 + - - +
200B GLN* 3.2 6.6 + - - +
201B LEU* 2.9 34.8 + - - +
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Residues in contact with CYS 198 (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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107B LEU* 4.0 14.1 - - - -
109B LEU* 3.7 27.6 - - - -
167B LEU* 4.1 4.0 - - - -
182B ALA* 3.8 25.1 - - + +
184B VAL* 3.9 11.4 - - + -
194B TYR 2.8 24.3 + - - +
195B TYR 3.9 2.5 - - - +
197B ARG* 1.3 71.4 - - - +
199B LEU* 1.3 63.2 + - - +
201B LEU* 3.0 8.7 + - - +
202B LEU* 2.9 27.9 + - - +
208B LEU* 4.0 11.7 - - + -
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Residues in contact with LEU 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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195B TYR* 3.0 22.8 + - + +
196B GLU* 3.7 5.8 - - - +
197B ARG 3.3 0.2 - - - -
198B CYS* 1.3 77.1 - - - +
200B GLN* 1.3 60.2 + - - +
202B LEU* 3.4 9.8 + - + -
208B LEU* 3.6 16.7 - - + +
242B ASP* 3.8 8.7 - - - +
244B ARG* 3.4 54.7 - - + +
245B VAL* 3.6 24.2 - - + -
261B LYS* 2.9 54.8 + - + +
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Residues in contact with GLN 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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171B LEU* 3.5 31.1 - - + +
176B ALA* 3.4 14.7 - - + +
177B GLY* 2.9 20.8 + - - -
196B GLU 3.2 14.2 + - - +
197B ARG* 3.2 8.9 + - - +
199B LEU* 1.3 79.2 - - - +
201B LEU* 1.3 58.8 + - - +
202B LEU 3.5 2.4 + - - +
261B LYS* 3.9 7.1 + - - +
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Residues in contact with LEU 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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107B LEU* 3.7 13.2 - - + -
167B LEU* 3.7 39.5 - - + +
170B LEU* 3.8 24.2 - - + -
171B LEU* 3.8 25.1 - - + -
175B GLU 3.6 21.5 - - - +
177B GLY 3.6 2.0 - - - +
178B THR 3.1 9.9 + - - -
179B PHE* 2.9 41.1 + - + +
197B ARG 2.9 20.7 + - - +
198B CYS* 3.0 5.8 + - - +
200B GLN* 1.3 75.9 - - - +
202B LEU* 1.3 58.3 + - - +
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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