Contacts of the helix formed by residues 190 - 201 (chain B) in PDB entry 3MZ2
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 ASP 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ASP* 4.6 4.8 - - - +
192A ALA* 3.7 24.1 - - - +
193A SER* 5.0 1.7 + - - -
188B VAL* 4.2 1.4 - - - +
189B HIS* 1.3 82.2 - - - +
191B GLY* 1.3 64.4 + - - +
192B ALA* 3.8 6.3 - - - +
193B SER* 3.0 23.9 + - - -
194B ALA* 3.2 15.6 + - - +
218B ASP* 3.5 12.8 - - - +
219B TYR* 3.4 19.1 + - - -
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Residues in contact with GLY 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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190B ASP* 1.3 71.2 - - - +
192B ALA* 1.3 60.0 + - - +
194B ALA* 3.4 2.0 + - - +
195B ARG* 2.8 30.3 + - - +
218B ASP* 2.8 21.3 + - - -
219B TYR* 3.5 21.7 - - - -
222B ASN* 3.5 22.8 - - - +
224B ILE* 4.2 0.2 - - - +
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Residues in contact with ALA 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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190A ASP* 4.0 10.5 - - - +
192A ALA* 3.8 29.4 - - + -
218A ASP* 5.9 3.1 - - - +
222A ASN* 6.1 0.9 - - - +
190B ASP* 3.3 6.1 + - - +
191B GLY* 1.3 78.7 - - - +
193B SER* 1.3 56.4 + - - +
195B ARG* 3.3 4.6 + - - +
196B PHE* 3.0 26.3 + - - +
218B ASP* 4.5 0.6 + - - -
222B ASN* 3.6 16.5 - - - +
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Residues in contact with SER 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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190A ASP* 5.2 2.3 + - - -
168B MSE 3.7 24.1 - - - -
187B THR 4.9 0.5 + - - -
188B VAL* 3.4 23.0 - - - +
189B HIS* 4.5 6.0 + - - -
190B ASP* 3.0 21.3 + - - -
192B ALA* 1.3 72.7 - - - +
194B ALA* 1.3 66.4 + - - +
196B PHE* 3.2 11.4 + - - +
197B PHE* 3.2 22.7 + - - -
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Residues in contact with ALA 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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188B VAL* 3.9 25.2 - - + +
190B ASP 3.2 11.2 + - - +
191B GLY 3.6 7.9 - - - +
193B SER* 1.3 79.7 + - - +
195B ARG* 1.3 57.2 + - - +
197B PHE 3.2 2.8 + - - -
198B TYR* 2.8 29.5 + - - +
206B PHE* 3.6 12.3 - - + -
219B TYR* 4.2 8.7 - - + -
224B ILE* 3.7 26.0 - - + -
229B ILE* 5.8 0.2 - - + -
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Residues in contact with ARG 195 (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 PG4 4.4 25.4 + - - -
191B GLY 2.8 17.9 + - - +
192B ALA* 3.6 5.6 - - - +
193B SER 3.2 0.2 - - - -
194B ALA* 1.3 78.0 - - - +
196B PHE* 1.3 62.9 + - - +
198B TYR* 4.3 3.1 - - + -
199B GLU* 2.3 68.3 + - + +
222B ASN* 3.5 41.1 + - - +
224B ILE* 3.5 10.8 - - + -
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Residues in contact with PHE 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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6B SO4 5.6 1.1 - - - -
168B MSE 3.3 61.9 - - + -
169B GLU* 3.8 32.1 - - + -
172B ALA* 5.0 0.4 - - + -
192B ALA 3.0 13.5 + - - +
193B SER* 3.2 8.7 + - - +
195B ARG* 1.3 77.2 - - - +
197B PHE* 1.3 71.5 + + - +
199B GLU* 3.7 7.9 + - - +
200B LYS* 3.3 42.7 + - + +
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Residues in contact with PHE 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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168B MSE 3.3 61.2 - - + -
171B THR* 4.1 7.2 - - + -
172B ALA* 4.0 13.0 - - + -
186B ILE* 3.6 43.3 - - + -
187B THR 5.2 0.9 - - - -
188B VAL* 3.9 11.9 - - + -
193B SER* 3.2 25.5 + - - -
194B ALA 3.2 3.1 + - - +
196B PHE* 1.3 81.6 - + - +
198B TYR* 1.3 58.9 + - - +
200B LYS* 3.0 7.1 + - - +
201B ASN 2.9 25.8 + - - -
204B PHE* 3.4 19.8 - + + -
206B PHE* 3.6 19.1 - - + -
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Residues in contact with TYR 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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194B ALA 2.8 20.5 + - - +
195B ARG* 4.0 4.3 - - + +
197B PHE* 1.3 72.8 - - - +
199B GLU* 1.3 67.8 + - + +
201B ASN 3.9 4.9 - - - -
202B PRO* 3.2 66.5 + - + +
204B PHE 5.1 0.4 - - - -
206B PHE* 4.2 18.4 - + + -
222B ASN 5.9 0.2 - - - -
223B GLY 4.2 12.3 - - - -
224B ILE* 4.1 16.6 - - + -
225B PRO* 3.5 38.6 - - + +
228B HIS* 4.6 7.2 + + - -
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Residues in contact with GLU 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 ARG* 2.3 76.6 + - + +
196B PHE* 3.9 6.6 - - - +
198B TYR* 1.3 83.6 - - + +
200B LYS* 1.3 60.1 + - + +
202B PRO* 5.0 2.8 - - - +
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Residues in contact with LYS 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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169B GLU* 3.1 32.3 + - - +
172B ALA* 4.4 19.5 - - + -
196B PHE* 3.3 37.2 + - + +
197B PHE 3.0 9.2 + - - +
199B GLU* 1.3 80.0 - - + +
201B ASN* 1.3 60.2 + - + +
202B PRO* 4.5 1.8 - - - +
204B PHE* 4.5 1.1 - - + -
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Residues in contact with ASN 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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176B THR* 2.9 27.2 + - + +
181B GLU* 2.9 31.9 + - - +
197B PHE 2.9 7.6 + - - +
198B TYR* 3.3 5.1 - - - +
199B GLU 3.4 0.2 - - - -
200B LYS* 1.3 80.8 - - - +
202B PRO* 1.3 64.9 - - - +
203B ASN* 2.9 35.7 + - - +
204B PHE* 3.1 42.7 + - + +
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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