Contacts of the helix formed by residues 196 - 210 (chain B) in PDB entry 3MA0
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.9 21.4 - - - +
169B TRP* 3.2 26.7 - - + +
194B ALA* 3.5 1.5 - - - +
195B SER* 1.3 79.5 - - - +
197B ASP* 1.3 60.3 + - - +
198B ALA* 3.7 4.6 - - - +
199B THR* 2.7 45.0 + - - +
200B ALA* 2.9 28.2 + - - +
220B GLY* 3.8 2.8 - - - -
221B GLN* 3.5 19.1 - - + +
222B ASP* 4.2 2.0 + - - -
401B XYP 2.9 30.1 + - - +
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Residues in contact with ASP 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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196B ASN* 1.3 70.6 - - - +
198B ALA* 1.3 61.4 + - - +
200B ALA* 4.0 5.4 - - - -
201B GLY* 2.8 25.8 + - - -
221B GLN 2.9 24.7 + - - +
222B ASP* 5.5 0.2 - - - -
223B ALA* 3.2 2.4 + - - -
224B ASP* 2.9 44.0 + - + +
227B GLY* 3.8 11.9 - - - -
230B ARG* 3.0 15.8 + - - +
236B GLN* 3.0 18.7 + - - -
239B THR* 2.7 28.6 + - - -
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Residues in contact with ALA 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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14B LEU* 3.6 30.7 - - + -
169B TRP 3.9 8.1 - - - +
171B PRO* 3.6 28.8 - - + +
196B ASN* 3.3 7.2 + - - +
197B ASP* 1.3 80.3 - - - +
199B THR* 1.3 61.9 + - - +
201B GLY* 3.4 7.1 + - - -
202B GLY 3.5 8.5 + - - -
222B ASP* 5.9 0.2 + - - -
224B ASP* 4.0 10.5 + - - +
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Residues in contact with THR 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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129B MET* 4.1 12.4 - - - +
130B GLY 5.3 1.1 + - - +
166B VAL* 3.9 24.0 - - + -
169B TRP* 3.6 37.6 - - + +
170B LEU 4.3 0.9 - - - +
171B PRO* 4.6 0.9 - - - -
174B ALA* 3.2 20.8 - - + +
194B ALA* 4.2 1.6 - - - +
195B SER 4.0 6.9 + - - -
196B ASN* 2.7 38.5 + - - +
198B ALA* 1.3 72.8 - - - +
200B ALA* 1.3 65.6 + - - +
202B GLY 3.1 2.4 + - - -
203B ALA* 3.0 21.3 + - - +
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Residues in contact with ALA 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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194B ALA* 4.0 4.4 - - + +
196B ASN 2.9 19.0 + - - +
197B ASP* 3.3 8.0 + - - +
199B THR* 1.3 77.3 + - - +
201B GLY* 1.3 51.6 + - - +
203B ALA* 3.1 2.8 + - - +
204B ILE* 2.7 41.6 + - + +
218B ILE* 3.9 15.7 - - + -
219B SER 3.5 21.8 - - - +
236B GLN* 4.0 18.4 - - - +
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 5.7 0.4 - - - -
197B ASP 2.8 12.9 + - - -
198B ALA 3.4 3.3 + - - -
199B THR 3.2 0.4 - - - -
200B ALA* 1.3 76.6 - - - +
202B GLY* 1.3 56.1 + - - +
204B ILE* 3.3 3.5 + - - +
205B GLN* 3.0 28.3 + - - +
230B ARG* 3.6 30.9 - - - +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 3.7 26.0 - - - +
175B LEU* 3.5 25.3 - - - +
198B ALA 3.5 6.9 + - - -
199B THR 3.1 7.3 + - - -
201B GLY* 1.3 70.9 - - - +
203B ALA* 1.3 65.6 + - - +
205B GLN* 3.4 6.9 + - - +
206B ALA* 3.2 17.0 + - - +
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Residues in contact with ALA 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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129B MET* 4.2 13.9 - - - -
174B ALA* 4.2 1.8 - - - +
178B MET* 3.7 30.0 - - + +
192B VAL* 4.4 1.6 - - + -
199B THR 3.0 12.5 + - - +
200B ALA 3.4 8.1 - - - +
202B GLY* 1.3 74.1 - - - +
204B ILE* 1.3 58.6 + - - +
206B ALA* 3.1 6.1 + - - +
207B LEU* 2.9 32.1 + - + +
218B ILE* 3.6 19.5 - - + -
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Residues in contact with ILE 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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200B ALA* 2.7 24.8 + - + +
201B GLY* 3.7 6.1 - - - +
203B ALA* 1.3 70.3 - - - +
205B GLN* 1.3 60.5 + - - +
207B LEU* 3.2 9.6 + - + +
208B SER* 2.8 30.2 + - - -
213B SER* 4.2 8.0 - - - -
218B ILE* 3.7 25.4 - - + -
230B ARG* 3.6 34.1 - - - +
235B THR* 3.0 46.2 - - + +
236B GLN* 3.8 12.3 - - + +
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Residues in contact with GLN 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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175B LEU* 4.1 28.3 - - + +
201B GLY 3.0 13.6 + - - +
202B GLY* 3.7 10.9 - - - +
203B ALA 3.3 0.2 - - - -
204B ILE* 1.3 75.7 - - - +
206B ALA* 1.3 63.6 + - - +
208B SER* 3.3 8.0 + - - -
209B ALA* 3.1 21.9 + - + +
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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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175B LEU* 3.8 17.8 - - + +
178B MET* 3.7 13.2 - - + -
179B GLU* 3.6 35.9 - - + +
182B LEU* 3.6 10.1 - - + +
202B GLY 3.2 3.3 + - - +
203B ALA 3.1 9.9 + - - +
205B GLN* 1.3 79.6 - - - +
207B LEU* 1.3 60.9 + - - +
209B ALA* 3.4 18.7 + - - +
210B GLN* 3.5 7.3 + - - +
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Residues in contact with LEU 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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178B MET* 4.7 5.8 - - + -
182B LEU* 3.9 28.7 - - + -
189B ILE* 5.5 0.7 - - + +
192B VAL* 4.7 11.0 - - + -
203B ALA* 2.9 20.6 + - + +
204B ILE* 3.2 21.7 + - + +
206B ALA* 1.3 73.8 - - - +
208B SER* 1.3 61.0 + - - +
210B GLN* 2.9 14.4 + - - -
212B LEU* 2.9 31.7 + - + +
213B SER* 3.9 16.6 - - - +
216B VAL* 3.9 48.9 - - + +
218B ILE* 4.8 6.7 - - + -
235B THR 6.0 0.2 - - - +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 2.8 18.9 + - - -
205B GLN* 3.5 9.2 - - - -
207B LEU* 1.3 73.6 - - - +
209B ALA* 1.3 65.1 + - - +
211B GLY* 3.0 14.0 + - - -
212B LEU 4.6 0.2 - - - +
213B SER* 3.8 23.2 + - - +
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Residues in contact with ALA 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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179B GLU* 6.2 2.5 - - + -
205B GLN* 3.1 13.1 + - + +
206B ALA* 3.5 13.0 - - - +
207B LEU 3.2 0.4 - - - -
208B SER* 1.3 74.8 - - - +
210B GLN* 1.3 71.8 + - - +
211B GLY 3.7 0.3 + - - -
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Residues in contact with GLN 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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182B LEU* 4.1 13.0 - - + -
183B THR* 5.8 1.4 + - - -
187B ASN* 3.1 42.3 + - - +
206B ALA 3.5 10.9 + - - +
207B LEU 2.9 9.5 + - - +
209B ALA* 1.3 89.2 + - - +
211B GLY* 1.3 62.6 + - - +
212B LEU* 3.5 17.3 + - + +
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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