Contacts of the helix formed by residues 196 - 206 (chain B) in PDB entry 2BM9
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 ALA 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B TRP 3.0 16.1 + - - +
195B TYR* 1.3 80.2 - - + +
197B PRO* 1.3 65.7 - - - +
198B GLN 3.1 3.1 + - - -
199B LEU* 4.1 11.4 - - + -
200B PHE* 3.0 20.1 + - - +
12C LEU* 4.1 14.1 - - + -
15C PHE* 4.2 15.3 - - + -
20C GLU* 3.2 22.2 - - + +
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Residues in contact with PRO 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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193B TYR* 3.2 36.9 - - + +
194B ARG 3.8 6.3 - - - +
195B TYR 3.4 7.6 - - - +
196B ALA* 1.3 89.9 - - - +
198B GLN* 1.3 64.9 + - + +
201B SER* 3.3 27.0 + - - -
20C GLU* 4.1 5.6 - - + +
51C SER* 6.0 6.3 - - - -
53C PHE* 6.0 0.9 - - + -
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Residues in contact with GLN 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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197B PRO* 1.3 81.7 - - + +
199B LEU* 1.3 63.8 + - + +
201B SER* 3.9 4.0 + - - -
202B GLU* 3.5 22.0 + - - +
20C GLU* 3.0 15.5 + - - +
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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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196B ALA* 3.3 6.9 + - + -
198B GLN* 1.3 76.3 - - + +
200B PHE* 1.3 61.8 + - - +
202B GLU* 3.3 13.4 + - - +
203B TYR* 2.9 70.5 + - + +
7C GLN* 5.3 0.4 - - - +
10C GLN* 4.2 16.6 - - - +
12C LEU* 4.8 6.7 - - + -
15C PHE* 3.9 29.2 - - + -
20C GLU* 3.0 30.4 + - + +
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Residues in contact with PHE 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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41A TRP* 3.5 35.9 - + - -
166B PHE* 3.8 22.9 - + - -
189B ILE* 3.5 35.7 - - + -
192B TRP* 3.5 20.2 - + + +
193B TYR* 3.6 26.7 - + + -
196B ALA 3.0 14.8 + - - +
199B LEU* 1.3 76.5 - - - +
201B SER* 1.3 66.4 + - - +
203B TYR* 3.3 2.3 + - - -
204B LEU* 2.9 53.3 + - + +
12C LEU* 3.7 13.1 - - + +
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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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38A LEU 5.0 2.6 - - - +
41A TRP* 4.7 10.7 - - - +
42A ALA* 5.1 4.5 - - - +
193B TYR* 4.1 15.8 - - - -
197B PRO 3.3 18.6 + - - -
198B GLN* 4.2 5.6 - - - -
199B LEU 3.4 0.2 - - - -
200B PHE* 1.3 81.3 - - - +
202B GLU* 1.3 57.2 + - - +
204B LEU* 4.0 4.7 - - - +
205B GLY* 3.1 23.7 + - - -
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Residues in contact with GLU 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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198B GLN 3.5 13.5 + - - +
199B LEU* 3.3 17.7 + - - +
200B PHE 3.0 0.2 - - - -
201B SER* 1.3 75.0 - - - +
203B TYR* 1.3 70.2 + - + +
204B LEU 2.9 4.9 + - - -
205B GLY* 3.0 11.3 + - - -
206B ALA* 3.1 14.0 + - - +
7C GLN* 2.7 38.7 + - - +
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Residues in contact with TYR 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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166B PHE* 3.4 28.5 - + + -
199B LEU* 2.9 38.4 + - + +
200B PHE* 3.9 2.9 - - - +
202B GLU* 1.3 79.8 - - - +
204B LEU* 1.3 56.5 + - - +
206B ALA* 4.0 2.2 - - - +
207B PHE* 3.0 30.7 - - - -
7C GLN* 3.4 27.9 + - - -
8C ASN 3.5 6.6 + - - -
9C PHE* 3.4 45.5 - + + -
10C GLN* 2.9 37.4 + - + -
12C LEU* 3.3 34.5 - - + -
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Residues in contact with LEU 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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38A LEU* 3.4 46.0 - - + +
41A TRP* 3.6 43.5 - - + +
166B PHE* 4.2 8.7 - - + -
169B MET* 5.0 8.5 - - + -
185B ILE* 5.9 1.1 - - + -
189B ILE* 5.5 4.5 - - + -
200B PHE* 2.9 41.5 + - + +
201B SER* 4.1 4.3 - - - +
203B TYR* 1.3 77.7 - - - +
205B GLY* 1.3 59.1 + - - +
206B ALA 3.1 6.1 + - - -
207B PHE* 3.3 11.1 + - - +
229B LEU* 4.6 17.0 - - + -
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Residues in contact with GLY 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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38A LEU* 3.9 21.5 + - - -
39A ASP* 4.4 6.7 - - - +
201B SER 3.1 14.6 + - - -
202B GLU* 3.0 6.0 + - - -
204B LEU* 1.3 72.9 - - - +
206B ALA* 1.3 62.4 + - - +
207B PHE 3.1 2.6 + - - -
208B ARG* 3.7 26.3 + - - +
3C ASP 5.3 1.2 + - - -
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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 GLU 3.1 13.3 + - - +
203B TYR* 4.0 4.7 - - - +
205B GLY* 1.3 79.5 - - - +
207B PHE* 1.3 65.7 + - + +
208B ARG* 3.4 4.2 + - - +
209B ASP* 4.7 4.2 + - - +
3C ASP* 3.7 31.2 - - - +
4C TYR* 3.4 39.3 - - + -
7C GLN* 5.3 4.3 - - - +
9C PHE* 5.1 3.8 - - + -
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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