Contacts of the helix formed by residues 187 - 196 (chain A) 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 ASP 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ASN* 4.8 5.4 + - - -
162A HIS* 4.3 5.3 + - - +
185A ILE 3.4 3.8 + - - -
186A GLU* 1.3 86.7 - - - +
188A MET* 1.3 63.2 + - - +
189A ILE 3.4 2.0 - - - -
190A PRO* 3.1 18.0 - - - +
191A TYR* 3.5 24.7 - - + -
222A SER 5.0 1.5 - - - +
223A GLN* 2.9 51.7 + - - +
224A LEU 5.4 0.4 - - - -
225A ASP 5.6 1.2 + - - -
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Residues in contact with MET 188 (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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162A HIS* 3.3 34.8 - - + -
185A ILE* 4.3 4.4 + - + -
186A GLU 3.2 4.8 + - - -
187A ASP* 1.3 80.0 - - - +
189A ILE* 1.3 56.0 + - - +
191A TYR* 2.6 52.2 + - - +
192A TRP* 3.0 53.5 + - + +
13E ASN* 3.4 21.1 - - - +
16E ARG* 4.6 24.2 - - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 3.8 48.5 - - + +
187A ASP 3.4 0.6 - - - -
188A MET* 1.3 73.7 - - - +
190A PRO* 1.3 70.7 - - + +
192A TRP* 3.5 12.2 + - + +
193A TYR* 3.1 21.7 + - - +
200A PHE* 3.6 23.6 - - + -
204A LEU* 4.9 8.1 - - + -
225A ASP 4.7 0.2 - - - +
226A ARG* 3.5 12.8 - - + +
227A GLY* 4.0 17.7 - - - -
229A LEU* 4.9 6.1 - - + -
41B TRP* 3.4 30.5 - - + +
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Residues in contact with PRO 190 (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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187A ASP 3.1 18.2 - - - +
189A ILE* 1.3 97.8 - - + +
191A TYR* 1.3 60.9 + - + +
193A TYR* 3.2 9.8 + - + +
194A ARG* 2.9 28.6 + - - +
222A SER 5.9 0.9 - - - +
225A ASP* 4.0 25.8 - - + +
226A ARG* 3.6 28.5 - - - +
41B TRP* 5.2 0.7 - - + -
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Residues in contact with TYR 191 (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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187A ASP* 3.5 33.4 - - + -
188A MET* 2.6 35.2 + - - +
190A PRO* 1.3 78.0 - - + +
192A TRP* 1.3 56.4 + - + +
194A ARG* 3.3 8.9 + - + -
195A TYR* 2.8 59.7 + + + -
16E ARG* 3.9 24.2 - - - +
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Residues in contact with TRP 192 (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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162A HIS* 3.8 19.3 - - + -
165A THR* 3.8 37.9 - - + -
166A PHE* 4.4 17.7 - + - -
185A ILE* 4.5 17.5 - - + -
188A MET* 3.0 45.0 + - + +
189A ILE* 3.9 10.8 - - + +
191A TYR* 1.3 75.5 - - + +
193A TYR* 1.3 58.0 + - - +
195A TYR* 4.4 5.6 - + + +
196A ALA* 2.7 38.0 + - - +
200A PHE* 4.0 26.4 - + + +
12E LEU* 3.9 43.6 + - + -
13E ASN* 3.5 18.3 + - - -
16E ARG* 6.1 2.2 - - + -
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Residues in contact with TYR 193 (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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189A ILE 3.1 15.4 + - - +
190A PRO* 3.2 10.1 + - + +
192A TRP* 1.3 76.1 - - - +
194A ARG* 1.3 62.8 + - + +
197A PRO* 3.4 38.5 - - + +
200A PHE* 4.1 15.2 - + + -
201A SER* 4.3 13.2 - - - -
226A ARG* 6.0 2.5 - - - -
41B TRP* 3.6 34.1 - + + -
42B ALA* 3.8 21.9 - - + +
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Residues in contact with ARG 194 (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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190A PRO 2.9 16.1 + - - +
191A TYR* 3.3 12.7 + - - +
193A TYR* 1.3 79.6 - - + +
195A TYR* 1.3 71.9 + - + +
197A PRO* 4.0 5.2 - - - +
51E SER* 4.9 4.1 + - - +
52E ASP* 3.4 20.0 + - - +
53E PHE* 3.4 72.4 + - + +
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Residues in contact with TYR 195 (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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191A TYR* 2.8 50.6 + + + +
192A TRP* 4.3 4.7 - + + +
194A ARG* 1.3 87.9 + - + +
196A ALA* 1.3 58.2 + - - +
197A PRO* 3.2 11.2 - - - +
12E LEU 5.6 1.6 - - - +
15E PHE* 3.6 20.2 - - + +
16E ARG* 3.7 28.7 + - + +
17E GLY* 3.5 26.3 + - - -
19E GLY* 3.0 26.0 - - - -
20E GLU* 3.7 2.6 + - - +
53E PHE* 3.4 39.4 - + - -
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Residues in contact with ALA 196 (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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192A TRP* 2.7 17.6 + - - +
195A TYR* 1.3 74.0 - - + +
197A PRO* 1.3 66.3 - - - +
198A GLN 3.2 0.4 + - - -
199A LEU* 3.4 5.3 + - + -
200A PHE* 3.0 21.1 + - - +
12E LEU* 4.0 17.9 - - + +
15E PHE* 3.9 20.0 - - + -
20E GLU* 3.2 24.7 - - + -
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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