Contacts of the helix formed by residues 193 - 201 (chain A) in PDB entry 2MBG
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 PRO 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ILE* 1.3 95.7 - - + +
194A LEU* 1.3 66.6 + - - +
195A ALA* 4.7 2.0 - - + +
196A ASP* 3.2 31.0 + - - +
197A ALA* 3.0 20.1 + - - +
274A LEU* 5.6 0.2 - - + -
275A PRO* 3.8 15.2 - - + -
276A GLU* 5.4 11.0 - - + +
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Residues in contact with LEU 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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192A ILE 3.9 0.2 + - - -
193A PRO* 1.3 72.5 - - - +
195A ALA* 1.3 52.9 + - - +
197A ALA* 2.9 7.3 + - + +
198A VAL* 2.7 39.6 + - + +
210A PRO* 4.3 23.6 - - + -
271A LEU* 6.2 0.2 - - + -
274A LEU* 3.5 28.6 - - + +
276A GLU* 5.1 15.4 + - + +
278A LEU* 4.5 14.1 - - + -
313A CYS* 3.7 24.2 - - + +
314A ASN* 3.1 42.6 - - - +
317A LEU* 4.7 10.8 - - + -
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Residues in contact with ALA 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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193A PRO* 3.5 2.1 - - + +
194A LEU* 1.3 77.4 - - - +
196A ASP* 1.3 58.6 + - - +
198A VAL* 3.0 11.2 + - - +
199A GLU* 2.8 44.4 + - + +
208A ARG* 6.6 0.2 - - - -
313A CYS* 4.5 8.9 - - - -
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Residues in contact with ASP 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 ILE* 4.1 12.7 - - + +
193A PRO* 3.2 43.7 - - + +
194A LEU 3.2 0.2 - - - -
195A ALA* 1.3 78.1 - - - +
197A ALA* 1.3 61.5 + - - +
199A GLU* 3.6 5.6 + - - +
200A ARG* 3.2 22.7 + - - +
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Residues in contact with ALA 197 (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* 5.4 1.1 - - + -
192A ILE* 3.5 23.5 - - + +
193A PRO 3.0 12.0 + - - +
194A LEU* 2.9 11.9 + - - +
196A ASP* 1.3 74.1 - - - +
198A VAL* 1.3 53.6 + - - +
200A ARG* 3.3 4.2 + - - +
201A THR* 2.6 44.1 + - + +
210A PRO* 4.2 5.2 - - + -
270A TYR* 3.2 26.7 - - - +
274A LEU* 5.2 2.0 - - + -
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Residues in contact with VAL 198 (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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194A LEU 2.7 32.2 + - - +
195A ALA* 3.0 11.9 + - - +
197A ALA* 1.3 73.1 - - - +
199A GLU* 1.3 62.1 + - - +
201A THR* 3.1 4.6 + - - -
202A MET* 2.9 56.9 + - + +
206A GLY 5.3 0.2 - - - -
208A ARG* 3.7 20.2 - - + +
209A LEU* 3.2 46.2 - - - +
210A PRO* 3.8 4.3 - - + -
313A CYS* 4.8 6.1 - - + -
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Residues in contact with GLU 199 (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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195A ALA* 2.8 27.0 + - + +
196A ASP* 4.1 6.1 - - - +
198A VAL* 1.3 76.9 - - - +
200A ARG* 1.3 66.9 + - - +
202A MET* 3.2 41.4 + - - +
208A ARG* 5.2 4.5 + - - -
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Residues in contact with ARG 200 (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 LYS* 3.6 42.5 - - - +
188A PRO 4.8 2.5 - - - +
189A ILE* 3.5 30.3 - - + -
192A ILE* 5.2 1.6 - - + -
196A ASP 3.2 12.7 + - - +
197A ALA* 3.4 9.4 - - - +
198A VAL 3.1 0.2 - - - -
199A GLU* 1.3 86.3 + - - +
201A THR* 1.3 58.1 + - + +
202A MET 3.4 4.5 + - - +
250A GLU* 2.7 42.2 + - + +
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Residues in contact with THR 201 (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* 4.0 24.2 - - + -
197A ALA* 2.6 29.0 + - + +
198A VAL* 3.4 2.7 - - - -
200A ARG* 1.3 77.3 - - + +
202A MET* 1.3 60.3 + - - +
203A MET* 4.7 1.1 - - - -
210A PRO* 3.2 8.9 - - + +
211A ALA* 2.8 40.8 + - + +
212A VAL* 4.8 12.6 - - + -
214A ARG* 3.1 20.1 + - - -
247A TYR* 5.8 3.4 - - + -
270A TYR* 5.6 0.2 - - - +
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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