Contacts of the helix formed by residues 191 - 199 (chain A) in PDB entry 1EBM
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 GLU 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLY 3.7 1.0 + - - -
190A PRO* 1.3 80.4 - - + +
192A VAL* 1.3 64.2 + - - +
193A GLU* 3.3 3.4 - - - +
194A ALA* 3.5 15.8 + - + +
195A HIS* 3.2 21.1 + - - +
213A ARG* 4.7 3.2 - - - +
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Residues in contact with VAL 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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166A PHE* 3.9 28.3 - - + -
186A ALA 3.5 22.7 - - - +
187A LEU* 3.6 24.5 - - + +
189A GLY* 3.1 26.3 + - - +
190A PRO 3.2 2.7 - - - +
191A GLU* 1.3 77.5 - - - +
193A GLU* 1.3 64.1 + - - +
195A HIS* 3.2 3.1 + - - +
196A LEU* 2.9 44.3 + - + +
208A VAL* 5.2 0.2 - - + -
209A SER* 4.5 9.6 + - - +
213A ARG* 5.6 0.2 - - - +
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Residues in contact with GLU 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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191A GLU* 3.3 1.3 - - - -
192A VAL* 1.3 79.0 - - - +
194A ALA* 1.3 64.0 + - - +
196A LEU* 3.2 2.5 + - - -
197A ARG* 2.9 51.4 + - - +
205A ALA* 3.6 15.8 - - - +
206A ARG* 3.0 69.7 + - - +
209A SER* 4.2 13.9 + - - +
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Residues in contact with ALA 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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191A GLU* 3.5 21.1 + - + +
192A VAL 3.3 0.4 - - - -
193A GLU* 1.3 80.9 - - - +
195A HIS* 1.3 61.9 + - - +
197A ARG* 3.4 10.9 + - - +
198A LYS* 3.3 25.9 + - - +
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Residues in contact with HIS 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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165A ALA* 4.2 13.9 + - + +
166A PHE* 3.6 28.3 - + + -
191A GLU 3.2 10.3 + - - +
192A VAL 3.2 9.3 + - - +
194A ALA* 1.3 78.5 - - - +
196A LEU* 1.3 62.1 + - - +
198A LYS* 3.1 13.6 + - + +
199A LEU* 3.1 42.8 + - + +
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Residues in contact with LEU 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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162A LEU* 4.4 19.5 - - + -
166A PHE* 3.8 24.0 - - + -
187A LEU* 5.7 0.4 - - + -
192A VAL* 2.9 37.0 + - + +
193A GLU 3.2 4.0 + - - +
195A HIS* 1.3 72.1 - - - +
197A ARG* 1.3 61.7 + - - +
199A LEU* 3.0 30.0 + - + +
200A GLY 3.1 8.1 + - - -
201A LEU* 3.1 22.8 + - + +
205A ALA* 3.6 23.3 - - + +
208A VAL* 3.8 33.9 - - + -
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Residues in contact with ARG 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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193A GLU* 2.9 51.1 + - - +
194A ALA* 3.7 9.6 - - - +
195A HIS 3.2 0.4 - - - -
196A LEU* 1.3 75.7 - - - +
198A LYS* 1.3 58.8 + - + +
200A GLY* 2.9 20.0 + - - +
201A LEU 4.5 3.6 - - - +
202A GLY* 3.7 25.1 + - - +
203A TYR* 3.9 18.0 - - - +
205A ALA* 3.5 10.5 - - + -
206A ARG* 4.0 23.8 - - - +
9D C 4.6 13.1 + - - -
10D T 4.4 10.5 + - - +
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Residues in contact with LYS 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 ALA 3.3 12.2 + - - +
195A HIS* 3.1 17.0 + - - +
197A ARG* 1.3 79.6 - - + +
199A LEU* 1.3 61.2 + - + +
200A GLY 3.1 3.0 + - - -
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Residues in contact with LEU 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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161A ARG* 2.8 79.5 + - + +
162A LEU 4.7 0.2 - - - +
165A ALA* 3.8 19.3 - - + -
195A HIS* 3.1 31.2 + - + +
196A LEU* 3.0 27.6 + - + +
198A LYS* 1.3 80.4 - - + +
200A GLY* 1.3 58.5 + - - +
201A LEU* 3.6 8.3 - - + +
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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