Contacts of the helix formed by residues 189 - 200 (chain B) in PDB entry 2E52
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 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B PHE* 4.7 6.4 - - - +
102B ASN 5.2 0.5 + - - -
103B TYR* 3.6 29.0 + - + +
138B TYR* 2.6 36.8 + - + +
187B SER* 3.1 19.0 + - - +
188B PHE* 1.3 75.5 - - - +
190B GLN* 1.3 71.7 + - + +
192B TRP* 3.3 11.8 + - - +
193B ASN* 3.2 17.8 + - - +
190C GLN* 3.4 28.9 - - - +
197C LYS* 2.7 30.8 + - - -
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Residues in contact with GLN 190 (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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138B TYR* 4.8 0.6 + - - -
187B SER 4.9 2.4 + - - +
188B PHE 3.1 1.6 + - - -
189B GLU* 1.3 82.4 - - + +
191B LEU* 1.3 63.1 + - - +
193B ASN* 3.0 31.1 + - - +
194B PHE 3.1 9.5 + - - -
197B LYS* 3.0 20.2 + - - +
218B TYR* 2.6 31.2 + - + +
222B LEU* 4.0 19.7 - - + -
101C PHE* 6.4 2.0 - - + -
102C ASN* 6.4 1.3 - - + -
138C TYR* 4.5 0.6 + - - -
189C GLU* 3.4 35.4 + - - +
190C GLN* 3.6 19.6 - - - +
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Residues in contact with LEU 191 (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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165B LEU* 3.6 10.9 - - + +
167B PHE* 4.0 14.4 - - + -
175B LEU* 4.1 7.9 - - + -
188B PHE 2.9 12.9 + - - +
190B GLN* 1.3 76.4 - - - +
192B TRP* 1.3 96.6 + - + +
194B PHE* 3.1 20.3 + - + +
215B PHE* 3.7 32.8 - - + -
218B TYR* 4.4 5.2 - - + -
219B PHE* 4.1 12.8 - - + -
222B LEU* 3.4 19.3 - - + +
223B PHE* 3.7 23.1 - - + -
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Residues in contact with TRP 192 (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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75B PHE* 3.5 31.9 - + - -
78B LEU* 4.2 15.3 - - + -
80B LEU* 4.6 4.7 - - + +
103B TYR* 2.9 46.0 + + - -
105B LEU* 3.7 13.4 - - + +
138B TYR* 3.6 32.5 - + + +
139B ALA 4.7 1.7 - - - +
140B VAL* 3.6 20.6 - - + -
163B ASN* 4.1 4.2 - - - +
165B LEU* 3.8 22.0 + - + +
167B PHE* 4.2 17.5 - + - -
188B PHE* 3.5 37.2 + + + -
189B GLU* 3.3 7.3 + - - +
191B LEU* 1.3 96.3 - - + +
193B ASN* 1.3 60.3 - - - +
194B PHE 3.7 0.3 + - - -
195B PRO* 3.7 10.6 - - - +
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Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.4 22.0 + - + -
163B ASN* 3.0 24.6 + - - -
189B GLU 3.2 15.4 + - - +
190B GLN* 3.0 33.7 + - - +
191B LEU 3.1 0.8 - - - -
192B TRP* 1.3 77.5 - - - +
194B PHE* 1.3 61.9 + - - +
195B PRO* 3.3 3.8 - - - -
196B LYS* 3.2 22.4 + - - +
197B LYS* 3.3 20.8 + - - +
218B TYR* 4.4 1.1 - - - -
138C TYR* 4.5 5.9 + - - -
193C ASN* 6.0 2.5 - - - +
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Residues in contact with PHE 194 (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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165B LEU* 3.9 11.0 - - + -
166B LEU 5.9 0.2 - - - -
190B GLN 3.1 8.6 + - - -
191B LEU 3.1 14.5 + - - +
193B ASN* 1.3 76.3 - - - +
195B PRO* 1.4 64.8 - - + +
197B LYS* 3.1 2.6 + - - +
198B GLN* 2.7 73.4 + - + +
211B PHE* 4.0 29.8 - + - -
214B ASP 4.2 0.9 - - - -
215B PHE* 3.7 48.5 - + + -
218B TYR* 3.4 47.6 - + + -
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Residues in contact with PRO 195 (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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159B SER* 3.3 33.2 - - - +
160B LEU* 3.5 12.8 - - + +
163B ASN* 3.3 16.8 - - - +
164B VAL 3.3 31.2 - - - +
165B LEU* 3.5 8.7 - - + +
192B TRP 3.7 8.1 - - - +
193B ASN 3.4 0.9 - - - -
194B PHE* 1.4 104.0 - - + +
196B LYS* 1.3 54.7 + - - +
199B SER* 2.8 32.6 + - - -
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Residues in contact with LYS 196 (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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160B LEU 5.0 5.6 + - - -
161B ASP 5.6 4.0 + - - -
163B ASN* 3.0 30.1 + - + +
193B ASN* 3.2 29.8 + - - +
195B PRO* 1.3 74.5 - - - +
197B LYS* 1.3 63.3 + - + +
199B SER* 2.8 29.3 + - - -
200B LYS* 3.7 26.2 + - + +
137C ASP* 5.4 1.1 - - - +
196C LYS* 5.6 12.3 - - - +
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Residues in contact with LYS 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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190B GLN* 3.0 21.4 + - - +
193B ASN* 3.6 18.6 - - - +
194B PHE 3.1 6.1 + - - +
196B LYS* 1.3 76.8 - - + +
198B GLN* 1.3 63.2 + - - +
200B LYS* 3.3 15.6 + - - +
201B LYS* 3.5 21.0 - - - +
218B TYR* 3.5 32.2 + - + +
102C ASN* 2.9 34.4 + - - +
103C TYR* 4.0 0.4 - - - -
137C ASP* 3.5 32.1 - - + +
138C TYR* 4.7 2.0 - - - +
189C GLU* 2.7 31.9 + - - +
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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
----------------------------------------------------------
160B LEU* 3.7 21.8 - - + -
194B PHE* 2.7 47.7 + - + +
197B LYS* 1.3 72.0 - - - +
199B SER* 1.3 60.9 + - - +
201B LYS* 3.0 35.1 + - - +
202B THR* 2.9 31.1 + - - +
211B PHE* 3.9 16.7 - - + +
214B ASP* 2.8 44.1 + - - +
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 3.9 19.9 + - - +
195B PRO 2.8 18.3 + - - -
196B LYS* 2.8 28.9 + - - -
198B GLN* 1.3 72.9 - - - +
200B LYS* 1.3 66.8 + - - +
202B THR* 3.2 14.0 + - - +
2002B ACT 3.3 40.1 - - - +
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Residues in contact with LYS 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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196B LYS* 3.9 28.5 - - + +
197B LYS 3.3 9.6 + - - +
198B GLN 3.2 1.0 - - - -
199B SER* 1.3 83.8 + - - +
201B LYS* 1.3 59.3 + - + +
202B THR 3.5 1.0 + - - +
133C ARG* 4.1 18.9 - - - +
134C GLU 3.7 17.7 - - - +
135C ASP* 3.5 38.6 - - - +
136C LYS 3.3 21.3 + - - +
137C ASP* 4.1 20.9 + - - +
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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