Contacts of the helix formed by residues 188 - 198 (chain B) in PDB entry 2EX4
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 LEU 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B MET* 3.6 29.2 - - + +
171B ALA 4.3 2.9 + - - +
187B ASP* 1.3 73.5 - - - +
189B ASP* 1.3 58.8 + - - +
191B VAL* 3.4 2.2 + - - +
192B ARG* 2.9 59.4 + - - +
219B TYR* 3.8 37.9 - - + +
221B PHE* 3.6 29.8 - - + -
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Residues in contact with ASP 189 (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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187B ASP* 3.0 13.1 + - - +
188B LEU* 1.3 77.7 - - - +
190B VAL* 1.3 66.2 + - - +
192B ARG* 3.4 17.6 + - - +
193B ARG* 2.9 42.1 + - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B GLY* 3.8 24.5 - - - +
144B ASP* 4.6 4.9 - - - +
174B GLY* 4.5 3.1 - - - +
175B VAL* 4.1 17.5 - - + -
186B ARG* 3.9 29.8 - - + +
187B ASP* 2.9 31.3 + - - +
189B ASP* 1.3 74.3 - - - +
191B VAL* 1.3 62.9 + - - +
193B ARG* 3.2 21.8 + - - +
194B ILE* 3.1 32.1 + - + +
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Residues in contact with VAL 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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139B ILE* 4.3 16.2 - - + -
147B LEU* 6.0 2.2 - - + -
166B ILE* 5.2 3.6 - - + -
169B ASN 5.7 0.2 - - - +
170B MET* 3.7 27.1 - - + -
186B ARG* 3.8 24.7 - - + -
187B ASP 3.1 12.9 + - - +
188B LEU* 3.9 6.1 - - - +
190B VAL* 1.3 75.4 - - - +
192B ARG* 1.3 63.2 + - - +
194B ILE* 3.2 9.7 + - + +
195B ILE* 3.0 41.1 + - + +
221B PHE* 4.0 20.6 - - + -
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Residues in contact with ARG 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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188B LEU* 2.9 47.0 + - - +
189B ASP* 3.7 15.7 + - - +
191B VAL* 1.3 77.6 - - - +
193B ARG* 1.3 61.6 + - - +
195B ILE* 3.3 9.5 + - + +
196B CYS* 3.0 33.7 + - - -
202B LEU* 4.2 12.6 - - + +
205B GLU* 2.3 47.1 + - - -
221B PHE* 4.3 11.2 - - + -
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Residues in contact with ARG 193 (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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0B GLY* 4.2 18.2 + - - -
189B ASP* 2.9 38.7 + - - +
190B VAL* 3.4 22.7 - - + +
192B ARG* 1.3 75.8 - - - +
194B ILE* 1.3 65.8 + - + +
196B CYS* 3.4 5.3 + - - +
197B SER* 3.1 25.6 + - - -
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Residues in contact with ILE 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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144B ASP* 3.5 38.1 - - + +
147B LEU* 3.9 22.4 - - + -
148B ALA* 3.9 31.6 - - + +
151B LEU* 4.3 6.1 - - + -
186B ARG* 3.7 17.9 - - - +
190B VAL* 3.1 23.5 + - + +
191B VAL* 3.2 7.8 + - + +
193B ARG* 1.3 77.6 - - + +
195B ILE* 1.3 62.0 + - + +
197B SER* 2.8 22.3 + - - +
198B ALA* 3.1 10.7 + - - +
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Residues in contact with ILE 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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151B LEU* 4.5 10.5 - - + -
166B ILE* 4.3 10.1 - - + -
191B VAL* 3.0 37.8 + - + +
192B ARG* 3.6 11.0 - - + +
194B ILE* 1.3 76.2 - - + +
196B CYS* 1.3 68.0 + - - +
198B ALA* 3.0 14.4 + - - +
200B LEU* 3.6 30.6 + - + +
202B LEU* 5.0 9.0 - - + +
221B PHE* 4.3 19.1 - - + -
223B LEU* 3.7 46.2 - - + -
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Residues in contact with CYS 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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192B ARG* 3.0 26.5 + - - +
193B ARG* 4.0 5.4 - - - +
195B ILE* 1.3 79.1 - - - +
197B SER* 1.3 57.6 + - - +
199B GLY* 3.0 21.0 + - - -
200B LEU 4.2 10.6 + - - +
202B LEU* 6.6 0.2 - - - -
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Residues in contact with SER 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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148B ALA* 3.9 15.2 - - - +
152B ARG* 2.7 30.4 + - - -
193B ARG* 3.1 15.1 + - - -
194B ILE* 2.8 20.8 + - - -
196B CYS* 1.3 77.7 - - - +
198B ALA* 1.3 48.6 + - - +
199B GLY 3.2 0.7 - - - -
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Residues in contact with ALA 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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148B ALA* 3.6 24.2 - - - +
151B LEU* 3.9 18.8 - - + -
152B ARG* 3.2 32.9 + - + +
155B LYS* 4.2 7.3 - - - +
194B ILE 3.1 11.5 + - - +
195B ILE 3.0 11.6 + - - +
197B SER* 1.3 76.4 - - - +
199B GLY* 1.3 61.8 + - - +
200B LEU* 3.2 11.2 + - + +
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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