Contacts of the helix formed by residues 186 - 197 (chain B) in PDB entry 5CVE
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 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B SER 4.8 1.0 - - - +
169B MET* 4.6 0.9 - - - -
170B ALA* 3.2 20.4 - - - +
171B GLN 4.0 3.8 - - - +
172B GLU* 3.6 11.4 - - - +
173B GLY* 2.7 42.4 + - - +
185B ARG* 1.3 78.2 - - - +
187B LEU* 1.3 64.9 + - - +
188B ASP* 2.9 21.9 + - - +
189B VAL* 2.9 20.3 + - - +
190B VAL* 3.2 19.6 + - - +
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Residues in contact with LEU 187 (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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169B MET* 3.8 23.5 - - + -
170B ALA 4.2 2.3 + - - +
186B ASP* 1.3 75.6 - - - +
188B ASP* 1.3 57.9 + - - +
190B VAL* 3.4 4.4 + - - +
191B ARG* 2.9 67.1 + - - +
204B GLU* 4.4 0.2 - - - +
218B TYR* 4.0 33.7 - - + +
220B PHE* 3.6 32.8 - - + -
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Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B HIS* 5.8 3.5 - - - -
186B ASP* 2.9 12.0 + - - +
187B LEU* 1.3 77.2 - - - +
189B VAL* 1.3 65.6 + - + +
191B ARG* 3.5 14.7 + - - +
192B ARG* 3.0 54.2 + - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B SER 4.6 1.8 - - - +
0B HIS* 3.7 33.2 - - + +
143B ASP* 4.6 4.7 - - - +
173B GLY 4.4 0.2 - - - +
174B VAL* 4.1 17.0 - - + -
185B ARG* 3.9 28.7 - - + +
186B ASP* 2.9 26.8 + - - +
188B ASP* 1.3 79.4 - - + +
190B VAL* 1.3 64.0 + - - +
192B ARG* 3.2 9.8 + - - +
193B ILE* 3.1 31.4 + - + +
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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
----------------------------------------------------------
138B ILE* 4.3 15.0 - - + -
146B LEU* 6.0 2.7 - - + -
165B ILE* 5.1 4.0 - - + -
169B MET* 3.7 25.6 - - + -
185B ARG* 3.8 23.6 - - + -
186B ASP 3.2 15.6 + - - +
187B LEU* 3.8 4.3 - - - +
189B VAL* 1.3 77.0 - - - +
191B ARG* 1.3 56.5 + - - +
193B ILE* 3.2 9.5 + - + +
194B ILE* 2.9 47.6 + - + +
220B PHE* 4.3 19.5 - - + -
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Residues in contact with ARG 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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187B LEU* 2.9 50.8 + - - +
188B ASP* 3.8 13.0 + - - +
190B VAL* 1.3 75.0 - - - +
192B ARG* 1.3 59.1 + - + +
194B ILE* 3.4 10.6 + - + +
195B CYS* 3.0 29.5 + - - +
201B LEU* 5.2 6.9 - - + +
204B GLU* 3.0 39.8 + - - -
220B PHE* 4.8 12.0 - - + -
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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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0B HIS 6.1 0.4 - - - -
188B ASP* 3.0 45.1 + - - +
189B VAL* 3.2 8.0 + - - +
191B ARG* 1.3 76.1 - - + +
193B ILE* 1.3 59.0 + - + +
195B CYS* 3.5 7.0 + - - +
196B SER* 3.0 28.2 + - - -
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Residues in contact with ILE 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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143B ASP* 3.4 39.7 - - + +
146B LEU* 3.8 23.8 - - + -
147B ALA* 3.8 32.3 - - + +
150B LEU* 4.3 5.2 - - + -
185B ARG* 3.6 17.9 - - - +
189B VAL* 3.1 21.0 + - + +
190B VAL* 3.2 7.4 + - - +
192B ARG* 1.3 76.5 - - + +
194B ILE* 1.3 65.5 + - + +
196B SER* 3.1 8.4 + - - -
197B ALA* 3.1 20.6 + - - +
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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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150B LEU* 4.4 11.0 - - + -
165B ILE* 4.2 14.4 - - + -
190B VAL* 2.9 39.4 + - + +
191B ARG* 3.7 9.2 - - + +
193B ILE* 1.3 77.0 - - + +
195B CYS* 1.3 63.0 + - - +
197B ALA* 3.1 13.0 + - - +
199B LEU* 3.3 35.2 + - + +
200B SER* 5.1 1.3 - - - -
201B LEU* 5.3 2.5 - - + +
220B PHE* 4.4 15.5 - - + -
222B LEU* 3.7 46.2 - - + -
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Residues in contact with CYS 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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191B ARG 3.0 17.6 + - - +
192B ARG* 3.6 8.5 - - - +
194B ILE* 1.3 77.2 - - - +
196B SER* 1.3 65.3 + - - +
198B GLY* 2.9 16.5 + - - -
199B LEU 3.9 10.0 + - - +
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Residues in contact with SER 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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147B ALA* 4.2 10.7 - - - +
151B ARG* 2.5 32.0 + - - -
192B ARG 3.0 15.1 + - - -
193B ILE* 3.1 12.5 + - - -
195B CYS* 1.3 78.3 - - - +
197B ALA* 1.3 54.0 + - - +
198B GLY* 3.2 4.2 + - - -
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Residues in contact with ALA 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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147B ALA 3.5 20.6 + - - +
150B LEU* 3.6 24.0 - - + -
151B ARG* 3.6 33.4 - - - +
154B LYS* 3.9 11.3 - - - +
193B ILE 3.1 10.4 + - - +
194B ILE 3.6 9.4 - - - +
195B CYS 3.1 1.2 - - - -
196B SER* 1.3 75.0 - - - +
198B GLY* 1.3 60.1 - - - +
199B LEU* 3.3 5.6 + - + +
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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