Contacts of the helix formed by residues 190 - 199 (chain B) in PDB entry 2PI8
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 SER 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B TYR* 3.7 25.4 + - - -
189B ARG* 1.3 73.4 - - - +
191B ILE* 1.3 61.9 + - - +
192B GLY* 3.5 11.8 + - - -
193B LYS* 3.9 19.8 + - - +
194B VAL* 3.4 16.6 + - - +
1F NAG 5.6 8.2 + - - +
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Residues in contact with ILE 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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157B PHE* 3.3 34.8 - - + -
188B TYR* 4.6 3.2 + - - +
189B ARG 4.2 3.1 - - - +
190B SER* 1.3 71.3 + - - +
192B GLY* 1.3 65.3 + - - +
193B LYS 3.2 2.0 - - - -
194B VAL* 3.2 5.8 + - + +
195B LEU* 3.1 26.8 + - + +
211B ILE* 5.0 13.2 - - + -
226B LEU* 3.1 57.7 - - + +
227B LEU* 4.3 5.4 - - + -
229B GLN* 3.8 17.0 - - + -
230B ASN* 4.0 15.3 - - + +
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Residues in contact with GLY 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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190B SER* 3.4 9.0 + - - -
191B ILE* 1.3 79.9 - - - +
193B LYS* 1.3 59.8 + - - +
195B LEU* 3.5 2.5 + - - -
196B ILE* 3.3 29.3 + - - +
206B MSE 3.4 29.7 - - - +
211B ILE* 4.6 9.6 - - - +
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Residues in contact with LYS 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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190B SER* 3.9 21.3 + - - +
191B ILE 3.2 0.2 - - - -
192B GLY* 1.3 74.5 - - - +
194B VAL* 1.3 61.8 + - + +
196B ILE* 3.2 9.0 + - - +
197B ASP* 2.9 61.5 + - - +
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Residues in contact with VAL 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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189B ARG* 6.1 1.1 - - + -
190B SER 3.4 19.1 - - - +
191B ILE* 3.2 11.2 + - + +
193B LYS* 1.3 80.2 - - + +
195B LEU* 1.3 56.7 + - - +
197B ASP* 3.8 5.6 - - - +
198B ARG* 2.8 66.6 + - - +
226B LEU* 3.9 15.0 - - + -
229B GLN* 3.9 28.7 - - + +
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Residues in contact with LEU 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 ILE* 3.1 22.1 + - + +
192B GLY* 3.7 6.7 - - - +
193B LYS 3.2 0.4 - - - -
194B VAL* 1.3 75.8 - - - +
196B ILE* 1.3 62.8 + - - +
198B ARG* 3.5 4.3 + - + +
199B GLY 3.3 12.1 + - - -
200B GLU* 3.4 7.9 + - + +
201B VAL* 3.3 42.4 + - + -
206B MSE 4.1 7.9 - - + -
211B ILE* 4.0 32.5 - - + -
214B TRP* 3.7 29.8 - - + +
226B LEU* 3.6 33.0 - - + -
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Residues in contact with ILE 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 GLY 3.3 19.5 - - - +
193B LYS* 3.2 9.3 + - - +
195B LEU* 1.3 74.8 - - - +
197B ASP* 1.3 69.7 + - - +
199B GLY* 3.2 13.5 + - - -
201B VAL 3.3 9.8 - - - +
202B LYS 3.5 13.0 - - - +
203B LYS* 3.6 53.2 - - + +
206B MSE 4.4 13.9 - - + -
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Residues in contact with ASP 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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193B LYS* 2.9 52.4 + - - +
194B VAL* 4.0 5.2 - - - +
196B ILE* 1.3 82.6 - - - +
198B ARG* 1.3 63.7 + - - +
199B GLY* 3.4 1.0 + - - -
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Residues in contact with ARG 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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194B VAL* 2.8 43.0 + - - +
195B LEU* 3.7 8.5 - - - +
196B ILE 3.2 0.2 - - - -
197B ASP* 1.3 77.9 - - - +
199B GLY* 1.3 60.3 + - - +
200B GLU* 3.5 27.1 - - + +
225B GLU* 3.2 34.5 + - - -
226B LEU* 4.6 7.5 - - - +
229B GLN* 4.1 15.4 + - - +
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Residues in contact with GLY 199 (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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195B LEU 3.3 0.6 + - - -
196B ILE 3.2 12.5 + - - -
197B ASP 3.2 4.1 - - - -
198B ARG* 1.3 79.3 - - - +
200B GLU* 1.3 62.9 + - - +
201B VAL 3.7 4.1 - - - +
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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