Contacts of the helix formed by residues 189 - 198 (chain B) in PDB entry 1QGN
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 VAL 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B PRO 5.3 2.7 - - - +
187B ALA 2.6 18.9 + - - +
188B ASP* 1.3 71.2 - - - +
190B GLY* 1.3 66.5 + - - +
192B LEU* 3.2 10.2 + - + +
193B GLU* 3.0 24.1 + - - +
218B ASP* 6.1 2.2 - - + -
221B LEU* 4.2 25.4 - - + -
222B VAL* 5.2 10.5 - - + -
225B LEU* 3.5 28.7 - - + -
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Residues in contact with GLY 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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188B ASP* 3.1 6.1 + - - -
189B VAL* 1.3 79.2 - - - +
191B ALA* 1.3 56.4 + - - +
193B GLU* 3.0 12.4 + - - +
194B LEU* 2.9 27.5 + - - +
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Residues in contact with ALA 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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184B ILE* 3.8 23.7 - - + +
188B ASP* 2.8 34.1 + - - +
189B VAL 3.2 0.2 - - - -
190B GLY* 1.3 77.5 - - - +
192B LEU* 1.3 56.5 + - - +
194B LEU* 3.7 10.0 - - + +
195B ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 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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157B VAL* 4.0 10.8 - - + -
184B ILE* 3.8 14.1 - - + +
188B ASP 3.6 3.3 + - - +
189B VAL* 3.2 12.3 + - + +
190B GLY 3.2 0.4 - - - -
191B ALA* 1.3 79.5 - - - +
193B GLU* 1.3 57.5 + - - +
195B ALA* 4.4 3.6 - - - +
196B LEU* 2.9 44.6 + - + +
204B PHE* 3.5 38.8 - - + -
222B VAL* 3.5 35.7 - - + +
225B LEU* 3.9 26.0 - - + -
226B CYS* 4.5 3.1 - - - -
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Residues in contact with GLU 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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189B VAL* 3.0 15.0 + - - +
190B GLY* 3.0 12.7 + - - +
192B LEU* 1.3 77.5 - - - +
194B LEU* 1.3 63.1 + - - +
196B LEU* 3.6 7.5 + - + +
197B ASN* 3.4 29.1 + - - +
225B LEU* 4.4 27.4 - - + +
228B GLU* 5.6 1.6 - - - +
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Residues in contact with LEU 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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190B GLY 2.9 14.2 + - - +
191B ALA* 3.7 8.7 - - - +
193B GLU* 1.3 75.1 - - - +
195B ALA* 1.3 54.5 + - + +
196B LEU 3.0 1.3 - - - -
197B ASN* 2.6 26.2 + - + +
198B GLN* 2.7 57.8 + - + +
199B LYS* 6.0 0.2 - - - +
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Residues in contact with ALA 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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157B VAL* 4.3 11.4 - - + -
182B THR* 3.8 29.6 - - + +
191B ALA 2.9 17.5 + - - +
192B LEU* 4.4 3.6 - - - +
194B LEU* 1.3 78.5 - - + +
196B LEU* 1.3 56.7 + - - +
197B ASN 3.1 1.2 + - - -
198B GLN* 4.3 2.7 - - - +
199B LYS* 2.9 46.7 + - + +
201B VAL* 3.7 7.6 - - - +
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Residues in contact with LEU 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 LEU* 2.9 38.3 + - + +
193B GLU* 3.7 10.3 - - + +
194B LEU 3.0 0.8 - - - -
195B ALA* 1.3 75.9 - - - +
197B ASN* 1.3 58.1 + - - +
199B LYS 4.1 5.2 - - - +
200B LYS* 5.9 0.2 - - - -
201B VAL* 3.9 31.0 + - + +
204B PHE* 5.7 0.2 - - + -
225B LEU* 4.4 4.9 - - + +
226B CYS* 3.7 34.3 - - - +
229B LYS* 3.3 53.7 - - + +
231B ALA* 4.0 12.6 - - + -
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Residues in contact with ASN 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 GLU* 3.4 20.4 + - - +
194B LEU* 2.6 14.1 + - + +
196B LEU* 1.3 79.7 - - - +
198B GLN* 1.3 63.2 + - + +
199B LYS 4.4 1.1 - - - -
229B LYS* 3.6 32.7 + - - +
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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
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194B LEU* 2.7 60.1 + - + +
195B ALA* 3.6 0.7 + - - -
197B ASN* 1.3 79.5 - - + +
199B LYS* 1.3 91.2 + - + +
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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