Contacts of the helix formed by residues 189 - 195 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H PRO 5.3 2.7 - - - +
187H ALA 2.6 18.8 + - - +
188H ASP* 1.3 69.5 - - - +
190H GLY* 1.3 59.6 + - - +
191H ALA 3.4 0.2 - - - -
192H LEU* 3.8 11.7 - - + -
193H GLU* 2.9 31.7 + - - +
218H ASP* 6.0 3.6 - - + +
221H LEU* 4.2 25.1 - - + -
222H VAL* 5.0 11.7 - - + -
225H LEU* 3.5 27.8 - - + -
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Residues in contact with GLY 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H ASP* 2.9 7.8 + - - -
189H VAL* 1.3 78.0 - - - +
191H ALA* 1.3 61.2 + - - +
193H GLU* 3.2 8.0 + - - +
194H LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H ILE* 3.5 29.3 - - + +
188H ASP* 2.9 27.7 + - - +
190H GLY* 1.3 75.7 - - - +
192H LEU* 1.3 64.4 + - - +
194H LEU* 3.2 6.8 + - - +
195H ALA* 3.1 26.9 + - - +
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Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H VAL* 4.3 5.2 - - + -
184H ILE* 3.4 22.7 - - + +
188H ASP 3.5 4.8 + - - +
189H VAL* 3.8 11.4 - - + +
190H GLY 3.2 0.4 - - - -
191H ALA* 1.3 79.8 - - - +
193H GLU* 1.3 60.9 + - - +
195H ALA* 3.9 2.7 + - - +
196H LEU* 2.9 56.5 + - + +
204H PHE* 3.9 27.8 - - + -
222H VAL* 3.2 40.8 - - + +
225H LEU* 4.2 17.7 - - + -
226H CYS* 4.2 7.4 - - - -
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Residues in contact with GLU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H VAL* 2.9 23.3 + - - +
190H GLY* 3.5 8.4 - - - +
191H ALA 3.2 0.2 - - - -
192H LEU* 1.3 76.9 - - - +
194H LEU* 1.3 63.0 + - - +
196H LEU* 3.5 7.3 - - - +
197H ASN* 3.0 34.9 + - - +
225H LEU* 3.6 33.6 - - + +
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Residues in contact with LEU 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H GLY 2.9 16.6 + - - +
191H ALA* 3.6 6.5 - - - +
193H GLU* 1.3 73.7 - - - +
195H ALA* 1.3 58.2 + - - +
197H ASN* 2.6 39.4 + - + +
198H GLN* 3.0 38.6 + - + +
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Residues in contact with ALA 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H HIS* 5.4 0.4 - - - +
157H VAL* 4.5 12.6 - - + -
182H THR* 4.1 30.3 - - + +
191H ALA 3.1 13.4 + - - +
192H LEU* 4.3 3.6 - - - +
194H LEU* 1.3 73.6 - - - +
196H LEU* 1.3 59.3 + - - +
197H ASN 2.8 7.5 + - - -
198H GLN* 3.4 15.7 + - - +
199H LYS* 2.9 34.3 + - + +
201H VAL* 3.9 5.3 - - + +
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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