Contacts of the helix formed by residues 193 - 204 (chain B) in PDB entry 2QH5
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 ALA 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ALA* 4.0 17.9 - - + +
99B SER* 4.4 0.2 - - - -
100B ASP 3.7 21.8 - - - +
101B LYS* 4.5 0.9 - - - -
103B ASP* 3.1 14.6 + - - +
105B LEU* 3.9 28.2 - - + +
191B PHE 3.7 0.8 + - - -
192B GLN* 1.3 71.3 - - - +
194B GLY* 1.3 60.8 + - - +
196B PHE* 3.7 4.9 - - - +
197B LEU* 3.0 35.8 + - + +
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Residues in contact with GLY 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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101B LYS* 2.7 38.6 + - - -
192B GLN* 3.2 8.4 + - - -
193B ALA* 1.3 71.5 - - - +
195B VAL* 1.3 59.6 + - - +
197B LEU* 3.3 4.5 + - - +
198B ASP* 2.9 37.1 + - - +
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Residues in contact with VAL 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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131B ALA 4.9 0.4 - - - +
134B GLY* 3.5 39.5 - - - +
135B PHE 4.7 1.3 - - - +
136B LEU* 4.0 19.1 - - + -
192B GLN* 3.0 41.0 + - + +
194B GLY* 1.3 72.5 - - - +
196B PHE* 1.3 51.3 + - - +
198B ASP* 3.2 10.9 + - - +
199B GLU* 2.7 44.8 + - + +
254B LYS* 4.6 6.1 - - + -
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.4 23.8 - - + -
93B ALA* 3.6 31.4 - - + -
96B ALA* 3.8 18.2 - - + -
136B LEU* 4.0 13.2 - - + +
191B PHE* 4.3 24.7 - + + -
192B GLN 3.2 14.4 + - - +
193B ALA* 3.7 9.4 - - - +
195B VAL* 1.3 79.4 - - - +
197B LEU* 1.3 61.8 + - + +
199B GLU* 3.3 1.9 + - - +
200B LEU* 2.8 36.8 + - + +
244B ILE* 3.6 24.2 - - + -
248B LEU* 3.5 29.2 - - + -
249B MET* 4.5 0.7 - - + -
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Residues in contact with LEU 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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93B ALA* 4.1 4.5 - - - +
96B ALA* 3.8 36.8 - - + +
97B LEU* 4.0 26.2 - - + +
101B LYS* 5.2 18.4 - - + +
193B ALA* 3.0 21.1 + - + +
194B GLY* 3.8 6.1 - - - +
196B PHE* 1.3 85.6 - - + +
198B ASP* 1.3 54.9 + - - +
200B LEU* 3.1 5.1 + - + +
201B LYS* 2.8 35.5 + - - +
208B LEU* 3.6 33.2 - - + +
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Residues in contact with ASP 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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101B LYS* 5.2 7.1 + - - -
194B GLY* 2.9 17.5 + - - +
195B VAL* 3.3 12.1 - - - +
197B LEU* 1.3 75.4 - - - +
199B GLU* 1.3 67.5 + - - +
201B LYS* 3.5 7.7 + - - +
202B LYS* 3.0 33.8 + - - +
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Residues in contact with GLU 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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136B LEU* 3.8 27.6 - - + -
195B VAL* 2.7 31.8 + - + +
196B PHE 3.7 3.8 - - - +
198B ASP* 1.3 75.1 - - + +
200B LEU* 1.3 61.4 + - - +
202B LYS* 2.9 36.4 + - - -
203B HIS* 3.1 28.3 + - - -
248B LEU* 3.3 18.7 - - + +
252B SER* 2.6 29.3 + - - -
253B HIS* 3.8 5.5 + - - +
254B LYS* 3.2 21.9 + - + +
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Residues in contact with LEU 200 (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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89B ALA 5.2 0.7 - - - +
93B ALA* 3.7 29.8 - - + -
196B PHE* 2.8 23.3 + - + +
197B LEU* 3.3 10.3 - - - +
199B GLU* 1.3 73.7 - - - +
201B LYS* 1.3 61.6 + - - +
204B ALA* 2.8 58.5 + - + +
207B ILE* 4.3 9.9 - - + -
208B LEU* 3.9 33.4 - - + +
244B ILE* 4.2 19.3 - - + -
247B ALA* 5.3 1.3 - - + -
248B LEU* 4.0 17.6 - - + +
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Residues in contact with LYS 201 (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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197B LEU 2.8 18.2 + - - +
198B ASP* 3.7 9.4 - - - +
200B LEU* 1.3 73.2 - - - +
202B LYS* 1.3 62.8 + - + +
205B PRO* 3.3 29.7 - - + +
208B LEU* 3.8 22.7 - - + +
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Residues in contact with LYS 202 (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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198B ASP* 3.0 24.1 + - + +
199B GLU* 2.9 37.1 + - - +
200B LEU 3.1 0.4 - - - -
201B LYS* 1.3 78.7 - - + +
203B HIS* 1.3 79.1 + - + +
205B PRO* 4.4 3.7 - - - +
253B HIS* 5.8 5.2 - - - -
254B LYS* 4.0 15.5 - - - +
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Residues in contact with HIS 203 (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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199B GLU* 3.1 36.6 + - - +
202B LYS* 1.3 100.8 + - + +
204B ALA* 1.3 60.9 + - - +
205B PRO* 3.5 6.5 - - - +
247B ALA 4.6 8.5 - - - +
248B LEU* 4.0 13.5 - - + +
251B GLN* 3.2 43.7 + - + +
252B SER* 4.1 7.2 - - - -
253B HIS* 4.3 18.0 - + - -
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Residues in contact with ALA 204 (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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200B LEU* 2.8 36.2 + - + +
203B HIS* 1.3 75.9 - - - +
205B PRO* 1.4 65.6 - - - +
206B THR* 3.3 3.4 - - - -
207B ILE* 3.1 24.2 + - + +
208B LEU* 3.0 18.7 + - - +
247B ALA* 4.2 14.6 - - - +
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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