Contacts of the helix formed by residues 188 - 197 (chain B) in PDB entry 2CXU
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 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ASP* 3.5 11.0 - - - +
343A GLN* 2.8 30.2 + - + +
412A THR* 4.3 8.7 + - - -
421A HIS* 4.8 1.3 + - - -
422A HIS* 4.9 1.8 + - - -
425A LEU* 3.7 29.5 - - + +
186B ASN* 3.0 26.0 + - + +
187B ILE* 1.3 77.8 - - - +
189B GLY* 1.3 61.0 + - - +
190B THR* 3.1 24.5 + - - -
191B HIS* 2.9 27.7 + - - +
192B ILE* 4.3 1.2 + - - +
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Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A THR* 5.4 1.0 + - - -
414A HIS* 4.3 8.7 - - - -
416A ILE* 3.7 13.4 - - - +
421A HIS* 3.6 26.3 - - - +
422A HIS* 5.1 1.4 + - - +
187B ILE 2.9 8.2 + - - -
188B ASP* 1.3 70.1 + - - +
190B THR* 1.3 64.8 + - - +
191B HIS 3.1 0.4 + - - -
192B ILE* 3.5 5.1 + - - +
193B ALA* 3.0 28.4 + - - +
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Residues in contact with THR 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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342A ASP* 5.4 1.4 + - - -
343A GLN* 4.1 11.0 - - + -
344A TYR* 3.4 49.5 - - + +
412A THR* 4.4 6.1 + - - -
413A GLN* 5.0 1.4 + - - +
414A HIS* 3.4 25.5 - - - +
188B ASP* 3.1 23.0 + - - -
189B GLY* 1.3 76.8 - - - +
191B HIS* 1.3 62.6 + - - +
194B LYS* 2.9 33.1 + - + +
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Residues in contact with HIS 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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343A GLN* 4.0 25.5 + - + +
386A ASN* 5.0 1.1 - - - -
183B PHE 3.3 20.3 + - - -
184B VAL* 4.4 4.3 - - + -
185B SER* 3.2 30.3 + - - -
186B ASN* 3.1 34.2 + - + +
188B ASP 2.9 15.2 + - - +
190B THR* 1.3 81.3 - - - +
192B ILE* 1.3 60.4 + - - +
194B LYS* 3.5 25.3 + - - +
195B THR* 2.8 31.1 + - - -
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Residues in contact with ILE 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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416A ILE* 3.5 28.5 - - + -
421A HIS* 3.9 6.7 - - + -
155B ILE* 4.4 16.2 - - + -
184B VAL* 3.8 29.0 - - + +
188B ASP 4.3 0.6 + - - -
189B GLY* 3.6 3.5 - - - +
191B HIS* 1.3 78.1 - - - +
193B ALA* 1.3 61.2 + - - +
195B THR* 3.2 2.8 + - - -
196B LEU* 2.9 66.2 + - + +
206B PHE* 4.8 2.2 - - + -
221B ASN* 3.7 28.0 + - - +
224B THR* 4.0 11.2 - - + -
225B ALA* 4.5 4.5 - - + +
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Residues in contact with ALA 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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414A HIS* 4.0 30.5 - - + +
416A ILE* 4.3 14.4 - - + -
189B GLY 3.0 20.3 + - - +
190B THR 3.9 1.8 - - - +
192B ILE* 1.3 79.3 - - - +
194B LYS* 1.3 62.2 + - - +
196B LEU* 4.0 6.3 - - - +
197B ALA* 3.1 24.6 + - - +
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Residues in contact with LYS 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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169A GLU* 5.3 7.3 + - - -
172A LYS* 6.3 0.9 - - + -
343A GLN* 4.1 18.1 - - - +
344A TYR* 4.3 24.2 - - + +
346A HIS* 5.8 2.8 + - - -
414A HIS* 5.4 3.3 - - + +
182B TRP* 5.3 0.7 - - - -
190B THR* 2.9 33.2 + - + +
191B HIS* 3.5 28.8 + - - +
193B ALA* 1.3 75.1 - - - +
195B THR* 1.3 68.2 + - - +
197B ALA* 3.7 12.6 + - - +
198B SER* 3.3 14.2 + - - -
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Residues in contact with THR 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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153B ILE* 4.3 3.8 - - + -
182B TRP* 3.9 37.4 - - + -
183B PHE 4.8 2.1 + - - +
184B VAL* 3.5 27.2 - - + +
191B HIS* 2.8 27.5 + - - -
192B ILE* 3.2 6.8 + - + -
194B LYS* 1.3 79.3 - - - +
196B LEU* 1.3 64.1 + - + +
198B SER* 3.3 15.5 + - - -
199B LEU* 3.3 28.8 - - + +
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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 ILE* 2.9 44.0 + - + +
193B ALA* 4.1 5.6 - - - +
195B THR* 1.3 75.9 - - - +
197B ALA* 1.3 65.4 + - - +
199B LEU* 3.1 27.3 + - + +
206B PHE* 3.6 36.8 - - + -
224B THR* 4.6 7.6 - - + +
225B ALA* 4.5 7.0 - - + -
228B TRP* 3.7 57.2 + - + +
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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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193B ALA 3.1 17.7 + - - +
194B LYS* 3.8 11.9 - - - +
195B THR 3.2 0.4 - - - -
196B LEU* 1.3 76.3 - - - +
198B SER* 1.3 58.0 + - - +
199B LEU 3.4 2.8 + - - +
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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