Contacts of the helix formed by residues 195 - 206 (chain B) in PDB entry 4UC5
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 LEU 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B ASN* 4.0 15.3 - - + +
193B GLY 3.0 7.0 + - - +
194B ASN* 1.3 70.7 + - - +
196B LYS* 1.3 65.5 + - - +
197B ILE 3.2 2.9 - - - -
198B ALA* 2.9 17.0 + - + +
199B ILE* 3.1 22.4 + - + -
233B VAL* 4.3 25.1 - - + -
234B ILE 5.3 0.4 - - - +
235B LEU* 4.1 21.3 - - + -
242B ASN* 6.1 1.1 - - - +
251B ALA* 3.5 37.0 - - + -
254B GLN* 3.9 21.1 - - - +
255B LEU* 5.8 0.4 - - + -
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Residues in contact with LYS 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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194B ASN* 2.7 17.3 + - - +
195B LEU* 1.3 74.1 - - - +
197B ILE* 1.3 57.2 + - + +
199B ILE* 3.0 13.1 + - - +
200B ASP* 2.8 43.9 + - - +
254B GLN* 4.7 5.2 + - - +
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Residues in contact with ILE 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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191A THR* 5.1 1.6 - - - +
166B ALA 4.4 4.9 - - - +
169B THR* 3.7 22.6 - - + +
170B GLU* 3.7 39.9 - - + +
175B ARG* 2.9 31.7 + - - +
188B LYS 4.7 0.4 - - - +
190B GLY* 3.7 29.6 - - - +
194B ASN* 3.2 35.2 + - + +
196B LYS* 1.3 76.0 - - + +
198B ALA* 1.3 60.6 + - - +
200B ASP* 3.5 4.4 + - - +
201B ALA* 3.0 15.9 + - - +
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Residues in contact with ALA 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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169B THR* 3.6 10.3 - - + -
187B PHE* 3.8 24.1 - - + +
188B LYS 3.8 15.7 - - - +
189B ASN* 4.2 6.3 - - - +
195B LEU* 2.9 12.3 + - + +
197B ILE* 1.3 78.2 - - - +
199B ILE* 1.3 66.3 + - - +
201B ALA* 3.2 4.1 + - - +
202B ILE* 3.2 25.6 + - - +
233B VAL* 3.8 15.4 - - + +
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Residues in contact with ILE 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* 3.1 27.3 + - + +
196B LYS* 3.0 9.1 + - - +
198B ALA* 1.3 75.9 - - - +
200B ASP* 1.3 67.4 + - - +
202B ILE* 3.3 15.5 + - - +
203B GLY* 3.3 9.5 + - - -
233B VAL* 4.3 6.5 - - + -
254B GLN* 3.5 43.5 - - + +
255B LEU* 3.8 26.5 - - + -
258B ALA* 3.7 30.7 - - + -
260B VAL* 4.4 4.2 - - + +
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Residues in contact with ASP 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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102A THR* 3.8 31.6 + - + +
175B ARG* 4.0 10.7 + - - +
196B LYS* 2.8 29.6 + - - +
197B ILE* 3.7 7.2 - - - +
199B ILE* 1.3 80.9 - - - +
201B ALA* 1.3 61.7 + - - +
203B GLY* 3.4 2.8 + - - +
204B ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 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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169B THR* 3.8 3.8 - - + +
175B ARG* 3.5 25.0 - - + +
187B PHE* 3.5 34.8 - - + -
197B ILE 3.0 15.2 + - - +
198B ALA 3.4 10.5 - - - +
199B ILE 3.2 0.6 - - - -
200B ASP* 1.3 74.1 - - - +
202B ILE* 1.3 59.4 + - - +
204B ALA* 3.2 1.7 + - - +
205B ALA* 2.7 33.3 + - - +
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Residues in contact with ILE 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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187B PHE* 4.4 4.0 - - + -
198B ALA 3.2 9.8 + - - +
199B ILE* 3.3 6.5 + - - +
201B ALA* 1.3 77.2 - - - +
203B GLY* 1.3 68.0 + - - +
205B ALA* 3.3 1.0 + - - +
206B SER* 3.0 23.9 + - - -
231B CYS* 4.1 29.9 - - + +
232B HIS* 3.7 27.1 - - - -
233B VAL* 3.4 29.2 - - + +
255B LEU* 4.2 14.8 - - + -
260B VAL* 3.9 26.0 - - + -
261B THR* 4.9 5.2 - - + -
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Residues in contact with GLY 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 ILE 3.3 9.5 + - - -
200B ASP* 3.4 3.1 + - - -
202B ILE* 1.3 78.7 - - - +
204B ALA* 1.3 59.9 + - - +
206B SER* 2.5 27.2 + - - -
207B HIS* 3.3 15.9 + - - -
260B VAL* 4.3 14.5 - - - +
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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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101A ARG 5.9 0.7 - - - +
102A THR* 4.1 21.9 + - - +
175B ARG* 4.3 24.2 - - + +
200B ASP 3.0 17.5 + - - +
201B ALA 3.6 4.0 - - - +
203B GLY* 1.3 75.4 - - - +
205B ALA* 1.3 56.8 + - - +
207B HIS* 3.1 20.7 + - - +
209B HIS* 2.9 32.8 + - + +
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Residues in contact with ALA 205 (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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175B ARG 3.9 16.4 - - - +
178B ALA* 4.1 4.7 - - + -
179B SER* 3.1 22.5 - - - +
187B PHE* 3.9 13.0 - - + -
201B ALA 2.7 20.2 + - - +
202B ILE 4.0 0.9 - - - +
204B ALA* 1.3 73.2 - - - +
206B SER* 1.3 58.7 + - - +
207B HIS 3.3 0.2 - - - -
228B ASN* 2.9 22.1 + - - +
231B CYS* 3.8 23.8 - - - -
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.0 13.6 + - - -
203B GLY* 2.5 24.1 + - - -
205B ALA* 1.3 78.2 - - - +
207B HIS* 1.3 70.8 + - - +
226B GLY 4.9 0.5 - - - +
227B GLY* 3.5 13.1 - - - -
228B ASN 3.5 19.4 + - - +
229B PRO* 5.1 4.5 - - - -
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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