Contacts of the helix formed by residues 194 - 208 (chain D) in PDB entry 2BKU
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 SER 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.0 40.6 + - - +
152D LYS* 6.0 1.1 - - - -
192D GLU* 2.7 15.6 + - - +
193D THR* 1.3 73.5 - - - +
195D LYS* 1.3 63.5 + - - +
196D ALA 3.2 9.5 + - - -
197D VAL* 3.3 24.1 + - - -
198D ARG* 3.1 23.3 + - - +
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Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D THR 3.8 3.8 + - - -
194D SER* 1.3 72.4 + - - +
196D ALA* 1.3 57.7 + - - +
198D ARG* 3.8 5.8 - - - +
199D LEU* 3.0 31.8 + - + +
237D ASP* 2.7 46.6 + - + +
238D ILE* 5.5 2.0 - - - +
239D GLU* 2.8 39.8 + - - +
240D VAL* 4.0 11.2 - - + +
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.7 15.3 - - + +
153D ARG* 3.6 24.7 - - + +
194D SER* 3.1 9.9 + - - +
195D LYS* 1.3 80.5 - - + +
197D VAL* 1.3 59.2 + - - +
199D LEU* 3.5 8.5 + - - +
200D ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.6 26.5 - - + +
152D LYS* 4.2 24.7 - - + -
153D ARG* 4.5 4.3 - - + +
156D LEU* 3.8 20.0 - - + +
187D GLY* 4.2 5.2 - - - +
192D GLU* 3.4 30.1 - - + +
194D SER* 3.3 20.1 + - - +
196D ALA* 1.3 73.3 - - - +
198D ARG* 1.3 61.9 + - - +
200D ALA* 3.3 7.1 + - - +
201D ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLY 3.4 14.1 + - - +
188D ALA* 3.1 26.1 + - - +
189D GLN 3.4 6.9 + - - +
190D SER* 3.3 38.4 + - - +
192D GLU* 4.1 11.4 + - + -
194D SER 3.1 17.1 + - - +
195D LYS* 3.8 5.4 - - - +
197D VAL* 1.3 77.7 - - - +
199D LEU* 1.3 61.3 + - - +
201D ALA* 3.2 2.4 + - - +
202D LEU* 3.0 31.9 + - + +
231D GLU* 4.3 4.2 + - - +
232D ALA* 3.7 25.2 - - - +
235D ALA* 3.5 26.2 - - - +
240D VAL* 3.7 27.0 - - + +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LYS* 3.0 21.5 + - - +
196D ALA* 3.6 9.6 - - - +
197D VAL 3.3 0.2 - - - -
198D ARG* 1.3 75.4 - - - +
200D ALA* 1.3 62.0 + - - +
201D ALA 3.2 0.3 + - - -
202D LEU* 3.2 6.5 + - - +
203D ASN* 3.0 41.2 + - - +
239D GLU* 3.3 58.1 - - + +
240D VAL* 3.8 11.1 - - + +
243D ALA* 3.8 9.9 - - + -
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Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ARG* 3.6 37.9 - - + +
156D LEU* 4.4 7.9 - - + +
157D LEU* 4.7 11.5 + - + +
196D ALA 2.9 18.5 + - - +
197D VAL 3.3 5.6 + - - +
199D LEU* 1.3 77.5 - - - +
201D ALA* 1.3 56.2 + - - +
203D ASN* 3.6 7.2 + - - +
204D ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 3.9 14.1 - - + +
184D ILE* 3.2 35.6 - - - +
187D GLY 3.4 20.9 - - - +
188D ALA* 3.6 4.4 - - - +
197D VAL 2.9 16.6 + - - +
198D ARG 3.6 2.0 - - - +
199D LEU 3.2 0.2 - - - -
200D ALA* 1.3 74.3 - - - +
202D LEU* 1.3 62.3 + - - +
204D ALA* 3.4 3.8 + - - -
205D LEU* 3.0 23.0 + - - +
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ALA* 3.7 21.3 - - + -
198D ARG* 3.0 25.1 + - + +
199D LEU* 3.7 0.9 - - - +
201D ALA* 1.3 74.8 - - - +
203D ASN* 1.3 58.9 + - - +
205D LEU* 3.3 6.5 + - + +
206D ALA* 3.0 22.4 + - - +
228D VAL* 5.1 0.7 - - + -
229D VAL* 4.9 15.3 - - + -
232D ALA* 4.0 21.3 - - + -
240D VAL* 3.6 41.3 - - + +
243D ALA* 3.7 23.6 - - + -
244D ALA* 4.2 8.7 - - - +
247D CYS* 3.2 17.1 - - - -
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Residues in contact with ASN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 5.9 6.3 - - + -
199D LEU* 3.0 38.3 + - - +
200D ALA* 3.9 6.0 - - - +
202D LEU* 1.3 76.2 - - - +
204D ALA* 1.3 57.5 + - - +
206D ALA* 3.2 8.7 + - - +
207D ASP* 2.9 38.4 + - - +
243D ALA* 3.8 19.1 - - - +
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 3.5 20.6 - - + +
157D LEU* 5.1 3.7 - - - +
160D GLY* 4.0 11.4 - - - -
184D ILE* 3.4 25.4 - - + -
200D ALA 2.9 19.0 + - - +
201D ALA* 3.7 6.1 - - - +
202D LEU 3.2 0.2 - - - -
203D ASN* 1.3 72.9 - - - +
205D LEU* 1.3 63.7 + - - +
207D ASP* 3.4 3.9 + - - +
208D SER* 2.7 33.6 + - - -
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D LEU* 3.9 16.6 - - + -
184D ILE* 3.6 12.7 - - + +
185D VAL* 4.5 11.0 - - + -
188D ALA* 5.9 3.8 - - + -
201D ALA 3.0 13.6 + - - +
202D LEU* 3.3 13.2 + - + +
204D ALA* 1.3 77.2 - - - +
206D ALA* 1.3 63.2 + - - +
208D SER* 3.1 15.5 + - - -
209D LEU* 3.1 23.1 + - + +
212D ILE* 3.9 26.9 - - + -
225D LEU* 3.9 19.1 - - + +
228D VAL* 6.1 1.6 - - + -
229D VAL* 3.9 28.9 - - + -
247D CYS* 4.0 8.1 - - - -
251D ILE* 5.4 0.4 - - + -
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D LEU 3.0 12.8 + - - +
203D ASN* 3.2 13.2 + - - +
205D LEU* 1.3 77.5 - - - +
207D ASP* 1.3 66.4 + - - +
208D SER 3.1 1.2 + - - -
209D LEU* 3.3 13.9 + - - +
243D ALA 5.9 0.4 - - - +
246D GLY 5.3 1.3 - - - -
247D CYS* 3.6 21.2 - - - +
250D LYS* 3.2 35.0 + - + -
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Residues in contact with ASP 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ARG* 5.2 0.7 - - - -
157D LEU* 5.1 4.2 - - - +
160D GLY* 3.8 21.8 - - - +
161D TYR* 4.0 23.1 + - - -
164D GLU* 3.3 43.6 - - + +
203D ASN* 2.9 25.3 + - - +
204D ALA* 3.9 5.4 - - - +
205D LEU 3.4 0.2 - - - -
206D ALA* 1.3 77.6 - - - +
208D SER* 1.3 56.7 + - - +
209D LEU 3.7 0.2 + - - -
210D ILE 5.0 0.2 + - - -
211D PHE* 3.3 12.5 - - - -
250D LYS* 4.8 5.6 + - - +
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Residues in contact with SER 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D GLY* 3.9 7.8 - - - -
163D CYS* 3.5 26.6 - - - +
180D ILE* 6.0 0.9 - - - -
181D LEU* 6.1 0.4 - - - -
184D ILE* 4.4 8.9 - - - +
204D ALA 2.7 21.8 + - - -
205D LEU* 3.1 9.8 + - - -
207D ASP* 1.3 75.4 - - - +
209D LEU* 1.3 64.9 + - - +
210D ILE 3.2 2.7 - - - -
211D PHE* 3.0 21.4 + - - -
212D ILE* 3.2 26.2 + - - +
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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