Contacts of the helix formed by residues 193 - 211 (chain D) in PDB entry 2W93
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 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ASN* 4.2 3.6 - - - +
192D ASN* 1.3 71.4 - - - +
194D ALA* 1.3 66.9 + - - +
195D GLU* 3.4 9.3 + - - +
196D SER* 3.0 38.4 + - - -
197D GLU* 3.0 22.7 + - - +
323D GLY 5.5 2.2 + - - -
324D VAL* 5.7 2.6 - - + +
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Residues in contact with ALA 194 (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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192D ASN 3.2 6.8 + - - +
193D ASP* 1.3 75.0 + - - +
195D GLU* 1.3 64.6 + - + +
197D GLU* 3.9 8.3 - - - +
198D LYS* 3.1 23.7 + - - +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LYS* 3.1 49.5 - - - +
317A ARG* 3.8 7.3 + - - -
318A ASN* 3.3 19.3 + - - +
193D ASP* 3.4 8.7 + - - +
194D ALA* 1.3 76.7 - - + +
196D SER* 1.3 67.5 + - - +
198D LYS* 3.4 6.6 + - - +
199D GLU* 3.2 17.7 + - - +
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Residues in contact with SER 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 3.5 29.8 + - - +
193D ASP* 3.0 24.4 + - - -
195D GLU* 1.3 76.1 - - - +
197D GLU* 1.3 63.6 + - - +
199D GLU* 3.4 3.6 + - - +
200D VAL* 3.1 26.5 + - - +
321D PHE* 3.7 10.4 - - - +
322D PRO 5.1 1.9 + - - -
324D VAL* 3.1 25.5 - - - +
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Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ASN* 2.8 42.2 + - + +
193D ASP 3.0 19.1 + - - +
194D ALA* 3.9 6.6 - - - +
196D SER* 1.3 75.0 - - - +
198D LYS* 1.3 60.1 + - - +
200D VAL* 3.4 2.4 + - - +
201D ILE* 3.0 39.7 + - + +
324D VAL* 4.2 10.6 - - + +
328D PHE* 3.4 16.7 - - - +
329D VAL* 4.3 8.3 - - + -
332D LYS* 2.6 40.9 + - - +
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Residues in contact with LYS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 6.0 4.1 - - - +
194D ALA 3.1 19.2 + - - +
195D GLU* 3.8 6.1 - - - +
196D SER 3.4 0.4 - - - -
197D GLU* 1.3 73.6 - - - +
199D GLU* 1.3 60.8 + - - +
201D ILE* 3.3 7.7 + - + +
202D ASP* 2.8 58.3 + - - +
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Residues in contact with GLU 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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316A ILE 4.1 4.3 - - - +
317A ARG* 3.5 32.3 - - - +
318A ASN* 3.0 34.9 + - - +
319A ALA* 4.0 11.6 - - - +
195D GLU 3.2 10.6 + - - +
196D SER 3.6 8.3 - - - +
197D GLU 3.3 0.2 - - - -
198D LYS* 1.3 79.1 - - - +
200D VAL* 1.3 58.2 + - - +
202D ASP* 3.4 5.4 + - - +
203D THR* 2.7 46.5 + - + +
321D PHE* 3.8 22.3 - - + -
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Residues in contact with VAL 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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196D SER 3.1 14.8 + - - +
197D GLU* 3.6 7.9 - - - +
199D GLU* 1.3 76.2 - - - +
201D ILE* 1.3 62.8 + - - +
203D THR* 4.7 0.2 - - - -
204D ILE* 3.0 49.3 + - + +
314D MET* 3.9 15.5 - - + -
316D ILE* 3.8 13.8 - - + +
321D PHE* 3.5 41.1 - - + -
324D VAL* 4.2 9.6 - - + -
329D VAL* 3.8 16.6 - - + -
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Residues in contact with ILE 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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197D GLU* 3.0 40.5 + - + +
198D LYS* 3.8 6.5 - - - +
200D VAL* 1.3 76.3 - - - +
202D ASP* 1.3 67.1 + - - +
204D ILE* 3.7 5.5 - - - +
205D LEU* 2.9 41.6 + - + +
329D VAL* 4.1 25.8 - - + +
332D LYS* 3.6 32.5 - - + +
333D LEU* 4.2 13.9 - - + +
336D ASN* 4.5 9.6 - - - +
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Residues in contact with ASP 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LYS* 2.8 57.6 + - - +
199D GLU* 3.8 6.4 + - - +
201D ILE* 1.3 77.0 - - - +
203D THR* 1.3 60.1 + - + +
205D LEU* 3.3 12.6 + - - +
206D ALA* 3.0 28.5 + - - +
209D LYS* 5.1 1.0 + - - -
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Residues in contact with THR 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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199D GLU* 2.7 39.2 + - + +
200D VAL* 3.8 3.1 - - - -
202D ASP* 1.3 75.3 - - + +
204D ILE* 1.3 67.0 + - - +
206D ALA* 3.2 9.0 + - - +
207D LEU* 3.0 28.0 + - - +
316D ILE* 3.9 24.8 - - + +
321D PHE* 5.6 2.7 - - + -
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Residues in contact with ILE 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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200D VAL* 3.0 39.2 + - + +
201D ILE* 3.7 3.8 - - - +
203D THR* 1.3 76.9 - - - +
205D LEU* 1.3 61.2 - - - +
207D LEU* 3.2 9.0 + - - +
208D VAL* 3.0 33.7 + - + +
283D LEU* 4.9 7.4 - - + -
307D VAL* 3.8 28.9 - - + -
309D PHE* 4.1 10.5 - - + -
314D MET* 4.0 8.7 - - + -
316D ILE* 3.8 12.6 - - + -
329D VAL* 4.0 12.1 - - + -
333D LEU* 3.8 26.0 - - + -
337D ILE* 5.1 0.4 - - + -
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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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201D ILE* 2.9 38.1 + - + +
202D ASP* 3.5 11.7 - - - +
204D ILE* 1.3 75.8 - - - +
206D ALA* 1.3 61.1 + - - +
208D VAL* 3.4 6.3 + - - +
209D LYS* 3.2 35.8 + - - +
333D LEU* 3.8 20.0 - - + -
336D ASN* 3.9 33.4 - - + +
337D ILE* 4.0 10.1 - - + -
340D ALA* 3.8 25.0 - - + +
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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 ASP 3.0 13.2 + - - +
203D THR* 3.2 12.1 + - - +
205D LEU* 1.3 74.5 - - - +
207D LEU* 1.3 65.8 + - + +
209D LYS* 3.4 35.1 + - - +
210D ASP* 3.5 13.8 + - - +
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Residues in contact with LEU 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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203D THR* 3.0 19.6 + - - +
204D ILE* 3.2 6.7 + - - +
206D ALA* 1.3 73.4 - - + +
208D VAL* 1.3 66.6 + - - +
210D ASP* 3.3 14.5 + - + +
211D ALA* 3.3 15.2 + - - +
281D LEU* 3.9 18.9 - - + +
305D ASN* 3.9 26.7 - - + +
307D VAL* 3.9 18.2 - - + -
316D ILE* 3.6 31.2 - - + -
317D ARG* 5.0 10.3 - - + -
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Residues in contact with VAL 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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204D ILE* 3.0 28.0 + - + +
205D LEU* 3.6 6.3 - - - +
206D ALA 3.3 0.2 - - - -
207D LEU* 1.3 75.9 - - - +
209D LYS* 1.3 63.2 + - - +
211D ALA* 3.2 18.0 + - - +
240D PHE* 3.9 28.2 - - + -
281D LEU* 3.9 19.3 - - + -
283D LEU* 4.8 4.3 - - + -
337D ILE* 4.0 24.9 - - + -
340D ALA* 3.7 31.0 - - + +
341D ALA* 4.1 3.6 - - + +
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Residues in contact with LYS 209 (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 ASP 5.1 1.0 + - - -
205D LEU* 3.2 21.9 + - - +
206D ALA* 3.4 33.9 - - - +
207D LEU 3.3 0.2 - - - -
208D VAL* 1.3 76.9 - - - +
210D ASP* 1.3 66.4 + - - +
211D ALA 3.5 3.1 + - - +
340D ALA* 3.8 24.7 - - + +
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Residues in contact with ASP 210 (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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206D ALA 3.5 11.0 + - - +
207D LEU* 3.3 10.4 + - + +
208D VAL 3.2 0.6 - - - -
209D LYS* 1.3 81.9 - - - +
211D ALA* 1.3 61.3 + - - +
212D LYS* 3.7 10.1 + - - +
280D ASP* 4.2 4.0 - - - +
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Residues in contact with ALA 211 (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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207D LEU 3.3 14.0 + - - +
208D VAL 3.2 12.6 + - - +
209D LYS 3.3 2.8 - - - +
210D ASP* 1.3 77.5 - - - +
212D LYS* 1.3 62.8 + - - +
214D PRO* 4.0 16.3 - - + +
280D ASP* 3.5 18.6 - - - +
281D LEU* 3.8 24.7 - - + -
344D TYR* 4.6 10.4 - - - +
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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
------------------------------------------------------------
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