Contacts of the helix formed by residues 193 - 211 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A PRO 3.9 0.4 + - - -
192A ASN* 1.3 69.0 - - - +
194A ALA* 1.3 60.9 + - - +
195A GLU* 3.4 8.4 + - - +
196A SER* 2.6 42.3 + - - +
197A GLU* 2.9 30.5 + - - +
323A GLY 5.5 2.0 + - - -
324A VAL* 5.6 3.2 - - + +
318D ASN* 4.1 2.9 - - - +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN 3.2 6.6 + - - +
193A ASP* 1.3 74.2 + - - +
195A GLU* 1.3 61.8 + - + +
197A GLU* 3.8 8.9 - - - +
198A LYS* 3.0 28.9 + - - +
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Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASP* 3.4 8.1 + - - +
194A ALA* 1.3 77.4 - - + +
196A SER* 1.3 61.3 + - - +
198A LYS* 3.4 8.3 + - + +
199A GLU* 3.0 23.6 + - - +
304D LYS* 3.6 45.8 - - + +
317D ARG* 4.7 6.0 + - - +
318D ASN* 3.4 21.6 + - - +
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Residues in contact with SER 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASP* 2.6 30.2 + - - +
195A GLU* 1.3 74.9 - - - +
197A GLU* 1.3 66.1 + - - +
199A GLU* 3.1 4.7 + - - +
200A VAL* 3.0 27.3 + - - +
321A PHE* 4.5 1.7 - - - -
322A PRO 5.8 0.2 - - - -
324A VAL* 3.6 22.9 - - - -
318D ASN* 3.1 32.6 + - - +
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 3.0 40.9 + - + +
193A ASP 2.9 18.6 + - - +
194A ALA* 3.8 7.8 - - - +
196A SER* 1.3 76.1 - - - +
198A LYS* 1.3 62.8 + - - +
200A VAL* 3.3 3.7 + - - +
201A ILE* 3.1 39.6 + - + +
324A VAL* 4.1 10.4 - - - +
328A PHE* 3.2 18.8 - - - +
329A VAL* 4.2 8.7 - - + -
332A LYS* 2.6 38.8 + - - +
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA 3.0 19.1 + - - +
195A GLU* 3.8 7.0 - - - +
196A SER 3.2 0.2 - - - -
197A GLU* 1.3 74.3 + - - +
199A GLU* 1.3 66.8 + - - +
201A ILE* 3.5 10.1 + - + +
202A ASP* 2.9 56.4 + - - +
304D LYS* 4.8 17.0 - - - +
317D ARG* 5.5 8.3 - - - +
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU 3.0 14.7 + - - +
196A SER 3.1 8.0 + - - +
198A LYS* 1.3 76.0 - - - +
200A VAL* 1.3 63.7 + - - +
202A ASP* 3.2 8.8 + - + +
203A THR* 3.0 39.6 + - + +
321A PHE* 3.7 25.0 - - + -
316D ILE 4.1 3.8 - - - +
317D ARG* 3.3 25.8 + - - +
318D ASN* 2.9 37.7 + - - +
319D ALA* 4.0 9.4 - - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER 3.0 17.8 + - - +
197A GLU* 3.6 8.3 - - - +
198A LYS 3.2 0.2 - - - -
199A GLU* 1.3 77.3 - - - +
201A ILE* 1.3 62.5 + - - +
203A THR* 3.4 1.7 + - - -
204A ILE* 3.2 47.4 + - + +
314A MET* 3.9 17.7 - - + -
316A ILE* 3.9 12.1 - - + -
321A PHE* 3.6 39.5 - - + -
324A VAL* 4.1 11.2 - - + -
329A VAL* 3.8 17.3 - - + -
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU* 3.1 38.9 + - + +
198A LYS* 3.9 8.3 - - + +
199A GLU 3.3 0.2 - - - -
200A VAL* 1.3 77.7 - - - +
202A ASP* 1.3 66.5 + - - +
204A ILE* 3.6 4.6 + - - +
205A LEU* 3.3 36.8 + - + +
329A VAL* 4.1 24.9 - - + +
332A LYS* 3.7 31.4 - - + +
333A LEU* 4.1 22.5 - - + +
336A ASN* 6.0 4.0 - - + -
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LYS* 2.9 49.5 + - - +
199A GLU* 3.6 9.6 - - - +
201A ILE* 1.3 78.5 - - - +
203A THR* 1.3 67.2 + - + +
204A ILE 3.4 0.2 + - - -
205A LEU* 3.4 23.2 + - - +
206A ALA* 3.5 11.8 + - - +
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.0 34.3 + - + +
200A VAL 3.8 4.0 - - - -
202A ASP* 1.3 77.1 - - + +
204A ILE* 1.3 64.2 + - - +
206A ALA* 3.2 15.4 + - - +
207A LEU* 3.3 17.7 + - - +
316A ILE* 3.8 27.6 - - + +
321A PHE* 5.3 3.4 - - + -
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.2 35.6 + - + +
201A ILE 3.8 4.5 - - - +
202A ASP 3.3 0.2 - - - -
203A THR* 1.3 79.9 + - - +
205A LEU* 1.3 63.4 + - - +
207A LEU* 3.2 11.8 + - - +
208A VAL* 3.0 37.0 + - + +
283A LEU* 4.8 14.4 - - + -
307A VAL* 3.7 29.6 - - + -
309A PHE* 3.9 17.9 - - + -
314A MET* 4.2 0.4 - - + -
316A ILE* 3.9 8.5 - - + -
329A VAL* 4.2 2.5 - - + -
333A LEU* 3.8 29.6 - - + -
337A ILE* 5.1 1.8 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.3 29.8 - - + +
202A ASP* 3.6 15.3 - - - +
203A THR 3.3 0.2 - - - -
204A ILE* 1.3 76.9 - - - +
206A ALA* 1.3 55.7 + - - +
208A VAL* 3.3 8.5 - - - +
209A LYS* 3.1 37.6 + - - +
333A LEU* 3.8 20.9 - - + -
336A ASN* 4.7 18.2 - - + +
337A ILE* 4.2 21.1 - - + +
340A ALA* 3.7 19.7 - - + +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASP 3.5 7.9 + - - +
203A THR* 3.2 12.2 + - - +
205A LEU* 1.3 77.3 - - - +
207A LEU* 1.3 66.7 + - + +
209A LYS* 3.5 9.4 + - - +
210A ASP* 3.4 27.0 + - - +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 3.3 14.8 + - - +
204A ILE* 3.2 7.2 + - - +
206A ALA* 1.3 75.6 - - + +
208A VAL* 1.3 66.6 + - - +
210A ASP* 3.3 7.5 + - + +
211A ALA* 3.1 23.6 + - - +
281A LEU* 4.0 15.1 - - + +
305A ASN* 3.8 28.7 + - - +
306A ILE 5.9 0.2 - - - +
307A VAL* 4.0 15.7 - - + -
316A ILE* 3.5 32.3 - - + -
317A ARG* 5.1 9.6 - - + -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 3.0 28.1 + - + +
205A LEU* 3.3 9.9 - - - +
207A LEU* 1.3 76.6 - - - +
209A LYS* 1.3 62.4 + - - +
210A ASP 3.2 0.9 + - - -
211A ALA* 3.2 17.7 + - - +
240A PHE* 4.1 18.2 - - + -
281A LEU* 4.1 17.5 - - + +
283A LEU* 4.8 7.2 - - + -
337A ILE* 4.1 21.8 - - + -
340A ALA* 3.3 31.4 - - + +
341A ALA* 3.8 16.7 - - + -
344A TYR* 6.1 1.2 - - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.1 25.6 + - - +
206A ALA* 3.8 12.9 - - - +
207A LEU 3.3 0.4 - - - -
208A VAL* 1.3 75.1 - - - +
210A ASP* 1.3 64.0 + - - +
211A ALA 3.7 2.8 + - - +
212A LYS* 5.2 4.7 + - - -
339A ASP* 4.3 17.0 + - - +
340A ALA* 3.2 34.6 - - - +
343A GLY* 5.8 3.8 - - - -
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Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA 3.4 14.4 + - - +
207A LEU* 3.3 8.8 + - + +
208A VAL 3.2 0.8 - - - -
209A LYS* 1.3 83.2 - - - +
211A ALA* 1.3 61.6 + - - +
212A LYS* 3.5 17.6 + - - +
280A ASP* 4.6 0.5 - - - +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU 3.1 16.3 + - - +
208A VAL 3.2 11.6 + - - +
209A LYS 4.5 1.6 - - - +
210A ASP* 1.3 77.4 - - - +
212A LYS* 1.3 66.7 + - - +
214A PRO* 3.8 16.3 - - + +
280A ASP* 3.6 10.5 - - - +
281A LEU* 3.6 33.9 - - + -
305A ASN* 5.4 1.8 - - - +
344A TYR* 4.6 11.4 - - - +
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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