Contacts of the helix formed by residues 198 - 218 (chain A) in PDB entry 2P3Z
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A HIS* 5.5 0.5 - - - -
56A GLU* 4.5 4.6 - - - +
194A TRP* 3.4 30.8 - - + -
195A GLY 2.8 30.4 + - - +
197A HIS* 1.3 99.7 + - - +
199A GLY* 1.3 63.4 + - - +
201A ALA* 3.4 11.9 + - + +
202A GLY* 3.2 26.3 + - - -
205A LYS* 5.4 1.5 + - - +
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Residues in contact with GLY 199 (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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195A GLY 3.6 2.8 + - - -
196A PRO 2.9 16.4 + - - -
197A HIS 3.4 1.0 - - - -
198A ASP* 1.3 76.8 - - - +
200A ASP* 1.3 65.3 + - - -
202A GLY 3.0 10.4 + - - -
203A ILE* 3.1 18.6 + - - +
235A TYR* 3.5 9.9 - - - -
238A LYS* 5.0 3.8 - - - -
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP 3.5 0.2 + - - -
199A GLY* 1.3 73.4 - - - -
201A ALA* 1.3 58.2 + - - +
203A ILE* 3.3 8.8 + - - +
204A ARG* 2.8 43.6 + - - +
238A LYS* 2.8 33.8 + - - -
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Residues in contact with ALA 201 (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 ASP* 3.4 9.3 + - + +
199A GLY 3.2 0.8 - - - -
200A ASP* 1.3 76.2 - - - +
202A GLY* 1.3 59.3 + - - +
204A ARG* 3.2 23.7 + - - +
205A LYS* 2.9 50.8 + - - +
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Residues in contact with GLY 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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194A TRP* 3.4 33.4 - - - -
198A ASP* 3.2 11.6 + - - +
199A GLY 3.0 7.5 + - - -
201A ALA* 1.3 77.9 - - - +
203A ILE* 1.3 62.5 - - - +
205A LYS* 3.3 1.3 + - - -
206A ASP* 3.1 23.9 + - - +
235A TYR* 3.3 11.2 + - - -
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Residues in contact with ILE 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 GLY 3.1 8.1 + - - +
200A ASP* 3.7 8.5 - - - +
202A GLY* 1.3 76.8 - - - +
204A ARG* 1.3 64.0 + - - +
207A ALA* 2.9 23.7 + - - +
235A TYR* 3.5 35.4 - - + -
238A LYS* 3.4 51.1 - - + +
239A LEU* 3.9 19.7 - - + +
242A ALA* 3.6 28.9 - - + -
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Residues in contact with ARG 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 ASP* 2.8 35.4 + - - +
201A ALA* 3.2 29.3 + - - +
203A ILE* 1.3 78.0 - - - +
205A LYS* 1.3 63.2 + - + +
207A ALA* 3.8 4.3 - - - +
208A ALA* 2.9 33.1 + - + +
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Residues in contact with LYS 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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194A TRP* 3.2 67.5 - - + +
198A ASP* 5.4 0.8 + - - +
201A ALA* 2.9 35.7 + - - +
202A GLY* 5.2 0.4 - - - +
203A ILE 3.2 0.2 - - - -
204A ARG* 1.3 79.8 - - + +
206A ASP* 1.3 65.5 + - - +
208A ALA* 3.2 7.2 + - - +
209A MET* 3.0 22.2 + - - +
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Residues in contact with ASP 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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192A THR* 3.5 20.1 - - + +
193A HIS* 3.0 26.2 + - - +
194A TRP* 3.1 40.3 + - - +
202A GLY 3.1 11.7 + - - +
205A LYS* 1.3 76.2 - - - +
207A ALA* 1.3 62.4 + - - +
209A MET* 3.3 23.9 + - + +
210A VAL* 3.2 25.6 + - - +
225A LEU* 5.2 1.6 - - + -
235A TYR* 4.6 1.7 + - - -
239A LEU* 4.2 17.8 - - + +
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Residues in contact with ALA 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 ILE 2.9 19.9 + - - +
204A ARG* 3.9 4.7 - - - +
206A ASP* 1.3 78.9 - - - +
208A ALA* 1.3 54.3 + - - +
210A VAL* 3.2 4.2 + - - +
211A ALA* 2.9 28.7 + - - +
239A LEU* 4.3 1.4 - - + +
242A ALA* 4.0 33.4 - - + +
243A CYS* 4.0 16.6 - - - -
246A PHE* 4.1 8.4 - - + -
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Residues in contact with ALA 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 ARG* 2.9 22.2 + - + +
205A LYS* 3.2 8.0 + - - +
207A ALA* 1.3 73.6 - - - +
209A MET* 1.3 61.5 + - - +
211A ALA* 3.7 8.2 - - - +
212A ASP* 2.9 31.6 + - - +
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Residues in contact with MET 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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175A ALA* 6.2 0.4 - - - +
190A MET* 3.9 22.7 - - + +
191A PRO* 3.4 22.4 - - - +
193A HIS* 3.8 24.0 - - - -
205A LYS 3.0 13.2 + - - +
206A ASP* 3.3 23.3 - - - +
207A ALA 3.2 0.2 - - - -
208A ALA* 1.3 79.1 - - - +
210A VAL* 1.3 62.2 + - + +
212A ASP* 3.4 6.3 + - - +
213A MET* 3.2 28.4 + - + +
225A LEU* 3.7 25.6 - - + -
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Residues in contact with VAL 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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190A MET* 3.9 14.8 - - + -
206A ASP 3.2 13.0 + - - +
207A ALA 3.2 8.0 + - - +
209A MET* 1.3 76.4 - - + +
211A ALA* 1.3 58.7 + - - +
213A MET 3.2 2.1 + - - +
214A ARG* 2.9 27.2 + - - +
223A LEU* 3.7 14.3 - - + +
225A LEU* 3.6 38.6 - - + -
243A CYS* 4.1 10.3 - - + -
246A PHE* 4.1 23.8 - - + +
248A LEU* 4.0 19.7 - - + -
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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 ALA 2.9 18.8 + - - +
208A ALA* 3.7 9.6 - - - +
210A VAL* 1.3 71.5 - - - +
212A ASP* 1.3 62.8 + - - +
214A ARG* 3.2 4.4 + - - +
215A GLU* 3.1 22.2 + - - +
246A PHE* 3.6 40.2 - - + -
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Residues in contact with ASP 212 (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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208A ALA 2.9 18.4 + - - +
209A MET* 3.6 6.7 - - - +
211A ALA* 1.3 73.1 - - - +
213A MET* 1.3 69.2 + - - +
215A GLU* 3.2 12.7 + - - +
216A LYS* 2.6 71.5 + - - +
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Residues in contact with MET 213 (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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175A ALA 4.0 18.8 - - - +
176A ARG* 4.5 6.3 - - - +
177A PRO* 3.9 5.6 - - + -
178A ASP* 3.7 50.0 - - - +
190A MET* 3.8 19.5 - - - -
209A MET* 3.2 19.1 + - + +
210A VAL 3.8 3.1 - - - +
212A ASP* 1.3 92.4 - - - +
214A ARG* 1.3 54.0 + - - +
216A LYS* 4.2 7.9 - - + +
217A CYS* 2.8 40.7 + - - +
223A LEU* 3.8 20.0 - - + -
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Residues in contact with ARG 214 (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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210A VAL 2.9 14.1 + - - +
211A ALA* 3.5 9.9 - - - +
213A MET* 1.3 74.5 - - - +
215A GLU* 1.3 65.2 + - - +
217A CYS* 5.1 1.0 - - - +
218A GLY* 2.7 57.2 + - - -
219A PRO* 3.6 16.9 + - - +
221A PHE* 2.8 25.7 + - - +
222A TRP* 4.8 1.2 - - - +
223A LEU* 3.4 36.6 - - + +
246A PHE* 2.8 47.0 + - + +
247A ASN* 3.2 23.7 + - - +
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Residues in contact with GLU 215 (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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211A ALA 3.1 11.9 + - - +
212A ASP* 3.2 14.6 + - - +
214A ARG* 1.3 80.9 - - - +
216A LYS* 1.3 76.1 + - - +
217A CYS 3.4 0.2 + - - -
218A GLY* 4.1 3.8 + - - -
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Residues in contact with LYS 216 (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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178A ASP* 4.0 33.9 + - + +
181A LYS* 5.1 4.0 + - - +
212A ASP* 2.6 52.7 + - - +
213A MET* 3.2 16.8 + - - +
215A GLU* 1.3 88.3 - - - +
217A CYS* 1.3 61.1 + - - +
218A GLY 3.7 0.4 + - - -
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Residues in contact with CYS 217 (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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177A PRO* 3.8 7.6 - - - -
178A ASP* 3.6 37.5 - - - -
181A LYS* 3.2 33.8 - - + +
213A MET* 2.8 23.8 + - - +
214A ARG* 4.9 1.6 - - - +
216A LYS* 1.3 80.5 - - - +
218A GLY* 1.3 62.7 + - - +
221A PHE* 3.5 39.7 + - + +
223A LEU* 4.6 2.5 - - + -
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Residues in contact with GLY 218 (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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214A ARG* 2.7 46.6 + - - -
215A GLU 4.1 3.1 + - - -
216A LYS 3.7 1.2 - - - -
217A CYS* 1.3 81.7 - - - +
219A PRO* 1.4 64.5 - - - +
220A ASP 3.5 1.7 + - - -
221A PHE 4.1 1.2 - - - +
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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