Contacts of the helix formed by residues 203 - 218 (chain A) in PDB entry 6EVO
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL* 3.0 25.9 + - + +
199A PHE* 4.2 0.8 + - - -
201A LEU* 3.6 3.3 - - + -
202A GLY* 1.3 72.9 - - - +
204A LEU* 1.3 64.6 + - - +
205A HIS 3.6 0.6 + - - -
206A ARG* 3.2 28.4 + - - +
207A ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 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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199A PHE* 3.7 33.0 - - + +
202A GLY* 3.4 20.4 + - - +
203A ASP* 1.3 72.5 + - - +
205A HIS* 1.3 68.3 + - + +
207A ALA* 3.2 8.4 + - - +
208A LEU 3.1 17.2 + - - -
231A PHE* 5.2 2.0 - - + -
234A LEU* 4.5 10.3 - - + -
235A LEU* 3.7 36.7 - - + +
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Residues in contact with HIS 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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203A ASP* 5.3 0.6 + - - -
204A LEU* 1.3 82.4 - - - +
206A ARG* 1.3 57.6 + - - +
208A LEU* 3.4 7.8 + - + +
209A GLU* 2.9 28.1 + - - +
235A LEU* 3.9 35.7 + - + +
237A GLU* 3.3 34.6 + - - -
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Residues in contact with ARG 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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171A GLU* 3.5 25.5 + - - -
174A LEU* 5.3 1.2 - - - +
194A LEU* 4.8 1.6 - - - +
198A VAL* 4.1 10.0 - - + +
203A ASP* 3.2 34.1 + - - +
204A LEU 3.2 0.2 - - - -
205A HIS* 1.3 75.8 - - - +
207A ALA* 1.3 60.0 + - - +
209A GLU* 3.2 34.5 + - - +
210A LEU* 2.8 64.3 + - + +
301A SO4 2.4 41.3 + - - -
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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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195A SER* 3.8 8.8 - - - +
198A VAL* 3.7 11.8 - - + +
199A PHE* 3.8 30.1 - - + -
203A ASP 3.0 14.4 + - - +
204A LEU 3.5 9.2 - - - +
206A ARG* 1.3 75.7 - - - +
208A LEU* 1.3 58.0 + - - +
210A LEU* 3.5 2.8 + - - +
211A THR* 2.8 35.5 + - - -
231A PHE* 4.0 13.9 - - + -
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Residues in contact with LEU 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 LEU 3.1 11.7 + - - +
205A HIS* 3.5 12.6 - - + +
206A ARG 3.2 0.2 - - - -
207A ALA* 1.3 73.2 - - - +
209A GLU* 1.3 65.4 + - - +
211A THR* 3.2 1.7 + - - -
212A ARG* 2.9 42.5 + - - +
228A LEU* 3.6 26.7 - - + -
231A PHE* 3.9 21.9 - - + +
232A GLU* 3.8 10.8 - - + -
235A LEU* 4.0 19.5 - - + -
237A GLU* 3.8 41.3 - - + +
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Residues in contact with GLU 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 HIS 2.9 16.0 + - - +
206A ARG* 3.2 34.7 + - - +
208A LEU* 1.3 77.3 - - - +
210A LEU* 1.3 58.3 + - - +
212A ARG* 3.3 12.7 + - - +
213A ARG* 2.6 56.7 + - - +
301A SO4 4.1 1.2 + - - -
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Residues in contact with LEU 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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174A LEU* 5.5 0.4 - - + -
191A LEU* 3.8 28.4 - - + +
194A LEU* 3.7 29.6 - - + -
195A SER* 3.8 18.6 - - - +
198A VAL* 3.9 20.0 - - + -
206A ARG* 2.8 61.6 + - + +
209A GLU* 1.3 76.9 - - - +
211A THR* 1.3 57.5 + - - +
213A ARG* 3.3 17.5 + - - +
214A LEU* 2.9 28.2 + - - +
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Residues in contact with THR 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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195A SER* 3.7 12.9 + - - -
207A ALA 2.8 21.8 + - - -
208A LEU* 3.2 4.7 + - - -
210A LEU* 1.3 75.2 - - - +
212A ARG* 1.3 63.9 + - - +
214A LEU* 3.3 9.0 + - + +
215A LEU* 3.0 24.1 + - - +
224A ALA* 3.6 27.5 - - + +
227A ASN* 4.0 10.1 + - + +
228A LEU* 3.6 25.1 - - + +
231A PHE* 3.3 19.7 - - - -
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Residues in contact with ARG 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 LEU* 2.9 33.8 + - - +
209A GLU* 3.6 11.7 - - - +
211A THR* 1.3 76.1 - - - +
213A ARG* 1.3 61.8 + - - +
215A LEU* 3.3 5.7 + - - +
216A SER* 3.0 23.4 + - - -
228A LEU* 3.5 21.8 - - + -
232A GLU* 3.1 26.3 + - - -
237A GLU* 3.3 42.4 + - - +
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Residues in contact with ARG 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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174A LEU* 5.4 2.4 - - - +
187A LYS* 5.3 10.5 - - - +
191A LEU* 3.7 23.5 - - + +
209A GLU* 2.6 47.5 + - - +
210A LEU* 3.7 22.9 - - - +
211A THR 3.2 0.4 - - - -
212A ARG* 1.3 75.1 - - - +
214A LEU* 1.3 63.0 + - - +
216A SER* 2.6 28.0 + - - +
217A LEU* 3.3 15.8 + - + +
301A SO4 3.2 37.3 + - - -
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Residues in contact with LEU 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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188A SER* 3.2 37.5 - - - +
191A LEU* 4.0 14.5 - - + +
192A ASP* 3.8 32.1 - - + +
195A SER* 4.4 7.6 - - - +
210A LEU 2.9 16.3 + - - +
211A THR* 3.5 9.0 - - + +
213A ARG* 1.3 76.5 - - - +
215A LEU* 1.3 63.2 + - - +
217A LEU* 3.1 6.0 + - - +
218A ASP* 3.0 19.0 + - + +
221A HIS* 4.0 15.9 - - + -
224A ALA* 3.6 27.8 - - + -
227A ASN* 5.9 2.2 - - - +
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Residues in contact with LEU 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 THR 3.0 16.3 + - - +
212A ARG* 3.9 4.9 - - - +
214A LEU* 1.3 78.4 - - - +
216A SER* 1.3 63.1 + - - +
218A ASP 3.1 19.8 + - - +
219A PRO* 3.2 43.1 - - + +
221A HIS 3.9 17.3 - - - +
224A ALA* 4.3 6.1 - - + +
225A GLY* 4.0 19.3 - - - +
228A LEU* 3.7 27.8 - - + -
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Residues in contact with SER 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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212A ARG 3.0 14.4 + - - -
213A ARG* 2.6 27.2 + - - +
215A LEU* 1.3 78.1 - - - +
217A LEU* 1.3 69.1 + - - +
219A PRO* 4.2 9.1 - - - +
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Residues in contact with LEU 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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187A LYS* 4.0 33.9 - - + -
188A SER* 4.1 15.2 - - - +
191A LEU* 4.1 14.4 - - + -
213A ARG* 3.4 18.8 - - + +
214A LEU 3.1 7.8 + - - +
216A SER* 1.3 86.5 - - - +
218A ASP* 1.3 61.7 + - - +
219A PRO* 3.8 4.6 - - - +
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Residues in contact with ASP 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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188A SER* 4.2 19.1 + - - -
214A LEU* 3.0 11.7 + - + +
215A LEU* 3.3 9.2 - - - +
217A LEU* 1.3 81.2 - - - +
219A PRO* 1.3 69.4 - - - +
220A SER* 3.2 7.4 + - - -
221A HIS* 3.0 49.6 + - + +
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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