Contacts of the helix formed by residues 206 - 218 (chain A) in PDB entry 6ABP
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 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ASN* 1.3 74.0 - - - +
207A SER* 1.4 57.9 + - - +
209A VAL* 3.2 1.6 + - - +
210A LEU* 2.7 40.3 + - + +
230A GLY* 3.1 19.7 - - - -
231A ILE 2.8 13.8 + - - +
232A ASN* 3.3 1.6 - - - +
233A GLY 3.1 23.0 + - - -
235A ASP* 3.2 35.1 - - + +
236A ALA* 3.5 12.5 + - - +
248A PHE* 3.5 3.5 - - - -
251A SER* 2.6 25.7 + - - -
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Residues in contact with SER 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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14A GLU* 4.3 14.5 + - - +
177A ASN 4.4 3.8 - - - -
178A ASP* 3.8 25.1 - - - -
179A ILE* 3.5 25.9 - - - +
205A ASN* 3.4 7.1 + - - -
206A ASP* 1.4 76.8 - - - +
208A THR* 1.4 63.7 + - - +
210A LEU* 3.3 5.6 + - - +
211A GLY 3.0 19.6 + - - -
235A ASP* 4.9 7.8 + - - +
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Residues in contact with THR 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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140A ILE* 3.6 43.3 - - + +
174A THR* 4.9 5.1 - - + +
177A ASN* 4.5 18.0 + - - +
178A ASP 4.5 1.7 + - - -
182A ALA* 3.2 18.6 - - + +
203A GLY* 3.8 18.4 - - - -
204A MET* 4.4 8.0 - - + +
205A ASN* 2.8 29.6 + - - -
207A SER* 1.4 77.3 - - - +
209A VAL* 1.4 64.9 + - - +
211A GLY 3.3 0.2 + - - -
212A GLY 3.2 16.6 + - - -
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Residues in contact with VAL 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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201A ILE* 4.0 17.3 - - + +
202A VAL 4.4 0.4 - - - -
203A GLY* 3.7 30.1 - - - +
205A ASN 3.1 15.5 + - - +
206A ASP 3.9 3.1 - - - +
208A THR* 1.4 79.5 - - - +
210A LEU* 1.3 57.6 + - - +
212A GLY* 3.2 2.9 + - - -
213A VAL* 2.9 27.0 + - + +
228A GLY* 3.6 33.4 - - - -
229A ILE 3.7 17.5 - - - +
230A GLY* 4.0 1.6 - - - -
248A PHE* 3.7 20.4 - - + -
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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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179A ILE* 4.1 20.9 - - + -
206A ASP* 2.7 33.1 + - + +
207A SER* 3.3 9.4 + - - +
209A VAL* 1.3 72.2 - - - +
211A GLY* 1.3 56.1 + - - +
213A VAL* 3.1 6.3 + - + +
214A ARG* 2.9 44.1 + - - +
235A ASP 4.5 15.9 - - - +
236A ALA* 5.1 0.7 - - - -
239A GLU* 3.5 43.1 - - + +
248A PHE* 3.6 26.9 - - + -
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Residues in contact with GLY 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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179A ILE* 3.6 34.4 - - - +
182A ALA* 3.9 2.9 - - - -
183A PHE* 3.5 18.1 - - - -
207A SER 3.0 12.3 + - - -
208A THR 3.9 2.5 - - - -
209A VAL 3.3 0.2 - - - -
210A LEU* 1.3 76.2 - - - +
212A GLY* 1.3 60.9 + - - +
214A ARG* 3.4 4.1 + - - +
215A ALA* 3.0 18.4 + - - +
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Residues in contact with GLY 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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140A ILE* 3.7 14.6 - - - -
182A ALA* 4.1 2.0 - - - +
186A ALA* 3.7 21.1 - - - +
201A ILE* 3.7 12.3 - - - -
208A THR 3.2 9.7 + - - -
209A VAL 3.2 4.4 + - - -
211A GLY* 1.3 75.1 - - - +
213A VAL* 1.4 60.5 + - - +
215A ALA* 3.3 3.8 + - - +
216A THR* 3.1 26.7 + - - +
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Residues in contact with VAL 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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201A ILE* 3.8 15.9 - - + -
209A VAL* 2.9 30.9 + - + +
210A LEU* 3.1 8.9 + - + +
212A GLY* 1.4 75.0 - - - +
214A ARG* 1.3 73.0 + - - +
216A THR* 2.5 28.8 + - - +
217A GLU* 3.1 25.4 + - + +
226A ILE* 4.3 1.3 - - + -
228A GLY* 4.6 1.6 - - - -
247A GLY* 4.1 25.4 - - - +
248A PHE* 4.0 22.4 - - + +
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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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179A ILE* 4.7 13.5 - - + +
183A PHE* 3.8 19.9 - - + -
210A LEU* 2.9 36.3 + - + +
211A GLY* 3.4 6.9 + - - +
213A VAL* 1.3 81.8 - - - +
215A ALA* 1.3 61.1 + - - +
217A GLU* 2.7 46.2 + - - +
218A GLY* 3.3 15.9 + - - -
239A GLU* 2.7 42.8 + - - -
242A LYS* 3.7 15.1 - - - +
246A THR* 3.9 5.1 - - - +
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Residues in contact with ALA 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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183A PHE* 3.5 38.7 - - + +
186A ALA* 3.7 18.4 - - + -
187A ASN* 3.8 12.7 - - - +
190A LEU* 3.6 11.6 - - + +
211A GLY 3.0 14.3 + - - +
212A GLY 3.7 0.2 - - - +
213A VAL 3.3 0.2 - - - -
214A ARG* 1.3 75.2 - - - +
216A THR* 1.3 63.3 + - - +
218A GLY* 3.1 11.3 + - - -
219A GLN* 3.2 12.0 + - - +
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Residues in contact with THR 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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138A MET* 4.5 4.7 - - + -
190A LEU* 3.7 27.1 - - + -
199A TRP* 4.9 1.6 - - + -
201A ILE* 3.6 19.7 - - + -
212A GLY 3.1 14.8 + - - +
213A VAL* 2.5 22.9 + - - +
215A ALA* 1.3 74.1 - - - +
217A GLU* 1.3 65.8 + - - +
219A GLN 3.1 6.9 + - - -
221A PHE* 3.1 30.1 + - - +
226A ILE* 3.7 35.3 - - + +
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Residues in contact with GLU 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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213A VAL* 3.1 18.5 + - + +
214A ARG* 2.7 54.4 + - - +
215A ALA 3.2 0.2 - - - -
216A THR* 1.3 86.3 + - - +
218A GLY* 1.3 60.5 + - - +
220A GLY* 3.2 14.2 + - - -
221A PHE 3.9 14.3 + - - +
226A ILE* 6.3 0.2 - - + -
246A THR* 4.0 13.7 - - - +
247A GLY 4.6 1.8 + - - +
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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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183A PHE* 6.0 4.0 - - - -
187A ASN* 5.6 0.7 - - - -
214A ARG 3.3 7.2 + - - -
215A ALA* 3.1 9.5 + - - -
217A GLU* 1.3 79.0 - - - +
219A GLN* 1.3 66.9 + - - +
220A GLY 3.2 2.5 + - - -
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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