Contacts of the helix formed by residues 209 - 219 (chain A) in PDB entry 2O9C
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 PRO 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A CYS* 4.5 4.3 - - - +
25A GLU* 3.4 31.0 - - + +
205A ALA 4.1 2.0 - - - +
206A SER 3.7 6.5 - - - +
208A ILE* 1.3 91.2 - - - +
210A ALA* 1.3 65.7 + - - +
211A GLN* 3.3 21.3 - - - +
212A ALA* 3.0 15.1 + - + +
213A ARG* 3.0 11.0 + - - +
328A LBV 3.4 51.1 - - + +
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Residues in contact with ALA 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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4A ASP 4.9 4.9 - - - +
5A PRO* 3.9 26.4 - - + +
6A LEU 5.3 0.2 - - - +
25A GLU* 2.8 20.8 + - + +
209A PRO* 1.3 72.3 - - - +
211A GLN* 1.3 55.8 + - - +
213A ARG* 3.3 32.1 + - - +
214A ALA* 2.9 28.2 + - - +
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Residues in contact with GLN 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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5A PRO* 3.8 16.7 - - + +
6A LEU 5.2 3.6 - - - +
8A PHE* 6.2 2.2 - - + -
24A CYS 3.0 24.7 + - - -
25A GLU* 3.3 21.0 + - - +
26A ARG 5.5 0.4 - - - -
27A GLU* 3.0 31.4 + - - +
29A ILE* 4.2 20.4 - - + +
30A HIS* 6.3 0.2 - - - +
209A PRO* 3.3 26.5 - - - +
210A ALA* 1.3 72.4 + - - +
212A ALA* 1.3 64.7 + - - +
214A ALA* 3.6 5.3 + - - +
215A LEU* 3.0 27.7 + - - +
328A LBV 4.8 0.8 - - - +
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Residues in contact with ALA 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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29A ILE* 3.6 23.1 - - + -
208A ILE* 4.1 8.5 - - + -
209A PRO* 3.0 18.5 + - + +
211A GLN* 1.3 80.1 + - - +
213A ARG* 1.3 60.9 + - - +
215A LEU* 3.1 1.8 + - - -
216A TYR* 2.8 46.8 + - + -
328A LBV 3.9 18.4 - - + -
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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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4A ASP 5.9 1.8 - - - +
25A GLU* 5.1 1.6 + - - -
178A PHE* 4.0 25.4 - - + -
182A ALA* 3.5 28.7 - - - +
205A ALA* 3.5 15.2 + - - +
208A ILE* 2.8 51.4 + - + +
209A PRO* 3.0 2.4 + - - +
210A ALA* 3.3 35.3 + - - +
212A ALA* 1.3 77.4 - - - +
214A ALA* 1.3 59.5 + - - +
216A TYR* 3.2 5.4 + - - +
217A THR* 2.9 27.2 + - - -
283A LEU* 3.8 21.7 - - + +
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Residues in contact with ALA 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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5A PRO* 4.1 22.2 - - + -
210A ALA 2.9 17.6 + - - +
211A GLN 3.7 5.2 - - - +
212A ALA 3.2 0.2 - - - -
213A ARG* 1.3 73.0 - - - +
215A LEU* 1.3 66.6 + - - +
217A THR* 3.0 21.8 + - - -
218A ARG* 3.7 12.2 + - - +
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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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29A ILE* 3.9 22.9 - - + -
30A HIS* 4.7 10.5 - - + -
211A GLN 3.0 17.8 + - - +
212A ALA* 3.1 5.4 + - - +
214A ALA* 1.3 76.0 - - - +
216A TYR* 1.3 67.3 + - + +
218A ARG* 3.0 32.3 + - - +
219A HIS* 2.9 46.6 + - + +
249A GLY* 3.9 15.7 - - - +
254A ARG* 3.7 32.5 - - - +
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Residues in contact with TYR 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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29A ILE* 5.1 0.2 - - + -
208A ILE* 4.0 20.9 - - + -
212A ALA* 2.8 30.4 + - + +
213A ARG* 3.7 7.2 - - - +
214A ALA 3.1 0.2 - - - -
215A LEU* 1.3 93.8 - - + +
217A THR* 1.3 59.3 + - - +
218A ARG 3.3 0.4 - - - -
219A HIS 3.7 8.1 - - - -
220A LEU* 3.6 5.0 - - - +
222A ARG* 3.3 45.3 - - + +
254A ARG* 4.5 0.4 - - - -
276A SER* 2.6 32.5 + - - +
283A LEU* 3.9 11.9 - - + +
286A LEU* 4.5 8.7 - - + -
328A LBV 2.7 68.3 + - + +
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Residues in contact with THR 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 ARG 2.9 14.2 + - - -
214A ALA* 3.0 12.8 + - - -
216A TYR* 1.3 81.6 - - - +
218A ARG* 1.3 61.5 + - + +
220A LEU* 3.8 10.5 - - - +
278A VAL* 4.4 17.5 - - + +
281A GLY 3.7 26.0 - - - +
282A GLN* 5.1 0.2 - - - -
283A LEU* 3.8 19.5 + - - +
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Residues in contact with ARG 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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30A HIS* 5.8 5.5 - - - +
95A ASP* 3.1 29.8 + - - +
96A ALA* 4.2 13.5 - - - +
214A ALA* 4.0 12.6 - - - +
215A LEU* 3.0 28.3 + - - +
217A THR* 1.3 83.9 - - + +
219A HIS* 1.3 84.0 + - + +
220A LEU* 4.0 8.0 + - - +
247A PRO* 6.1 3.2 - - - +
249A GLY* 5.9 1.0 - - - -
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Residues in contact with HIS 219 (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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95A ASP* 3.4 41.4 + - + -
96A ALA* 4.1 9.1 - - - +
116A HIS* 5.1 0.7 - + - -
215A LEU* 2.9 28.8 + - + +
216A TYR* 3.7 2.6 - - - -
218A ARG* 1.3 110.5 + - + +
220A LEU* 1.3 60.7 + - - +
221A LEU 3.4 6.4 + - - +
222A ARG* 2.9 19.1 + - - -
249A GLY* 3.4 31.4 - - - +
250A GLY* 3.4 23.8 + - - -
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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