Contacts of the helix formed by residues 208 - 218 (chain I) in PDB entry 6O81
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 LYS 208 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209E ARG* 5.2 7.1 - - - +
99I THR 5.6 0.2 - - - -
100I ASP* 3.4 18.8 - - - +
101I VAL* 5.4 0.8 - - - +
121I PHE* 3.6 26.2 - - - -
125I ASP* 4.4 18.2 + - - -
126I ALA 3.6 17.0 + - - -
127I SER* 3.5 17.5 + - - +
207I LEU* 1.3 78.2 - - - +
209I LYS* 1.3 73.0 + - + +
210I TYR* 3.4 34.3 - - + +
211I ILE* 3.3 16.2 + - + +
212I VAL* 3.4 12.6 + - - +
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Residues in contact with LYS 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I TYR* 3.6 13.6 + - - -
97I LEU* 3.8 40.4 - - + -
98I LYS* 4.7 12.1 - - - +
99I THR* 4.3 13.5 - - - +
100I ASP* 3.9 9.2 + - - +
208I LYS* 1.3 80.7 - - + +
210I TYR* 1.3 57.0 + - - +
212I VAL* 3.3 7.9 - - + +
213I ASP* 2.8 65.1 + - - +
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Residues in contact with TYR 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I SER* 3.5 12.9 + - - -
208I LYS* 3.6 29.1 - - + +
209I LYS* 1.3 76.0 - - - +
211I ILE* 1.3 82.4 + - + +
213I ASP* 3.4 12.8 + - + +
214I PHE* 2.9 29.6 + - + +
261I LEU* 3.5 36.3 - - + +
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Residues in contact with ILE 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I SER* 3.4 28.3 - - - +
128I LEU* 5.5 3.6 - - + -
207I LEU* 3.7 24.9 - - + -
208I LYS* 3.5 17.7 - - + +
209I LYS 3.2 0.8 - - - -
210I TYR* 1.3 109.2 - - + +
212I VAL* 1.3 58.6 + - + +
214I PHE* 3.2 12.1 + - + +
215I LEU* 2.9 29.0 + - + +
228I LEU* 5.2 10.5 - - + +
232I LEU* 5.7 6.7 - - + -
261I LEU* 5.1 6.3 - - + -
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Residues in contact with VAL 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I LEU* 4.0 30.3 - - + +
94I TYR* 4.1 10.1 - - + -
97I LEU* 3.8 30.1 - - + -
101I VAL* 4.3 13.7 - - + -
207I LEU* 4.4 13.2 - - + -
208I LYS 3.4 11.4 + - - +
209I LYS* 3.3 18.8 - - + +
211I ILE* 1.3 75.6 - - + +
213I ASP* 1.3 60.2 + - - +
215I LEU* 3.6 15.2 - - + +
216I MET* 2.9 27.9 + - - +
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Residues in contact with ASP 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I TYR* 2.4 36.4 + - - +
209I LYS* 2.8 52.5 + - - +
210I TYR* 3.4 12.6 - - + +
211I ILE 3.2 0.2 - - - -
212I VAL* 1.3 77.6 - - - +
214I PHE* 1.3 56.6 + - - +
216I MET* 3.3 3.3 + - - +
217I GLU* 2.9 28.5 + - - +
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Residues in contact with PHE 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I TYR* 2.9 18.8 + - + +
211I ILE* 3.6 9.6 - - + +
213I ASP* 1.3 73.4 - - - +
215I LEU* 1.3 60.8 + - - +
217I GLU* 3.6 10.2 - - + -
218I ASN* 2.8 47.2 + - + +
231I TYR* 3.6 45.8 - + - -
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Residues in contact with LEU 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I ALA* 3.5 40.8 - - + +
90I LEU* 3.8 27.4 - - + -
91I ARG* 3.9 14.6 - - + +
211I ILE* 2.9 19.7 + - + +
212I VAL* 3.6 14.6 - - + +
213I ASP 3.3 0.4 - - - -
214I PHE* 1.3 80.8 - - + +
216I MET* 1.3 59.9 + - + +
218I ASN* 2.9 24.0 - - - +
219I GLY* 4.1 3.3 + - - -
221I ILE* 5.1 7.9 - - + -
224I ILE* 5.0 8.1 - - + -
227I GLU* 6.4 1.1 - - + -
228I LEU* 5.3 10.8 - - + +
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Residues in contact with MET 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I ARG* 5.1 10.3 - - + -
94I TYR* 4.1 36.6 - - + -
212I VAL 2.9 16.9 + - - +
213I ASP 3.3 4.5 + - - +
215I LEU* 1.3 80.1 - - - +
217I GLU* 1.3 59.2 + - - +
218I ASN 3.7 0.3 + - - -
219I GLY* 4.7 4.0 + - - -
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Residues in contact with GLU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213I ASP 2.9 17.1 + - - +
214I PHE* 3.3 14.3 + - + +
216I MET* 1.3 79.1 - - - +
218I ASN* 1.3 55.2 + - - +
219I GLY 3.9 2.2 + - - -
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Residues in contact with ASN 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214I PHE* 2.8 37.6 + - + +
215I LEU* 2.9 18.2 - - - +
217I GLU* 1.3 75.8 - - - +
219I GLY* 1.3 58.3 + - - +
220I SER* 3.2 13.3 + - - +
221I ILE* 4.0 11.8 + - + +
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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