Contacts of the helix formed by residues 207 - 217 (chain C) in PDB entry 5OA3
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 ALA 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32 C 3.9 4.8 + - - -
42 C 3.4 39.5 + - - +
52 U 4.6 0.2 - - - +
206C SER* 1.3 90.6 + - - +
208C PRO* 1.3 78.0 - - + +
209C VAL 3.4 0.9 - - - +
210C PRO* 3.2 18.0 - - + +
211C LYS* 3.1 6.6 - - - +
236C PHE* 4.0 9.6 - - + -
18J ARG* 3.8 5.4 - - - +
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Residues in contact with PRO 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42 C 4.3 7.0 - - - +
52 U 5.3 3.1 - - - +
206C SER 4.6 0.2 - - - +
207C ALA* 1.3 88.4 - - + +
209C VAL* 1.3 61.6 + - + +
211C LYS* 3.2 13.3 - - + +
212C LYS* 2.9 39.7 + - - +
18J ARG* 3.7 26.9 - - - +
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52 U 5.7 4.7 - - - +
107C LEU* 4.6 18.0 - - + +
207C ALA* 4.6 0.4 - - - +
208C PRO* 1.3 79.1 - - + +
210C PRO* 1.4 74.4 - - + +
212C LYS* 3.1 24.1 + - - +
213C LEU* 3.5 7.3 + - + +
233C LEU* 4.0 34.8 - - + -
236C PHE* 4.5 12.6 - - + -
237C ALA* 4.6 28.3 - - + +
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Residues in contact with PRO 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 5.1 2.9 - - + -
206C SER* 4.1 13.5 - - - +
207C ALA 3.2 16.4 - - - +
209C VAL* 1.4 96.6 - - + +
211C LYS* 1.3 56.1 + - - +
213C LEU* 3.2 4.2 + - + +
214C LEU* 2.9 39.0 + - + +
224C THR* 5.0 5.6 - - + -
236C PHE* 3.7 33.7 - - + -
240C THR* 3.7 36.6 - - + +
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C ILE* 4.1 38.1 + - + +
206C SER* 3.3 17.7 + - - +
207C ALA 3.1 17.7 - - - +
208C PRO* 3.2 14.1 - - + +
209C VAL 3.1 0.2 - - - -
210C PRO* 1.3 79.4 - - - +
212C LYS* 1.3 62.9 + - - +
214C LEU* 3.8 5.9 - - - +
215C MET* 2.9 43.2 + - + +
21J GLU* 5.0 8.9 + - - -
23J SER* 5.2 11.5 + - - -
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Residues in contact with LYS 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLU* 3.8 31.4 - - + +
107C LEU* 4.4 19.7 - - + +
208C PRO* 2.9 26.8 + - - +
209C VAL* 3.1 12.1 + - - +
211C LYS* 1.3 76.1 - - + +
213C LEU* 1.3 63.6 + - + +
215C MET* 3.1 10.8 + - + +
216C MET* 3.0 42.4 + - + +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 4.6 6.5 - - + -
129C ALA* 3.5 31.9 - - + -
137C VAL* 3.9 9.1 - - + +
138C GLY 5.1 3.1 - - - +
139C LEU* 4.3 10.8 - - + -
209C VAL 3.5 6.6 + - - +
210C PRO* 3.2 9.3 + - + +
212C LYS* 1.3 79.2 - - + +
214C LEU* 1.3 52.4 + - - +
216C MET* 3.1 9.4 + - + +
217C ALA* 2.8 35.9 + - - +
237C ALA* 3.9 13.2 - - + +
240C THR* 3.9 26.9 - - + +
241C PHE* 4.0 24.5 - - + +
244C ILE* 4.0 16.6 - - + -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 3.7 45.8 - - + -
204C ILE* 4.1 24.9 - - + -
206C SER* 5.0 0.4 - - - +
210C PRO* 2.9 29.6 + - + +
211C LYS 4.0 3.1 - - - +
213C LEU* 1.3 73.4 - - + +
215C MET* 1.3 62.6 + - - +
217C ALA* 3.5 4.5 + - - +
219C ILE* 3.0 51.5 + - + +
222C CYS* 4.7 4.3 - - + -
224C THR* 3.9 11.7 - - - +
240C THR* 4.4 9.0 - - - +
244C ILE* 3.8 20.0 - - + -
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Residues in contact with MET 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C TYR* 3.5 22.3 - - + +
204C ILE* 3.6 31.2 - - + -
211C LYS* 2.9 36.5 + - + +
212C LYS* 3.3 11.0 - - + +
213C LEU 3.1 0.2 - - - -
214C LEU* 1.3 76.2 - - - +
216C MET* 1.3 60.3 + - + +
218C GLY* 2.9 19.1 + - - -
219C ILE 4.3 8.0 + - - +
220C ASP* 5.1 6.1 - - - +
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Residues in contact with MET 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LYS 4.6 5.4 - - - +
104C ASP* 5.0 0.4 - - - -
105C GLU* 3.9 15.0 - - + -
129C ALA* 3.8 34.3 - - + +
130C ILE 5.2 0.2 - - - -
131C GLY* 3.6 30.7 - - - +
132C ASP 2.9 25.5 + - - +
133C TYR* 3.2 40.3 - - + +
136C HIS 4.0 0.5 - - - +
137C VAL* 4.1 4.7 - - + -
212C LYS* 3.0 46.5 + - + +
213C LEU* 3.8 7.0 - - + +
215C MET* 1.3 78.0 - - + +
217C ALA* 1.3 57.9 + - - +
218C GLY 3.0 1.6 + - - -
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ASP 4.5 0.4 - - - -
134C ASN* 3.7 12.3 - - - +
135C GLY 4.2 0.2 + - - -
136C HIS 4.6 2.2 + - - -
137C VAL* 3.5 20.1 - - + +
165C VAL* 3.5 33.1 - - + +
167C ARG* 4.7 0.5 + - - -
213C LEU 2.8 17.1 + - - +
214C LEU* 3.6 11.7 - - - +
215C MET 3.1 0.4 - - - -
216C MET* 1.3 75.9 - - - +
218C GLY* 1.3 60.4 + - - +
219C ILE* 3.2 15.5 + - + +
244C ILE* 4.7 5.6 - - + -
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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