Contacts of the helix formed by residues 213 - 225 (chain C) in PDB entry 6V99
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 THR 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C ILE* 4.2 6.5 - - + -
122C GLU* 6.3 1.6 - - + -
125C ALA* 5.8 1.1 - - - -
126C PRO* 2.9 40.9 + - + +
127C GLU 2.8 16.9 + - - -
128C TYR 3.2 14.2 + - - -
129C MET* 3.4 22.8 - - + +
211C PHE 3.5 1.4 + - - -
212C HIS* 1.3 71.2 - - - +
214C LYS* 1.3 64.0 + - - +
216C LEU* 3.2 2.6 + - - +
217C MET* 3.0 44.4 + - + +
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Residues in contact with LYS 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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212C HIS* 3.2 4.0 - - + +
213C THR* 1.3 80.0 - - - +
215C PHE* 1.3 64.3 + - - +
217C MET* 3.4 7.0 + - - +
218C GLU* 3.3 21.2 + - + +
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Residues in contact with PHE 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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155C ASP* 3.6 57.0 - - + -
211C PHE* 4.0 15.5 - + + -
212C HIS* 3.3 19.7 + - + +
214C LYS* 1.3 82.6 - - - +
216C LEU* 1.3 59.4 + - - +
218C GLU* 3.4 7.6 + - + +
219C ALA* 2.9 38.2 + - + +
241C ILE* 4.1 22.4 - - + -
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Residues in contact with LEU 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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114C VAL* 4.6 3.6 - - + -
129C MET* 3.8 31.0 - - + -
131C ILE* 4.2 13.9 - - + -
211C PHE* 3.8 39.5 - - + -
212C HIS 3.1 15.9 + - - +
213C THR* 3.7 4.5 - - - +
215C PHE* 1.3 81.0 - - - +
217C MET* 1.3 61.3 + - + +
219C ALA* 3.1 8.9 + - + +
220C LEU* 2.7 62.3 + - + +
233C PHE* 4.1 6.5 - - + -
237C ILE* 5.2 1.6 - - + -
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Residues in contact with MET 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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118C ILE* 3.6 34.6 - - - +
121C ILE* 4.3 24.0 - - + -
122C GLU* 4.2 13.0 - - + +
129C MET* 4.2 5.2 - - + -
213C THR* 3.0 36.2 + - + +
214C LYS* 3.9 6.5 - - + +
216C LEU* 1.3 98.4 - - + +
218C GLU* 1.3 63.4 + - - +
220C LEU* 3.4 9.6 + - + +
221C ARG* 3.0 46.6 + - - +
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Residues in contact with GLU 218 (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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214C LYS* 3.3 11.4 + - + +
215C PHE* 3.7 10.1 - - + +
216C LEU 3.3 0.4 - - - -
217C MET* 1.3 79.8 - - - +
219C ALA* 1.3 61.7 + - - +
221C ARG* 3.3 2.4 + - - +
222C ARG* 3.0 58.1 + - - +
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Residues in contact with ALA 219 (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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211C PHE* 5.9 0.4 - - + -
215C PHE* 2.9 34.7 + - + +
216C LEU* 3.1 14.6 + - + +
218C GLU* 1.3 77.4 - - - +
220C LEU* 1.3 62.3 + - - +
222C ARG* 3.4 6.0 + - - +
223C ASP* 3.0 23.4 + - - +
237C ILE* 4.2 16.9 - - + +
241C ILE* 5.4 3.6 - - + -
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Residues in contact with LEU 220 (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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111C ALA* 3.6 37.0 - - + +
114C VAL* 3.7 31.2 - - + -
115C TYR* 4.0 22.5 - - + +
118C ILE* 4.2 8.3 - - + -
216C LEU* 2.7 47.5 + - + +
217C MET* 3.8 12.6 - - + +
219C ALA* 1.3 70.8 - - - +
221C ARG* 1.3 58.2 + - - +
223C ASP* 3.0 7.6 + - - +
224C ALA* 2.7 29.1 + - - +
231C ARG* 5.0 0.3 + - - -
233C PHE* 4.2 8.1 - - + -
237C ILE* 4.5 6.1 - - + -
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Residues in contact with ARG 221 (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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115C TYR* 4.2 22.0 - - + -
118C ILE* 3.6 20.9 - - + +
122C GLU* 3.0 34.6 + - - -
217C MET* 3.0 35.7 + - - +
218C GLU* 3.7 4.7 - - - +
220C LEU* 1.3 75.7 - - - +
222C ARG* 1.3 86.5 + - - +
224C ALA* 3.1 4.5 + - - +
225C ALA* 3.0 22.3 + - - +
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Residues in contact with ARG 222 (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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218C GLU* 3.0 47.0 + - - +
219C ALA* 4.0 5.4 - - - +
221C ARG* 1.3 99.6 - - - +
223C ASP* 1.3 61.8 + - - +
225C ALA* 3.4 8.1 + - - +
226C ASP* 3.3 20.1 + - - +
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Residues in contact with ASP 223 (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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111C ALA* 4.0 6.5 - - + +
219C ALA 3.0 14.9 + - - +
220C LEU* 3.3 9.2 - - - +
222C ARG* 1.3 75.0 - - - +
224C ALA* 1.3 65.3 + - - +
226C ASP* 3.0 25.8 + - - +
229C SER* 2.8 28.4 + - - -
231C ARG* 3.1 35.3 + - - -
236C ASP* 3.5 15.4 - - - +
237C ILE* 3.5 23.1 + - + +
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Residues in contact with ALA 224 (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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115C TYR* 3.5 36.1 - - + +
220C LEU 2.7 16.2 + - - +
221C ARG 3.1 8.3 + - - +
223C ASP* 1.3 74.6 + - - +
225C ALA* 1.3 59.7 + - - +
226C ASP 3.1 5.1 + - - +
231C ARG* 3.6 29.4 + - - +
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Residues in contact with ALA 225 (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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221C ARG 3.0 14.6 + - - +
222C ARG* 3.9 8.5 - - - +
223C ASP 3.2 0.6 - - - -
224C ALA* 1.3 76.0 - - - +
226C ASP* 1.3 56.7 + - - +
227C PRO* 3.2 14.9 - - - +
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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