Contacts of the helix formed by residues 213 - 218 (chain C) in PDB entry 6F0X
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 ASN 213 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 3.0 33.3 + - - +
121C ALA 3.8 9.8 + - - +
123C ASN* 5.1 11.9 - - - +
211C GLU* 2.9 13.8 + - + +
212C ILE* 1.3 70.1 - - - +
214C SER* 1.3 64.5 + - - +
215C HIS* 4.0 7.8 + - - +
216C SER* 2.1 48.9 + - - +
217C LEU* 3.4 2.9 + - - +
232C MET* 5.7 1.8 - - - +
230D THR* 4.5 16.7 - - - +
279D ALA* 5.4 1.9 - - - +
282D THR* 5.3 4.3 + - - -
283D GLN* 4.7 11.0 + - - +
286D GLN* 5.9 1.2 - - - +
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Residues in contact with SER 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 ILE* 2.7 20.8 + - - -
213C ASN* 1.3 70.3 + - - +
215C HIS* 1.3 64.2 + - - +
216C SER 2.6 0.9 + - - -
217C LEU* 2.4 39.1 + - - +
218C PHE* 4.1 4.1 + - - -
251C ILE* 5.1 1.3 - - - -
252C ASP 4.2 14.3 + - - -
253C GLN* 4.9 0.8 + - - +
256C SER* 2.8 31.7 + - - -
257C LEU* 4.4 18.2 - - - -
278D ASN* 4.5 3.1 + - - +
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Residues in contact with HIS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ASN* 3.5 5.7 + - - +
214C SER* 1.3 81.9 + - - +
216C SER* 1.3 60.7 + - - +
218C PHE* 4.1 12.9 + - - +
256C SER* 3.8 7.6 - - - +
223D SER 5.3 3.3 - - - +
226D GLY* 4.3 20.1 - - - +
227D LYS* 4.7 3.6 + - - +
230D THR* 5.2 2.7 - - + -
275D ARG* 4.1 21.7 - - + +
278D ASN* 4.6 1.3 - - - +
279D ALA* 3.6 31.4 - - + -
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Residues in contact with SER 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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119C ILE* 6.3 2.0 - - - -
120C ILE 3.5 21.8 - - - -
121C ALA* 3.7 14.4 + - - -
213C ASN* 2.1 43.9 + - - +
214C SER 2.6 5.1 + - - -
215C HIS* 1.3 73.2 - - - +
217C LEU* 1.3 66.3 + - - -
218C PHE 2.8 15.7 + - - +
228C LEU* 5.4 0.5 - - - +
232C MET* 6.0 0.9 - - - -
227D LYS* 6.0 2.2 - - - +
230D THR* 5.6 4.2 - - - +
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Residues in contact with LEU 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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212C ILE* 5.6 0.7 - - + -
213C ASN 4.3 2.9 - - - +
214C SER* 2.4 33.7 + - - +
216C SER* 1.3 71.2 + - - +
218C PHE* 1.3 65.0 + - + +
225C SER 4.2 3.1 - - - +
228C LEU* 3.1 37.3 - - + +
229C VAL* 3.7 47.8 - - + -
232C MET* 3.8 42.0 - - + -
257C LEU* 3.6 26.5 - - + -
280C VAL* 4.6 3.4 - - + -
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Residues in contact with PHE 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 SER 4.1 2.9 + - - -
215C HIS* 4.6 9.4 - - - +
216C SER 2.8 15.0 + - - +
217C LEU* 1.3 89.0 - - + +
219C SER* 1.3 61.0 + - - +
225C SER* 4.0 7.0 - - - +
228C LEU* 5.0 2.8 - - - +
256C SER* 3.0 26.9 - - - -
257C LEU* 3.6 25.4 - - + -
273C ALA* 6.1 2.5 - - - -
276C VAL* 3.7 32.1 - - + -
277C VAL* 5.9 0.4 - - + -
222D PHE* 3.5 18.2 - + + -
223D SER* 3.2 20.4 + - - +
275D ARG* 3.2 44.6 - - + -
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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