Contacts of the helix formed by residues 213 - 221 (chain C) in PDB entry 6QPA
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 ASP 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212C LEU* 1.3 74.5 - - - +
214C PRO* 1.3 75.5 - - + +
215C GLU* 3.3 15.2 + - - +
216C GLY* 3.1 27.0 + - - -
217C ALA* 2.9 19.6 + - - +
230C GLU 4.6 1.7 - - - +
232C ASN* 3.3 44.0 + - - +
233C THR* 3.5 19.7 - - - +
234C ASN* 3.7 7.2 - - - +
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Residues in contact with PRO 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 LEU 4.8 0.4 - - - +
213C ASP* 1.3 88.9 - - + +
215C GLU* 1.3 63.3 + - + +
217C ALA* 3.2 8.7 + - + +
218C MET* 3.1 30.2 + - + +
234C ASN* 3.6 15.0 - - - +
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Residues in contact with GLU 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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38B SER* 6.0 1.7 - - - -
213C ASP* 3.3 11.2 + - - +
214C PRO* 1.3 77.1 - - + +
216C GLY* 1.3 66.5 + - - +
218C MET* 3.2 15.8 + - - +
219C LYS* 2.9 38.3 + - + +
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Residues in contact with GLY 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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212C LEU* 3.9 11.2 - - - -
213C ASP* 3.1 22.5 + - - -
215C GLU* 1.3 77.4 - - - +
217C ALA* 1.3 57.2 + - - +
219C LYS* 3.7 0.8 - - - -
220C ALA* 2.8 32.4 + - - +
229C PRO* 3.7 22.8 - - - +
230C GLU 5.1 1.8 - - - -
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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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210C PHE* 6.3 0.2 - - - -
212C LEU* 4.1 11.1 - - + +
213C ASP 2.9 13.3 + - - +
214C PRO* 3.4 12.6 - - + +
216C GLY* 1.3 77.6 - - - +
218C MET* 1.3 74.5 + - + +
220C ALA* 3.4 15.6 + - - +
221C VAL* 3.6 12.3 + - - +
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Residues in contact with MET 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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34B ILE* 4.1 15.6 - - + +
214C PRO* 3.1 20.5 + - + +
215C GLU* 3.5 20.2 - - - +
217C ALA* 1.3 87.1 - - + +
219C LYS* 1.3 65.4 + - + +
220C ALA 3.2 0.7 + - - -
221C VAL* 3.3 18.2 + - + +
222C SER* 2.8 18.4 + - - -
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Residues in contact with LYS 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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35B THR* 4.7 9.9 - - - +
38B SER* 4.1 20.4 + - - -
95B ASN* 2.6 31.7 + - - -
98B GLU* 4.9 13.3 - - + +
215C GLU* 2.9 30.3 + - + +
216C GLY 4.0 2.9 - - - +
218C MET* 1.3 78.6 - - + +
220C ALA* 1.3 57.0 + - - +
222C SER* 2.8 32.7 + - - +
223C THR* 3.5 11.3 - - - +
227C ASN 4.6 2.7 - - - +
228C PRO 5.4 0.7 - - - -
229C PRO* 4.0 22.7 - - + -
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Residues in contact with ALA 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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31B LYS* 5.4 0.2 - - - -
100C PHE* 3.6 27.1 - - + -
104C SER* 5.2 0.9 + - - -
107C LEU* 5.8 3.1 - - - +
210C PHE* 3.7 34.5 - - + -
212C LEU* 4.4 5.6 - - + -
216C GLY 2.8 23.0 + - - +
217C ALA* 3.5 9.9 - - - +
218C MET 3.2 0.4 - - - -
219C LYS* 1.3 73.2 - - - +
221C VAL* 1.3 62.8 + - + +
223C THR* 3.7 8.9 - - - +
229C PRO* 4.4 2.4 - - + +
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Residues in contact with VAL 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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31B LYS* 3.0 44.6 - - + +
34B ILE* 3.9 25.7 - - + +
107C LEU* 6.2 4.0 - - + -
210C PHE* 6.1 2.9 - - + -
217C ALA 3.7 10.8 - - - +
218C MET* 3.4 17.5 - - + +
220C ALA* 1.3 78.9 - - + +
222C SER* 1.3 56.3 + - - +
223C THR 3.3 4.9 - - - -
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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