Contacts of the helix formed by residues 207 - 215 (chain A) in PDB entry 4IRC
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A CYS* 1.3 79.4 - - - +
208A LEU* 1.3 62.3 + - - +
209A VAL* 2.8 34.8 + - - +
210A MET* 3.2 46.3 + - + +
211A LEU* 3.6 11.1 + - - +
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A CYS 3.8 2.2 + - - -
207A ASP* 1.3 72.1 + - - +
209A VAL* 1.3 61.3 + - - +
210A MET 3.2 1.8 - - - -
211A LEU* 3.2 9.4 + - + +
212A LEU* 2.9 63.6 + - + +
219A GLY 4.9 1.3 - - - +
220A ARG* 4.5 19.5 - - - +
223A TRP* 3.6 54.9 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ASP* 2.8 31.4 - - - +
208A LEU* 1.3 73.4 - - + +
210A MET* 1.3 56.0 + - + +
212A LEU* 3.3 11.8 + - + +
213A LYS* 2.8 42.5 + - + +
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 4.3 20.4 - - + -
206A CYS* 5.0 9.0 - - - -
207A ASP* 3.2 35.1 + - + +
209A VAL* 1.3 73.4 - - + +
211A LEU* 1.3 58.5 + - + +
213A LYS* 2.8 46.5 + - - +
214A ARG* 2.9 47.2 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 4.4 3.8 - - + -
197A LEU* 4.0 24.9 - - + -
203A VAL* 3.7 30.3 - - + +
206A CYS* 5.2 5.8 - - + -
207A ASP 3.6 13.0 + - - +
208A LEU* 3.2 9.4 + - + +
210A MET* 1.3 79.3 - - + +
212A LEU* 1.3 58.4 + - - +
215A PHE* 2.9 49.3 + - + +
219A GLY* 3.3 29.8 - - - +
222A LEU* 4.3 13.9 - - + -
223A TRP* 3.9 20.6 - - + +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 2.9 48.6 + - + +
209A VAL* 3.6 12.8 - - + +
211A LEU* 1.3 78.3 - - - +
213A LYS* 1.3 62.4 + - + +
215A PHE 2.6 17.0 - - - +
216A GLY* 4.3 10.1 - - - +
220A ARG* 3.8 53.2 - - + +
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 2.8 22.9 + - + +
210A MET* 2.8 37.2 + - - +
212A LEU* 1.3 78.3 - - - +
214A ARG* 1.3 63.6 + - + +
215A PHE 3.7 0.7 + - - -
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 3.3 29.8 - - - +
195A MET* 2.9 45.0 - - + +
210A MET* 2.9 41.5 + - - +
213A LYS* 1.3 78.5 - - + +
215A PHE* 1.3 89.6 + - + +
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Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A SER* 5.4 3.4 - - - -
191A LYS* 3.9 22.2 - - + -
192A LEU* 3.5 29.6 - - + -
195A MET* 3.9 19.1 - - + -
211A LEU* 2.9 44.7 + - + +
212A LEU* 2.6 25.1 - - - +
213A LYS 3.4 1.5 - - - -
214A ARG* 1.3 99.9 - - + +
216A GLY* 1.3 66.5 + - - +
218A PHE* 3.6 25.4 - + + -
219A GLY* 3.3 21.1 - - - +
222A LEU* 5.1 0.4 - - + -
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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