Contacts of the helix formed by residues 206 - 214 (chain A) in PDB entry 2I6A
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 TYR 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.0 12.0 - - - +
172A LEU* 4.3 9.4 - - + -
173A THR* 3.1 54.9 - - + +
201A PHE* 3.5 24.9 - + - -
202A ILE* 3.2 25.3 + - + +
205A PHE* 1.3 98.8 - + + +
207A LYS* 1.3 67.0 + - - +
208A GLU* 2.9 5.1 + - - -
209A SER* 3.0 21.5 + - - +
210A LEU* 3.0 9.5 + - + +
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Residues in contact with LYS 207 (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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202A ILE 3.5 3.2 + - - -
203A SER* 2.9 26.5 - - - +
204A GLN 3.6 19.7 - - - +
205A PHE 3.8 0.6 - - - -
206A TYR* 1.3 71.3 - - - +
208A GLU* 1.3 57.3 + - - +
210A LEU* 3.7 11.2 - - + -
211A MET* 2.7 45.9 + - + +
233A GLU* 3.8 37.7 + - + +
234A GLN* 4.6 7.4 - - - +
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Residues in contact with GLU 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 TYR 2.9 2.9 + - - -
207A LYS* 1.3 78.7 - - - +
209A SER* 1.3 57.6 + - - +
211A MET* 4.1 2.7 - - - +
212A LYS* 3.1 55.6 + - - +
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Residues in contact with SER 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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172A LEU* 4.0 23.5 + - - -
176A PRO* 2.9 35.9 - - - +
206A TYR* 3.0 12.7 + - - -
208A GLU* 1.3 77.7 - - - +
210A LEU* 1.3 61.8 + - - +
212A LYS* 3.6 7.4 + - - +
213A VAL* 3.2 30.0 + - - +
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Residues in contact with LEU 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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172A LEU* 3.6 17.7 - - + +
195A LEU* 3.5 29.6 - - + -
196A ASN 5.2 1.6 - - - +
197A LEU* 4.1 11.2 - - + -
202A ILE* 4.3 19.1 - - + +
203A SER* 3.9 13.2 - - - +
206A TYR 3.0 15.7 + - - +
207A LYS* 3.7 6.7 - - + +
209A SER* 1.3 77.7 - - - +
211A MET* 1.3 60.2 + - - +
213A VAL* 3.2 3.0 + - - +
214A MET* 2.9 41.1 + - + +
230A PHE* 3.7 30.7 - - + -
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Residues in contact with MET 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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207A LYS* 2.7 31.2 + - + +
208A GLU* 4.4 2.5 - - - +
210A LEU* 1.3 75.7 - - + +
212A LYS* 1.3 58.7 + - - +
214A MET* 3.8 22.5 - - + +
215A PRO* 3.1 24.1 - - - +
230A PHE* 3.9 23.3 - - - -
234A GLN* 3.2 39.3 - - - +
251A LEU* 4.4 18.2 - - + -
252A PRO* 6.1 2.2 - - + -
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Residues in contact with LYS 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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180A LEU* 3.9 34.7 - - + +
208A GLU* 3.1 53.8 + - - +
209A SER* 3.8 8.3 - - - +
210A LEU 3.2 0.2 - - - -
211A MET* 1.3 77.1 - - - +
213A VAL* 1.3 62.7 + - - +
215A PRO* 3.4 9.3 - - - +
216A TYR* 4.0 6.9 - - - -
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Residues in contact with VAL 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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172A LEU* 3.9 16.8 - - + -
176A PRO* 4.9 2.9 - - + +
179A VAL* 4.1 14.1 - - + -
180A LEU* 4.1 25.4 - - + +
183A ALA* 5.1 1.6 - - + -
193A PHE* 4.2 10.3 - - + -
195A LEU* 4.0 34.1 - - + -
209A SER 3.2 18.6 + - - +
210A LEU* 3.2 4.9 + - - +
212A LYS* 1.3 77.9 - - - +
214A MET* 1.3 54.5 + - - +
215A PRO* 3.2 6.3 - - - -
216A TYR* 3.1 26.8 + - - +
217A VAL* 3.7 9.3 + - + -
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Residues in contact with MET 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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197A LEU* 4.6 0.4 - - + -
210A LEU* 2.9 36.9 + - + +
211A MET* 3.8 16.4 - - + +
213A VAL* 1.3 69.4 - - - +
215A PRO* 1.3 60.8 - - + +
216A TYR 3.0 7.6 + - - -
217A VAL* 3.3 21.2 + - - +
220A LEU* 3.9 36.3 - - + -
230A PHE* 3.4 37.7 - - + -
251A LEU* 4.0 22.9 - - + -
252A PRO 4.3 0.4 - - - +
260A ARG* 2.7 39.9 + - - +
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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