Contacts of the helix formed by residues 199 - 206 (chain D) 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 ALA 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D GLN* 4.0 11.9 - - + +
170D PHE* 3.5 22.0 - - + -
197D LEU* 2.6 17.3 + - - +
198D SER* 1.3 78.0 - - - +
200D PRO* 1.3 78.2 - - + +
201D PHE* 3.7 22.0 - - + -
202D ILE* 3.1 14.6 + - + +
203D SER* 3.8 2.9 + - - -
226D GLU* 3.5 9.6 + - - +
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Residues in contact with PRO 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP* 5.7 6.1 - - - +
38D GLN* 4.9 9.2 - - + +
199D ALA* 1.3 87.0 - - + +
201D PHE* 1.3 54.0 + - - +
203D SER* 2.8 28.3 + - - +
204D GLN* 3.1 24.6 + - - +
225D THR* 4.4 20.4 - - - +
226D GLU* 3.7 15.5 - - + +
229D THR* 3.6 27.5 - - - +
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Residues in contact with PHE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN 3.2 29.1 + - - +
39D ILE* 3.9 19.1 - - + -
40D LEU* 3.6 38.4 - - + -
170D PHE* 3.7 26.5 - + - -
173D THR* 4.0 3.1 - - + -
199D ALA* 3.1 19.6 + - + -
200D PRO* 1.3 77.0 - - - +
202D ILE* 1.3 79.1 + - + +
204D GLN* 3.3 13.3 + - - +
205D PHE* 2.7 50.6 + + + +
206D TYR* 3.8 10.9 + + - -
500D 5I5 4.3 1.6 - - + -
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Residues in contact with ILE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D GLY* 3.5 29.4 - - - +
170D PHE* 4.3 6.7 - - + -
172D LEU* 4.2 17.3 - - + -
173D THR* 3.5 22.9 - - + -
197D LEU* 3.6 19.5 - - - +
199D ALA 3.1 15.6 + - - +
201D PHE* 1.3 108.3 - - + +
203D SER* 1.3 60.1 + - - +
206D TYR* 3.0 37.7 + - + -
207D LYS* 3.5 0.5 + - - -
210D LEU* 4.5 13.7 - - + +
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Residues in contact with SER 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LEU* 4.8 6.2 + - - +
199D ALA 3.8 1.4 + - - -
200D PRO* 2.8 13.2 + - - -
202D ILE* 1.3 80.6 - - - +
204D GLN* 1.3 55.4 + - - -
207D LYS* 2.8 33.6 - - - +
210D LEU* 4.0 11.1 - - - +
226D GLU* 4.3 2.9 + - - -
229D THR* 3.6 20.2 - - - -
230D PHE* 3.5 37.8 + - - +
233D GLU* 3.8 6.0 - - - +
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Residues in contact with GLN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D PRO* 3.1 17.8 + - - +
201D PHE* 3.6 23.2 + - - +
203D SER* 1.3 73.2 - - - +
205D PHE* 1.3 89.9 + - + +
207D LYS* 3.2 27.6 - - - +
229D THR* 3.8 17.4 + - + +
233D GLU* 3.9 22.1 + - - +
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Residues in contact with PHE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PHE* 2.7 31.3 + + + +
204D GLN* 1.3 102.5 - - + +
206D TYR* 1.3 80.9 + + + -
207D LYS* 3.7 1.6 - - - -
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Residues in contact with TYR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.9 12.0 - - + +
172D LEU* 4.5 7.4 - - + -
173D THR* 3.3 54.6 + - + -
201D PHE* 3.9 21.8 - + - -
202D ILE* 3.0 33.7 + - + +
205D PHE* 1.3 96.1 - + + +
207D LYS* 1.3 64.4 - - - +
208D GLU* 3.2 4.6 + - - -
209D SER* 3.4 14.7 + - - -
210D LEU* 3.0 20.6 + - - +
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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