Contacts of the helix formed by residues 209 - 215 (chain D) in PDB entry 3G1Q
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 ILE 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D PHE* 3.5 11.4 + - - +
207D SER 3.8 5.3 + - - +
208D LEU* 1.3 77.6 - - - +
210D PRO* 1.3 61.2 - - + +
211D ALA* 3.9 14.8 - - + +
212D ALA* 2.9 26.9 + - + +
218D LEU* 3.9 28.7 - - + -
223D LEU* 3.8 29.4 - - + -
225D GLN* 4.3 21.1 - - + +
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Residues in contact with PRO 210 (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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105D PHE* 3.7 28.9 - - + -
208D LEU 3.8 6.1 - - - +
209D ILE* 1.3 87.5 - - + +
211D ALA* 1.3 60.5 + - - +
212D ALA 3.0 1.6 + - - -
213D VAL* 3.1 24.3 + - - +
214D PHE* 4.6 3.9 - - - -
460D MET* 3.6 38.1 - - + -
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Residues in contact with ALA 211 (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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45D ILE* 6.4 1.6 - - + -
209D ILE* 3.1 13.7 + - + +
210D PRO* 1.3 77.5 - - - +
212D ALA* 1.3 57.5 + - - +
213D VAL 3.1 0.2 - - - -
214D PHE* 2.9 17.4 + - + +
215D LEU* 2.8 38.1 + - + +
218D LEU* 4.5 3.4 - - + -
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Residues in contact with ALA 212 (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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104D SER* 4.9 0.2 + - - -
105D PHE* 4.1 7.2 - - + -
209D ILE* 2.9 21.6 + - + +
211D ALA* 1.3 79.1 - - - +
213D VAL* 1.3 62.4 + - - +
215D LEU 3.2 24.4 - - - +
216D PRO* 3.2 8.7 - - - +
218D LEU* 3.9 24.9 - - + -
219D LEU* 3.9 28.1 - - + +
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Residues in contact with VAL 213 (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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75D LYS* 5.6 0.9 - - - -
101D GLU 4.1 15.6 - - - +
102D VAL* 3.4 36.8 - - + +
104D SER* 4.7 3.4 - - - +
105D PHE* 3.6 18.6 - - + +
210D PRO* 3.4 15.0 - - + +
211D ALA 3.1 0.2 - - - -
212D ALA* 1.3 78.6 - - - +
214D PHE* 1.3 82.6 + - + +
216D PRO* 4.0 11.6 - - - +
360D MET* 4.3 12.3 - - + -
379D ILE* 4.2 15.1 - - + +
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Residues in contact with PHE 214 (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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72D ILE* 3.6 45.3 - - + +
73D VAL* 4.6 7.4 - - + +
75D LYS* 3.3 39.8 + - + -
77D VAL* 3.6 19.3 - - + -
210D PRO 4.8 2.9 - - - -
211D ALA* 2.9 17.4 + - + +
213D VAL* 1.3 90.7 - - + +
215D LEU* 1.3 64.9 - - + +
216D PRO* 3.4 4.7 - - - +
360D MET* 4.1 26.9 - - + -
379D ILE* 3.2 33.9 - - + -
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Residues in contact with LEU 215 (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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73D VAL* 3.6 32.5 - - + -
75D LYS* 5.2 3.1 - - - +
211D ALA* 2.8 26.6 + - + +
212D ALA* 3.2 6.1 - - - +
214D PHE* 1.3 80.8 - - + +
216D PRO* 1.3 62.2 - - - +
217D ILE* 2.9 16.8 + - + -
218D LEU* 3.0 39.2 + - + +
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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