Contacts of the helix formed by residues 210 - 219 (chain O) in PDB entry 6CNB
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 PRO 210 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105O LYS* 4.1 20.0 - - + +
106O TYR 4.8 1.6 - - - +
107O LEU* 4.3 11.2 - - + -
121O TYR* 3.4 42.4 - - + -
209O THR* 1.3 91.7 - - + +
211O ILE* 1.3 60.8 + - - +
212O GLU* 3.2 6.5 - - + +
213O ASP* 3.7 18.5 - - + +
214O LEU* 2.9 27.9 + - - +
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Residues in contact with ILE 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O LYS* 5.0 9.6 - - - +
207O HIS 5.2 8.1 - - - +
209O THR 3.0 7.8 + - - +
210O PRO* 1.3 71.4 - - - +
212O GLU* 1.3 64.4 + - - +
214O LEU* 3.1 25.4 - - + +
215O TRP* 2.9 22.3 + - + +
249O PHE* 4.5 22.0 - - + -
253O ILE* 6.1 3.4 - - + -
330O LEU* 4.5 20.0 - - + +
331O THR* 5.3 1.3 - - + +
333O THR* 4.6 17.7 - - + +
334O GLY* 5.6 0.2 - - - -
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Residues in contact with GLU 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.7 32.6 - - + +
118A THR* 4.2 6.3 + - - -
73O ARG* 4.3 15.4 + - - +
210O PRO* 4.8 5.0 - - + +
211O ILE* 1.3 78.8 - - - +
213O ASP* 1.3 84.8 + - - +
215O TRP* 2.9 23.5 + - - +
216O GLN* 2.9 21.3 + - - +
333O THR* 5.1 5.4 + - + +
334O GLY* 4.2 31.6 - - - +
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Residues in contact with ASP 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 4.4 11.4 + - - -
107O LEU* 3.0 39.4 - - + +
121O TYR* 5.9 2.0 - - - +
209O THR* 4.7 2.9 - - + +
210O PRO* 3.1 20.4 + - + +
212O GLU* 1.3 94.2 + - - +
214O LEU* 1.3 57.6 + - - +
216O GLN* 3.3 13.1 + - - +
217O PHE* 2.8 26.5 + - - +
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Residues in contact with LEU 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206O LEU* 4.5 15.7 - - + +
209O THR* 4.1 22.6 - - + +
210O PRO 2.9 10.6 + - - +
211O ILE* 3.1 44.6 - - + +
213O ASP* 1.3 74.6 - - - +
215O TRP* 1.3 62.7 + - - +
217O PHE* 3.7 9.1 - - + +
218O LEU* 2.9 31.3 + - + +
249O PHE* 3.5 34.8 - - + -
252O ILE* 4.7 15.7 - - + -
253O ILE* 6.2 0.9 - - + -
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Residues in contact with TRP 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211O ILE* 2.9 12.1 + - + +
212O GLU* 2.9 13.5 + - - +
214O LEU* 1.3 83.2 - - + +
216O GLN* 1.3 59.8 + - + +
218O LEU* 3.5 6.6 + - + +
219O TYR* 2.9 38.5 + + + +
242O LYS* 4.5 12.1 - - + -
245O ALA* 3.7 43.0 - - + +
246O LYS* 4.1 20.2 - - + -
249O PHE* 3.9 25.4 - + + -
331O THR* 4.2 18.6 - - + -
334O GLY* 3.4 25.3 + - - +
335O LEU* 3.8 31.9 - - + +
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Residues in contact with GLN 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 4.5 19.4 - - + +
118A THR* 5.3 7.6 - - - +
212O GLU* 2.9 19.7 + - - +
213O ASP* 3.5 20.2 - - - +
214O LEU 3.2 0.2 - - - -
215O TRP* 1.3 81.7 - - + +
217O PHE* 1.3 60.0 + - - +
219O TYR* 3.0 53.8 - - - +
220O GLU* 3.9 2.9 + - - +
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Residues in contact with PHE 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213O ASP* 2.8 19.9 + - - +
214O LEU* 3.7 9.0 - - + +
215O TRP 3.2 0.4 - - - -
216O GLN* 1.3 73.2 - - - +
218O LEU* 1.3 61.2 + - + +
219O TYR 2.9 3.8 - - - -
220O GLU* 2.9 48.7 + - - +
221O LYS* 5.5 9.1 - - + +
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Residues in contact with LEU 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214O LEU* 2.9 18.8 + - + +
215O TRP* 3.6 6.5 - - + +
217O PHE* 1.3 80.8 - - + +
219O TYR* 1.3 56.4 + - - +
220O GLU 2.8 18.8 - - - +
221O LYS* 5.6 7.0 - - + -
222O HIS* 3.0 23.4 - - - +
245O ALA* 3.3 34.2 - - + +
248O ASP* 3.9 19.3 - - + +
249O PHE* 3.4 33.9 - - + +
252O ILE* 4.6 10.5 - - + -
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Residues in contact with TYR 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215O TRP* 2.9 28.9 + + - +
216O GLN* 3.0 40.8 - - - +
217O PHE 2.9 0.8 - - - -
218O LEU* 1.3 72.2 - - - +
220O GLU* 1.3 63.2 + - - +
222O HIS* 4.3 4.1 - - - +
223O TYR* 3.1 72.2 + + + +
241O ALA* 6.2 0.4 - - + -
242O LYS* 6.0 4.0 - - + -
245O ALA* 5.4 4.3 - - - -
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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