Contacts of the helix formed by residues 215 - 220 (chain F) in PDB entry 4DEM
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 THR 215 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74F ARG* 5.4 0.4 - - - +
211F VAL 3.0 10.0 + - - -
213F TYR 3.3 0.4 - - - -
214F LYS* 1.3 84.6 - - - +
216F ALA* 1.3 68.2 + - - +
217F PHE 3.5 2.0 + - - -
218F TYR* 3.6 7.8 + - + -
219F SER* 3.1 33.2 + - - +
220F PHE* 4.9 0.2 - - + -
250F GLY 4.1 10.8 - - - +
253F PHE* 3.7 27.1 - - + -
254F GLN* 2.7 34.1 + - + +
401F YS4 3.5 11.1 - - + -
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Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F VAL 3.1 10.5 + - - +
212F LYS* 3.4 17.6 + - - +
215F THR* 1.3 74.4 - - - +
217F PHE* 1.3 65.9 + - - +
220F PHE* 3.1 21.9 + - - +
221F TYR 3.4 6.2 + - - -
247F LEU* 3.7 39.6 - - + +
250F GLY* 3.7 20.6 - - - -
251F GLU 4.2 0.4 - - - +
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Residues in contact with PHE 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F SER* 4.7 5.5 + - - +
180F GLN* 3.3 55.0 - - + +
181F THR* 5.1 0.2 - - - +
212F LYS* 3.2 46.3 + - + -
213F TYR* 3.9 28.9 + + - +
215F THR 3.5 0.6 - - - -
216F ALA* 1.3 80.9 - - - +
218F TYR* 1.3 60.5 + - + +
221F TYR* 3.3 17.5 + + + +
222F LEU* 2.9 27.1 + - - +
243F LYS* 4.3 17.3 - - + -
247F LEU* 3.9 31.6 - - + -
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Residues in contact with TYR 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG* 3.5 24.0 + - - -
106F VAL* 4.2 6.0 - - + +
109F LEU* 4.2 20.4 - - + -
110F GLN* 2.6 34.9 + - - -
113F PHE* 3.8 25.9 - + - +
177F SER* 4.5 5.8 - - - -
181F THR* 3.4 23.9 + - + +
213F TYR 5.5 0.2 + - - -
214F LYS 3.3 26.7 - - - -
215F THR* 3.6 13.2 + - - +
217F PHE* 1.3 80.2 - - - +
219F SER* 1.3 72.4 + - - +
222F LEU* 3.4 16.7 - - + +
223F PRO* 3.4 15.1 - - - +
401F YS4 4.0 23.6 + + - -
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Residues in contact with SER 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG* 2.8 46.3 + - - +
77F THR* 5.7 0.5 + - - +
215F THR* 3.1 24.9 + - - +
218F TYR* 1.3 91.2 - - - +
220F PHE* 1.3 86.3 + - - +
223F PRO* 3.5 13.9 - - - +
253F PHE* 5.1 0.9 - - - -
358F LEU* 5.7 1.2 - - - +
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Residues in contact with PHE 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F THR* 4.9 0.4 - - + -
216F ALA* 3.1 8.6 + - - +
218F TYR 3.4 0.2 - - - -
219F SER* 1.3 100.3 - - - +
221F TYR* 1.3 68.2 + - - +
222F LEU 3.4 0.4 - - - -
223F PRO* 3.5 11.4 - - - +
224F ILE* 3.7 9.0 + - - +
246F LEU* 3.4 39.1 - - + +
249F MET* 4.0 12.6 - - + -
250F GLY* 3.4 17.3 - - - -
253F PHE* 3.5 47.6 - + + -
358F LEU* 3.9 35.2 - - + +
362F ILE* 3.9 23.3 - - + -
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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