Contacts of the helix formed by residues 209 - 215 (chain D) in PDB entry 1PYB
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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72C LEU* 5.9 0.4 - - + -
73C LYS* 3.3 31.0 - - + +
76C LYS* 6.1 4.7 - - + -
77C ILE* 4.8 12.8 - - + -
207D ILE* 2.8 20.8 + - + -
208D GLY* 1.3 78.8 - - - +
210D GLU* 1.3 70.0 + - + +
211D ASP 3.2 1.3 - - - +
212D PHE* 3.2 5.5 + - - +
213D LEU* 3.0 41.4 + - + +
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Residues in contact with GLU 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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207D ILE* 3.6 35.4 + - + +
209D ILE* 1.3 80.3 - - + +
211D ASP* 1.3 67.0 + - - +
213D LEU* 3.4 27.4 + - + +
214D LYS* 3.6 18.7 - - - +
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Residues in contact with ASP 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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206D LEU* 5.2 5.7 - - - +
207D ILE* 2.9 29.8 + - - +
208D GLY* 5.2 3.1 - - - -
209D ILE 3.2 0.6 - - - +
210D GLU* 1.3 76.8 - - - +
212D PHE* 1.3 65.3 + - - +
214D LYS* 3.3 35.4 + - - +
215D VAL* 3.6 12.0 + - - +
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Residues in contact with PHE 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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69C VAL* 6.2 0.9 - - + -
72C LEU* 6.1 3.4 - - + -
85C MET* 4.3 7.6 - - + -
87C LEU* 3.7 31.0 - - + -
208D GLY 4.1 16.8 - - - +
209D ILE* 3.2 11.0 + - - +
211D ASP* 1.3 75.5 - - - +
213D LEU* 1.3 72.5 + - + +
214D LYS 3.0 2.2 - - - -
215D VAL* 3.1 37.3 + - + +
216D ASP* 4.9 0.5 - - - +
217D LEU* 4.5 20.6 - - + -
310D LEU* 4.6 5.8 - - + -
311D SER* 3.4 37.9 - - - -
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Residues in contact with LEU 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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209D ILE* 3.0 38.2 + - + +
210D GLU* 3.4 20.2 - - + +
211D ASP 3.2 0.4 - - - -
212D PHE* 1.3 84.2 - - + +
214D LYS* 1.3 57.6 + - + +
216D ASP* 3.2 23.0 - - - +
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Residues in contact with LYS 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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6C LEU* 5.8 9.9 - - + -
210D GLU* 3.6 20.0 - - - +
211D ASP* 3.4 24.2 + - - +
212D PHE 3.0 0.4 - - - -
213D LEU* 1.3 78.7 - - - +
215D VAL* 1.3 61.9 + - + +
216D ASP* 3.0 6.3 - - - +
271D ASN* 3.0 29.1 + - - +
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Residues in contact with VAL 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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6C LEU* 6.2 3.4 - - + -
211D ASP 3.6 13.2 + - - +
212D PHE* 3.1 29.2 + - + +
214D LYS* 1.3 75.2 - - + +
216D ASP* 1.3 61.0 + - - +
217D LEU* 3.5 28.0 + - + +
269D VAL* 3.9 15.7 - - + -
271D ASN* 4.2 3.4 - - - -
272D LEU* 4.2 25.1 - - + -
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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