Contacts of the helix formed by residues 228 - 235 (chain D) in PDB entry 1D1T
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 LYS 228 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D LEU* 3.7 25.4 + - + +
201D GLY* 4.3 4.8 - - - -
205D LEU* 4.9 0.3 - - - +
223D ASP* 3.4 21.3 - - - +
225D ASN* 3.1 26.0 + - - +
227D ASP* 1.3 82.2 - - + +
229D PHE* 1.3 63.5 + - - +
230D GLU 3.4 0.2 - - - -
231D LYS* 3.3 10.1 + - + +
232D ALA* 3.0 19.8 + - - +
365D GLY* 3.4 33.1 + - - -
367D SER 4.5 8.5 + - - +
368D ILE* 3.9 20.8 - - + +
4377D NAD 2.7 38.7 + - - +
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Residues in contact with PHE 229 (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 LEU* 3.7 8.5 - - + -
223D ASP* 3.4 37.7 - - + -
225D ASN 3.9 7.9 - - - -
226D LYS* 3.3 42.7 + - + +
228D LYS* 1.3 75.3 - - - +
230D GLU* 1.3 67.3 + - - +
232D ALA* 3.2 2.0 + - - +
233D MET* 2.9 31.7 + - + +
240D CYS* 3.5 35.9 - - + -
241D ILE* 3.4 33.4 - - - -
242D SER 4.0 1.3 - - - -
245D ASP* 5.4 0.2 - - - -
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Residues in contact with GLU 230 (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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226D LYS 4.6 1.4 + - - -
227D ASP 4.2 8.7 + - - +
228D LYS 3.4 0.8 - - - -
229D PHE* 1.3 79.8 - - - +
231D LYS* 1.3 64.0 + - - +
233D MET* 3.2 7.8 + - - +
234D ALA* 3.0 22.0 + - + +
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Residues in contact with LYS 231 (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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205D LEU* 4.0 22.7 - - + -
227D ASP 5.0 1.3 + - - +
228D LYS* 3.3 11.1 + - - +
229D PHE 3.2 0.2 - - - -
230D GLU* 1.3 76.0 - - - +
232D ALA* 1.3 67.5 + - - +
234D ALA* 2.9 18.4 + - + +
235D VAL* 3.0 18.1 + - + +
343D ASP 5.2 0.6 + - - -
344D GLN* 3.0 60.7 + - + +
347D THR* 4.2 15.3 - - + +
368D ILE* 4.6 11.7 - - + -
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Residues in contact with ALA 232 (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 LEU* 3.6 20.6 - - + -
205D LEU* 3.4 19.6 - - + +
208D ILE* 4.0 9.3 - - + +
228D LYS 3.0 8.2 + - - +
229D PHE 3.2 8.3 + - - +
231D LYS* 1.3 75.5 - - - +
233D MET* 1.3 58.3 + - - +
235D VAL* 3.3 10.3 - - - +
237D ALA* 3.0 25.3 + - + +
240D CYS* 3.5 21.5 - - - -
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Residues in contact with MET 233 (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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229D PHE* 2.9 23.0 + - + +
230D GLU* 3.6 9.0 - - - +
231D LYS 3.1 0.2 - - - -
232D ALA* 1.3 73.9 - - - +
234D ALA* 1.3 66.5 + - - +
236D GLY* 3.3 11.4 + - - -
237D ALA 3.5 21.9 - - - +
238D THR 3.4 21.3 - - - +
239D GLU* 3.8 20.2 - - - -
240D CYS* 4.1 12.6 - - - -
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Residues in contact with ALA 234 (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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212D LYS* 5.0 4.9 + - - -
230D GLU* 3.0 13.7 + - + +
231D LYS* 2.9 14.7 + - + +
233D MET* 1.3 79.0 - - - +
235D VAL* 1.3 59.0 + - - +
236D GLY 3.5 0.7 + - - -
344D GLN* 4.2 29.0 - - - +
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Residues in contact with VAL 235 (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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205D LEU* 3.7 31.0 - - + +
208D ILE* 3.4 21.7 - - + +
209D MET* 4.1 27.7 + - + +
212D LYS* 3.7 18.6 + - - +
231D LYS* 3.5 17.7 - - + +
232D ALA 3.3 14.4 - - - +
234D ALA* 1.3 78.6 - - - +
236D GLY* 1.3 54.4 + - - +
344D GLN* 4.0 29.4 - - + -
345D LEU* 5.2 1.3 - - + -
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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