Contacts of the helix formed by residues 226 - 234 (chain A) in PDB entry 1HDZ
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 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ILE 3.8 1.7 - - - +
225A ASN* 1.3 74.5 + - - +
227A ASP* 1.3 62.3 + - - +
228A LYS 3.0 1.6 + - - -
229A PHE* 3.0 41.3 + - + +
230A ALA 4.6 0.5 + - - -
242A ASN* 3.7 21.3 - - + +
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Residues in contact with ASP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASN* 3.2 22.2 + - - +
226A LYS* 1.3 77.3 - - - +
228A LYS* 1.3 61.7 - - + +
229A PHE 3.3 0.6 + - - -
230A ALA* 4.2 11.7 + - - +
231A LYS* 4.8 2.1 + - - +
365A GLY 4.5 9.7 - - - +
366A LYS* 5.8 4.0 - - - +
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 2.8 43.5 + - + +
201A GLY* 4.0 5.9 - - - -
205A LEU* 4.8 2.8 - - + +
223A ASP* 4.2 4.9 - - - +
225A ASN* 3.4 38.8 - - + +
226A LYS 3.0 1.0 + - - -
227A ASP* 1.3 78.0 - - + +
229A PHE* 1.3 65.7 + - - +
230A ALA 3.4 0.2 - - - -
231A LYS* 3.2 9.2 + - - +
232A ALA* 3.0 21.0 + - - +
365A GLY* 4.3 9.0 - - - +
367A SER 3.8 23.5 + - - -
368A ILE* 4.1 17.9 - - + +
377A NAD 2.8 32.5 + - - -
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Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.9 11.9 - - + -
221A ALA 4.5 0.7 - - - -
223A ASP* 3.5 36.1 - - + -
225A ASN 4.0 2.9 - - - -
226A LYS* 3.0 34.3 + - + +
228A LYS* 1.3 75.4 - - - +
230A ALA* 1.3 57.6 + - - +
232A ALA* 3.1 4.6 + - - +
233A LYS* 2.8 50.8 + - - +
240A CYS* 3.6 28.7 - - + -
241A ILE 3.4 30.5 - - - -
242A ASN* 3.7 12.3 - - + -
245A ASP* 5.8 0.2 - - - -
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LYS 4.6 0.6 + - - -
227A ASP 4.2 8.8 + - - +
228A LYS 3.4 0.4 - - - -
229A PHE* 1.3 76.9 - - - +
231A LYS* 1.3 61.2 + - + +
233A LYS* 3.6 10.0 + - - +
234A GLU* 3.0 29.2 + - - +
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.2 7.2 - - + -
227A ASP 4.8 1.7 + - - +
228A LYS* 3.2 10.6 + - - +
230A ALA* 1.3 78.3 - - + +
232A ALA* 1.3 60.2 + - - +
234A GLU* 3.2 25.9 + - - +
235A LEU* 2.8 38.5 + - + +
344A ALA* 2.7 43.1 + - + +
346A ILE 5.6 0.2 + - - -
347A THR* 3.9 17.4 - - - +
368A ILE* 3.7 23.8 - - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.9 22.9 - - + -
205A LEU* 3.4 18.5 - - + +
208A VAL* 3.9 3.3 - - + +
221A ALA* 4.1 3.8 - - + -
228A LYS 3.0 12.7 + - - +
229A PHE 3.3 8.1 - - - +
231A LYS* 1.3 75.4 - - - +
233A LYS* 1.4 57.4 + - - +
235A LEU* 3.0 4.7 + - - +
236A GLY 2.9 13.0 + - - -
237A ALA* 2.9 33.5 + - + +
240A CYS* 4.0 5.8 - - - -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PHE* 2.8 31.7 + - - +
230A ALA* 3.7 7.6 - - - +
232A ALA* 1.4 74.4 - - - +
234A GLU* 1.3 63.4 + - - +
236A GLY* 3.0 13.9 + - - -
237A ALA 3.7 20.8 + - - +
238A THR 5.1 7.6 - - - +
239A GLU* 5.2 2.9 - - - -
240A CYS* 3.4 30.2 - - - +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS* 5.8 1.9 + - - -
230A ALA 3.0 17.5 + - - +
231A LYS* 3.4 33.7 - - - +
233A LYS* 1.3 75.9 - - - +
235A LEU* 1.3 63.5 + - + +
236A GLY 3.6 0.3 + - - -
344A ALA* 4.0 19.5 - - - +
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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