Contacts of the helix formed by residues 225 - 235 (chain A) in PDB entry 3ZUU
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 ASN 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLU* 3.2 45.7 + - + +
223A PRO 3.2 2.2 - - - -
224A LYS* 1.3 73.6 - - - +
226A PHE* 1.3 57.5 + - - +
227A ARG* 2.9 46.1 + - - +
228A LYS* 3.6 19.9 + - + +
229A THR* 3.0 31.7 + - - -
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Residues in contact with PHE 226 (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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178A GLY 5.0 5.6 - - - -
179A THR* 5.6 0.4 - - - -
180A PRO* 3.9 32.5 - - + -
218A GLU* 5.3 0.7 - - - -
223A PRO 3.5 21.8 - - - -
224A LYS* 3.2 25.6 + - + -
225A ASN* 1.3 69.3 - - - +
227A ARG* 1.3 59.2 + - - +
229A THR* 3.7 6.0 - - - -
230A ILE* 2.9 43.8 + - + +
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Residues in contact with ARG 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* 2.9 41.4 + - - +
226A PHE* 1.3 80.6 - - - +
228A LYS* 1.3 69.1 + - - +
230A ILE* 3.5 6.7 - - - +
231A HIS* 2.9 22.2 + - + +
1321A AU 4.2 15.3 - - - -
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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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217A PHE 5.6 0.2 - - - +
219A ASP* 3.2 28.6 + - + +
222A GLU* 3.2 26.1 + - - +
225A ASN* 3.3 25.3 + - + +
227A ARG* 1.3 86.4 - - - +
229A THR* 1.3 65.2 + - - +
231A HIS* 3.2 10.5 - - + +
232A ARG* 3.0 63.3 + - + +
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Residues in contact with THR 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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180A PRO* 3.8 24.5 - - + -
181A ALA 4.6 4.3 - - - +
217A PHE* 4.2 10.5 - - + +
218A GLU* 3.6 41.9 + - + +
219A ASP 4.2 2.9 + - - -
222A GLU 4.5 2.3 + - - -
223A PRO 4.6 1.9 + - - -
225A ASN 3.0 19.1 + - - -
226A PHE* 3.7 8.5 - - - -
228A LYS* 1.3 76.1 - - - +
230A ILE* 1.3 64.4 + - - +
232A ARG* 2.9 6.8 + - - +
233A ILE* 2.9 32.7 + - + +
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Residues in contact with ILE 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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180A PRO* 4.7 18.2 - - + -
188A LEU* 4.2 28.7 - - + -
226A PHE* 2.9 37.4 + - + +
227A ARG* 3.5 6.3 - - - +
229A THR* 1.3 67.5 - - - +
231A HIS* 1.3 68.6 + - - +
233A ILE* 3.1 10.0 + - + +
234A LEU* 2.9 42.1 + - + +
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Residues in contact with HIS 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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227A ARG 2.9 12.5 + - - +
228A LYS* 3.2 12.5 + - + +
230A ILE* 1.3 80.1 - - - +
232A ARG* 1.3 64.2 + - - +
234A LEU* 3.1 7.4 + - + +
235A ASN* 3.1 45.9 + - - +
237A GLN* 4.0 22.5 + - - -
1321A AU 3.5 24.4 - - - -
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Residues in contact with ARG 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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217A PHE* 3.2 32.6 + - - +
218A GLU 4.7 0.8 + - - -
219A ASP* 3.8 22.0 + - - +
220A PRO* 5.4 1.2 - - - +
228A LYS* 3.0 51.3 + - + +
229A THR 2.9 7.4 + - - +
231A HIS* 1.3 76.9 - - - +
233A ILE* 1.3 57.4 + - - +
236A VAL* 2.8 8.7 + - - -
237A GLN* 2.8 69.3 + - + +
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Residues in contact with ILE 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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180A PRO* 3.2 36.6 - - + +
181A ALA* 4.0 6.5 - - - +
183A ILE 3.7 19.5 - - - +
185A PRO* 3.5 26.6 - - + +
188A LEU* 4.0 18.6 - - + -
201A TRP* 4.0 6.9 - - + -
217A PHE* 3.8 27.1 - - + -
229A THR* 2.9 24.3 + - + +
230A ILE* 3.1 13.2 + - - +
232A ARG* 1.3 76.6 - - - +
234A LEU* 1.3 63.0 + - - +
236A VAL* 3.1 13.7 + - - +
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Residues in contact with LEU 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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185A PRO* 4.1 19.5 - - + +
188A LEU* 4.1 16.4 - - + -
189A LEU* 3.8 41.1 - - + -
230A ILE* 2.9 34.3 + - + +
231A HIS* 3.6 9.6 - - - +
233A ILE* 1.3 75.5 - - - +
235A ASN* 1.3 66.7 + - - +
236A VAL* 3.3 6.5 + - - +
260A ALA* 4.4 10.0 - - - +
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Residues in contact with ASN 235 (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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231A HIS* 3.1 40.9 + - - +
234A LEU* 1.3 81.8 + - - +
236A VAL* 1.3 71.7 + - - +
237A GLN* 3.1 31.1 + - + +
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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