Contacts of the helix formed by residues 221 - 229 (chain A) in PDB entry 1ZM9
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A GLY* 5.0 6.7 - - - -
209A VAL 4.2 9.4 - - - +
210A ALA* 3.9 13.0 - - + -
220A PHE* 1.3 85.6 - - - +
222A ILE* 1.3 70.2 + - - +
223A ARG* 3.2 5.7 + - - -
224A GLN* 2.6 37.1 + - - +
225A PHE* 3.5 3.5 + - - -
333A ALA* 3.8 24.2 - - + +
336A GLU* 2.9 29.9 + - - +
337A MET* 4.3 7.0 - - + -
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Residues in contact with ILE 222 (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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204A PRO* 3.2 37.2 + - + +
205A ALA* 4.5 1.6 - - - +
207A GLY* 5.4 0.4 - - - -
209A VAL 4.8 2.0 + - - +
211A PHE* 3.9 15.9 - - + -
220A PHE* 4.3 2.2 - - + -
221A THR* 1.3 74.3 - - - +
223A ARG* 1.3 58.3 + - - +
224A GLN 3.1 0.3 + - - -
225A PHE 3.3 2.0 + - - +
226A ALA* 3.0 24.8 + - - +
241A MET* 3.3 39.0 - - + +
244A LEU* 3.5 20.2 - - + +
245A TRP* 4.7 7.4 - - + -
273A PHE* 3.5 32.3 - - + -
277A ILE* 3.8 11.0 - - + -
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Residues in contact with ARG 223 (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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81A MET* 6.0 0.4 - - - -
85A ASP* 2.6 37.2 + - - +
88A GLU* 2.6 36.4 + - - -
206A ARG 6.0 0.2 - - - -
207A GLY* 4.6 12.1 - - - -
221A THR* 2.9 11.7 + - - +
222A ILE* 1.3 80.8 - - - +
224A GLN* 1.3 57.9 + - - +
226A ALA* 3.8 7.3 - - - +
227A THR* 2.8 32.5 + - - +
237A LYS* 3.4 10.7 - - - +
241A MET* 3.8 27.0 - - + -
336A GLU* 2.8 42.0 + - - +
340A LEU* 3.6 21.7 - - - +
341A HIS* 5.7 2.9 - - - -
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Residues in contact with GLN 224 (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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219A ALA 3.7 5.2 + - - +
220A PHE* 3.1 35.1 - - + +
221A THR* 2.6 24.1 + - - +
223A ARG* 1.3 70.5 - - - +
225A PHE* 1.3 64.3 + - + +
226A ALA 3.1 1.9 + - - -
227A THR* 3.3 13.2 + - - -
228A ARG* 3.4 12.6 + - - +
328A LEU* 4.9 10.0 - - + +
329A PRO* 5.1 4.6 + - - +
332A ASP* 4.3 12.1 + - - +
333A ALA* 3.7 25.3 - - - +
336A GLU* 3.3 20.0 + - - +
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Residues in contact with PHE 225 (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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220A PHE* 3.7 33.0 - + + -
221A THR 3.5 3.0 + - - -
222A ILE 3.3 5.9 + - - +
224A GLN* 1.3 80.7 - - + +
226A ALA* 1.3 58.0 + - - +
228A ARG* 3.6 21.3 - - - +
229A TYR* 2.9 57.4 + + + -
244A LEU* 4.1 3.8 - - + -
276A PHE 4.1 6.7 - - - -
277A ILE* 3.4 48.5 - - + -
280A PRO* 5.3 2.7 - - + -
281A ILE* 3.8 19.7 - - + -
327A PHE* 4.1 19.1 - + - -
328A LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 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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222A ILE 3.0 17.9 + - - +
223A ARG* 3.9 6.5 - - - +
224A GLN 3.1 0.2 - - - -
225A PHE* 1.3 79.4 - - - +
227A THR* 1.3 57.6 + - - +
230A ALA* 3.1 24.9 + - - +
237A LYS* 3.5 15.7 - - + +
240A MET* 3.9 8.8 - - + +
241A MET* 3.3 38.4 - - + +
244A LEU* 3.8 6.7 - - + +
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Residues in contact with THR 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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223A ARG* 2.8 26.2 + - - +
224A GLN* 3.3 7.4 + - - -
225A PHE 3.2 0.6 - - - -
226A ALA* 1.3 77.1 - - - +
228A ARG* 1.3 60.1 + - - +
230A ALA* 3.0 19.2 - - + +
237A LYS* 3.7 30.7 + - + +
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Residues in contact with ARG 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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224A GLN 3.4 9.5 + - - +
225A PHE* 3.6 30.1 - - - +
226A ALA 3.2 0.2 - - - -
227A THR* 1.3 79.6 - - - +
229A TYR* 1.3 79.3 + - + +
230A ALA* 2.8 10.3 + - - +
231A LYS 4.0 3.5 + - - -
232A LYS* 4.9 3.3 + - - +
303A LEU* 4.3 21.4 + - - +
327A PHE* 4.3 32.9 + - - -
328A LEU* 5.2 6.3 - - - +
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Residues in contact with TYR 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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225A PHE* 2.9 46.7 + + + +
226A ALA 4.1 0.2 - - - -
228A ARG* 1.3 86.9 - - + +
230A ALA* 1.3 64.7 + - - +
231A LYS 3.0 2.9 + - - -
232A LYS* 3.4 22.0 + - + -
233A PHE* 3.9 29.3 + + + -
235A VAL* 4.3 2.1 - - - +
240A MET* 4.2 19.9 - - + +
244A LEU* 4.9 6.5 - - + -
276A PHE* 2.6 61.7 + + + -
280A PRO* 3.7 12.8 - - - +
303A LEU* 6.0 0.7 - - - +
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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