Contacts of the helix formed by residues 222 - 233 (chain A) in PDB entry 1IS0
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 SER 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.5 17.3 - - - -
220A PHE* 3.3 11.2 + - - +
221A SER* 1.3 85.3 + - - +
223A LEU* 1.3 63.4 + - - +
224A GLN* 3.0 33.1 - - - +
225A GLN* 3.0 14.8 + - - +
226A LEU* 3.1 16.6 + - - +
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Residues in contact with LEU 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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148A TRP* 3.8 13.9 - - + -
149A TYR* 4.3 11.9 - - + -
174A VAL* 4.1 13.7 - - + -
184A TYR* 4.1 33.2 - - + -
204A ILE* 3.8 33.0 - - + -
212A PHE* 3.7 33.3 - - + -
222A SER* 1.3 71.4 - - - +
224A GLN* 1.3 70.4 + - - +
226A LEU* 3.1 5.9 + - + +
227A VAL* 2.8 34.7 + - + +
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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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148A TRP* 3.7 24.7 - - + -
212A PHE* 5.9 0.2 - - - -
222A SER* 3.0 22.9 - - - +
223A LEU* 1.3 95.7 - - - +
225A GLN* 1.3 54.5 + - - +
227A VAL* 3.5 1.4 + - - +
228A ALA* 3.0 29.2 + - - +
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Residues in contact with GLN 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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219A GLN 4.5 0.8 + - - -
220A PHE* 3.0 23.0 - - + +
221A SER* 2.7 46.3 + - - +
222A SER* 3.0 20.0 + - - +
224A GLN* 1.3 73.7 - - - +
226A LEU* 1.3 65.2 + - - +
228A ALA* 3.5 6.4 + - + +
229A TYR* 3.1 24.5 + - + +
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Residues in contact with LEU 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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186A LEU* 4.2 19.1 - - + -
204A ILE* 3.8 44.2 - - + -
212A PHE* 4.6 4.9 - - + -
213A TYR* 4.7 2.7 - - - +
214A ILE* 4.3 11.0 - - + -
220A PHE* 3.6 39.2 - - + -
222A SER 3.1 10.9 + - - +
223A LEU* 3.1 10.4 + - + +
225A GLN* 1.3 77.2 - - - +
227A VAL* 1.3 74.8 + - + +
229A TYR* 3.2 2.4 + - - +
230A TYR* 3.1 42.8 + - + -
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Residues in contact with VAL 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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148A TRP* 3.7 32.3 - - + +
172A PHE* 3.7 30.1 - - + -
174A VAL* 3.8 29.2 - - + -
186A LEU* 5.1 0.2 - - + -
223A LEU 2.8 23.2 + - - +
224A GLN 3.9 3.6 - - - +
226A LEU* 1.3 81.1 - - + +
228A ALA* 1.3 59.6 + - - +
230A TYR 3.5 0.2 + - - -
231A SER* 2.7 37.2 + - - +
241A LEU* 3.8 8.2 - - + +
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Residues in contact with ALA 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 3.0 18.9 + - - +
225A GLN* 3.8 7.9 - - + +
227A VAL* 1.3 77.2 - - - +
229A TYR* 1.3 61.8 + - - +
231A SER* 3.4 8.3 + - - -
232A LYS* 3.2 27.7 + - + +
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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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218A THR* 3.9 20.4 - - + +
220A PHE* 3.5 25.6 - + + -
225A GLN* 3.1 18.9 + - + +
226A LEU 3.2 4.5 + - - +
228A ALA* 1.3 78.2 - - - +
230A TYR* 1.3 79.9 + + - +
232A LYS* 3.1 16.3 + - + +
233A HIS* 3.0 49.9 + + - -
235A ASP* 2.6 37.0 + - + -
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Residues in contact with TYR 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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186A LEU* 4.6 2.0 - - + -
214A ILE* 3.8 22.2 - - + +
215A THR* 4.3 4.0 - - - +
218A THR* 4.0 20.4 + - - -
220A PHE* 3.8 22.1 - + - -
226A LEU* 3.1 31.6 + - + +
229A TYR* 1.3 92.3 - + - +
231A SER* 1.3 62.4 + - - +
232A LYS 3.2 0.2 - - - -
233A HIS 3.4 12.1 - - - +
234A ALA* 3.3 26.1 - - - -
235A ASP* 4.2 6.1 + - - -
237A LEU* 3.8 12.6 - - + -
240A ARG* 3.6 6.8 - - - +
241A LEU* 2.9 42.3 + - + -
255C ILE* 3.5 29.8 - - + +
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Residues in contact with SER 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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172A PHE* 4.6 3.8 - - - -
227A VAL* 2.7 30.8 + - - +
228A ALA* 3.6 9.1 - - - -
230A TYR* 1.3 76.3 - - - +
232A LYS* 1.3 59.2 + - - +
240A ARG* 2.8 32.7 + - - -
241A LEU* 3.4 26.4 + - - +
191B PHE* 5.7 0.3 - - - -
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Residues in contact with LYS 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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228A ALA 3.2 15.7 + - - +
229A TYR* 3.1 13.4 + - + +
231A SER* 1.3 80.4 - - - +
233A HIS* 1.3 80.6 + - + +
240A ARG* 4.6 0.2 - - - -
163B LEU* 2.8 32.2 + - - +
164B ASN* 5.0 0.2 - - - +
165B PRO* 3.8 25.4 - - + +
191B PHE* 4.9 1.2 - - - -
196B GLY* 3.2 5.7 - - - -
197B LEU* 2.7 54.1 + - + +
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Residues in contact with HIS 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 TYR* 3.0 58.1 + + - +
230A TYR* 3.4 16.5 - - - -
231A SER 3.5 0.2 - - - -
232A LYS* 1.3 113.2 - - - +
234A ALA* 1.3 66.2 + - - +
235A ASP* 3.4 8.9 + - + +
240A ARG* 4.6 0.9 - - - -
163B LEU* 4.5 17.9 - - + +
195B LYS 3.1 12.1 - - - +
196B GLY* 4.2 1.1 - - - -
197B LEU* 3.5 20.1 + - - +
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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