Contacts of the helix formed by residues 222 - 233 (chain A) in PDB entry 4H1S
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 GLY 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A SER* 1.3 79.7 - - - +
223A PHE* 1.3 60.3 + - - -
224A GLU 3.3 2.7 - - - -
225A MET 3.3 3.4 + - - -
226A ASP* 2.9 35.6 + - - +
242A GLY 3.2 19.7 + - - -
243A HIS* 3.4 9.3 - - - +
244A SER* 3.6 8.5 - - - -
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Residues in contact with PHE 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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222A GLY* 1.3 71.2 - - - -
224A GLU* 1.3 66.7 + - + +
226A ASP* 3.2 7.9 + - - +
227A LYS* 3.1 64.0 + - + +
244A SER* 2.9 11.9 + - - +
246A THR* 3.3 36.1 - - + +
248A LEU* 4.2 17.7 - - + -
260A ALA* 5.0 11.7 - - + -
265A PHE* 3.8 31.2 - + + -
277A VAL* 3.9 26.5 - - + -
279A GLN* 4.1 7.0 - - + +
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Residues in contact with GLU 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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222A GLY 3.3 1.0 - - - -
223A PHE* 1.3 83.1 - - + +
225A MET* 1.3 62.4 + - - +
227A LYS* 2.8 38.6 + - - +
228A LEU* 3.2 25.6 + - - +
444A GLN* 3.4 43.1 - - + +
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Residues in contact with MET 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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195A ASP* 5.0 6.7 - - - +
196A GLU* 4.0 28.5 - - - +
197A ILE* 4.3 16.6 - - + -
221A SER* 3.5 37.6 + - - +
222A GLY 3.3 3.6 + - - +
224A GLU* 1.3 77.7 - - - +
226A ASP* 1.3 57.2 + - - +
228A LEU* 3.2 17.4 + - + -
229A ILE* 2.9 47.8 + - + +
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Residues in contact with ASP 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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176A TYR* 2.6 35.5 + - - -
221A SER 4.6 0.3 + - - -
222A GLY 2.9 30.7 + - - +
223A PHE* 3.2 8.8 + - - +
225A MET* 1.3 75.5 - - - +
227A LYS* 1.3 57.6 + - - +
229A ILE* 3.4 5.5 + - - +
230A ALA* 3.0 26.9 + - - +
239A VAL* 3.8 18.8 - - + +
241A GLY* 3.4 23.4 - - - -
242A GLY 3.9 0.3 + - - -
277A VAL* 3.8 14.8 - - + +
278A VAL 4.9 0.3 - - - +
279A GLN* 3.4 16.6 + - - -
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Residues in contact with LYS 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 PHE* 3.1 50.5 + - + +
224A GLU* 2.8 45.2 + - - +
225A MET 3.2 0.2 - - - -
226A ASP* 1.3 73.2 - - - +
228A LEU* 1.3 62.3 + - + +
230A ALA* 3.3 3.6 + - - +
231A GLN* 3.0 28.6 + - - +
265A PHE* 3.5 30.5 - - + -
267A VAL* 3.8 24.6 - - + +
277A VAL* 4.5 2.9 - - + -
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Residues in contact with LEU 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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197A ILE* 4.0 18.6 - - + -
224A GLU 3.2 15.0 + - - +
225A MET* 3.6 26.7 - - + +
227A LYS* 1.3 78.3 - - + +
229A ILE* 1.3 57.6 + - - +
231A GLN* 3.2 19.8 + - - +
232A LYS* 2.8 51.8 + - - +
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Residues in contact with ILE 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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176A TYR* 3.5 39.7 - - + +
196A GLU* 4.2 3.1 - - + -
197A ILE* 4.1 14.6 - - + -
200A LEU* 3.7 26.9 - - + -
217A ALA* 4.3 12.3 - - + -
225A MET* 2.9 31.5 + - + +
226A ASP* 3.7 5.2 - - - +
228A LEU* 1.3 76.4 - - - +
230A ALA* 1.3 63.6 + - - +
233A VAL* 3.0 44.1 + - + +
236A VAL* 4.7 4.0 - - + +
239A VAL* 4.2 14.4 - - + -
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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 ASP 3.0 15.1 + - - +
227A LYS 3.5 8.7 - - - +
229A ILE* 1.3 77.4 - - - +
231A GLN* 1.3 60.4 + - - +
233A VAL 4.8 2.8 + - - +
236A VAL* 5.2 2.7 - - - +
239A VAL* 3.8 9.4 - - + +
267A VAL* 3.7 11.2 - - + -
269A SER* 3.4 17.2 - - - -
273A ARG* 4.9 2.9 + - - -
275A VAL* 3.6 32.5 - - + +
277A VAL* 3.7 17.7 - - + -
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Residues in contact with GLN 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 LYS 3.0 16.6 + - - +
228A LEU* 3.7 22.8 - - - +
229A ILE 3.2 0.2 - - - -
230A ALA* 1.3 80.1 - - - +
232A LYS* 1.3 72.5 + - + +
233A VAL 5.5 0.6 - - - -
267A VAL* 3.8 8.3 - - + +
268A THR 3.9 14.8 + - - +
269A SER* 3.6 8.4 - - - +
270A ASP* 2.8 55.8 + - - +
271A ASP 4.7 0.2 + - - -
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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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197A ILE* 4.2 26.7 - - + +
201A GLN* 3.5 5.9 - - - +
228A LEU* 2.8 36.8 + - + +
231A GLN* 1.3 99.8 + - + +
233A VAL* 1.3 60.5 + - - +
234A ARG* 3.2 20.2 + - - +
270A ASP* 3.1 30.0 - - - +
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Residues in contact with VAL 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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197A ILE* 3.8 40.6 - - + +
200A LEU* 4.2 7.4 - - + -
201A GLN* 3.4 24.2 - - - +
204A VAL* 3.9 18.4 - - + -
229A ILE* 3.0 31.1 + - + +
230A ALA 4.9 2.6 - - - +
231A GLN 5.5 0.2 - - - -
232A LYS* 1.3 75.4 - - - +
234A ARG* 1.3 61.4 + - - +
235A GLY 3.4 0.5 + - - -
236A VAL* 3.3 35.5 + - + +
273A ARG* 4.2 4.2 + - - -
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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