Contacts of the helix formed by residues 227 - 238 (chain A) in PDB entry 4HHM
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLU* 5.4 0.4 - - - +
226A LEU* 1.3 74.5 - - - +
228A PHE* 1.3 62.3 + - - +
229A PRO* 3.0 15.8 - - - +
230A HIS* 2.8 60.0 + - + +
231A GLY* 3.0 19.1 + - - -
190B ASP* 3.1 36.8 + - + -
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Residues in contact with PHE 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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196A ILE* 4.6 0.9 - - + -
216A PRO* 3.6 28.3 - - + -
217A GLU 3.2 23.1 - - - -
218A VAL* 3.3 40.2 - - + -
221A GLU* 3.4 27.6 - - + +
222A GLN* 4.5 18.2 + - + +
226A LEU 3.7 5.1 + - - -
227A ASN* 1.3 68.5 - - - +
229A PRO* 1.3 70.8 - - + +
231A GLY* 3.1 2.2 + - - +
232A ILE* 2.8 56.7 + - + +
244A ILE* 4.0 6.3 - - + -
267A ALA* 5.7 0.6 - - + +
271A LEU* 3.8 25.1 - - + -
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Residues in contact with PRO 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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227A ASN* 3.0 13.2 - - - +
228A PHE* 1.3 95.6 - - + +
230A HIS* 1.3 60.9 + - + +
232A ILE* 3.2 7.6 + - + -
233A ALA* 2.8 26.0 + - - +
267A ALA* 3.4 35.7 - - + +
270A TRP* 4.0 24.5 - - + +
271A LEU* 3.9 14.4 - - + +
274A LEU* 3.3 16.2 - - + +
151B VAL* 5.7 0.2 - - - -
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 2.8 43.3 + - + +
229A PRO* 1.3 81.0 - - + +
231A GLY* 1.3 62.7 + - - +
233A ALA* 3.0 18.5 + - - +
234A GLN* 3.1 13.7 + - - +
142B GLY 5.4 0.2 - - - -
143B ALA* 4.8 17.8 - - + +
145B SER 5.4 3.4 + - - -
146B GLY* 5.7 5.1 + - - -
149B LYS* 4.9 5.9 + - + -
151B VAL* 3.5 30.4 - - + +
190B ASP* 3.9 26.1 - - + +
191B ILE 5.2 2.2 + - - -
192B LEU* 4.1 18.2 - - + +
194B PRO* 6.4 2.7 - - + -
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Residues in contact with GLY 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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196A ILE* 3.6 26.8 - - - +
221A GLU* 5.5 1.1 - - - -
227A ASN 3.0 13.5 + - - -
228A PHE* 3.1 3.5 + - - -
230A HIS* 1.3 76.0 - - - +
232A ILE* 1.3 61.3 + - - +
234A GLN* 3.3 7.2 + - - +
235A ALA* 3.0 22.0 + - - +
198B HIS* 4.8 15.5 - - - -
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Residues in contact with ILE 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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196A ILE* 4.6 0.2 - - + -
216A PRO* 3.8 24.5 - - + -
228A PHE* 2.8 56.4 + - + +
229A PRO* 3.5 9.0 - - + +
231A GLY* 1.3 73.1 - - - +
233A ALA* 1.3 52.9 + - - +
235A ALA* 3.0 5.2 + - - +
236A LEU* 2.8 40.6 + - + +
241A LEU* 4.0 11.2 - - + -
244A ILE* 3.8 12.3 - - + -
271A LEU* 3.8 9.0 - - + -
274A LEU* 3.7 16.2 - - + -
275A LEU* 4.0 24.0 - - + -
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Residues in contact with ALA 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 PRO 2.8 12.2 + - - +
230A HIS 3.0 9.8 + - - +
232A ILE* 1.3 76.5 - - - +
234A GLN* 1.3 56.3 + - - +
236A LEU* 3.4 5.2 + - - -
237A TRP* 2.8 28.9 + - - +
274A LEU* 3.5 16.5 - - + +
151B VAL* 3.4 30.3 - - + +
152B ARG* 3.7 17.0 - - + +
155B LEU* 4.7 1.6 - - - -
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Residues in contact with GLN 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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200A LEU* 4.4 11.0 - - + +
230A HIS 3.1 11.5 + - - +
231A GLY* 3.8 9.2 - - - +
232A ILE 3.2 0.4 - - - -
233A ALA* 1.3 73.2 - - - +
235A ALA* 1.3 65.6 + - - +
237A TRP* 3.2 8.2 + - + +
238A ALA* 3.0 24.2 + - + +
151B VAL* 5.5 0.4 - - + -
155B LEU* 3.8 25.7 - - + +
193B LEU* 3.8 15.5 + - - +
194B PRO* 5.0 0.2 - - - +
198B HIS* 3.0 61.4 + - + +
201B ALA* 3.9 8.7 - - - +
202B PHE* 3.8 14.6 - - - +
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Residues in contact with ALA 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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196A ILE* 4.3 6.7 - - + -
200A LEU* 4.3 12.5 - - - +
214A VAL* 4.1 25.8 - - + -
216A PRO* 4.8 1.6 - - + -
231A GLY 3.0 13.3 + - - +
232A ILE* 3.0 10.9 + - - +
234A GLN* 1.3 78.2 - - - +
236A LEU* 1.3 56.5 + - - +
238A ALA* 3.4 1.7 + - - +
239A GLY 3.1 6.4 + - - -
240A LYS* 2.9 27.4 + - - -
241A LEU* 4.2 17.5 - - + -
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Residues in contact with LEU 236 (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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232A ILE* 2.8 22.8 + - + +
233A ALA* 3.8 4.0 - - - +
235A ALA* 1.3 73.4 - - - +
237A TRP* 1.3 66.9 + - - +
239A GLY* 3.0 15.3 + - - +
241A LEU* 3.7 30.1 - - + -
274A LEU* 3.8 27.1 - - + +
275A LEU* 5.0 3.8 - - + -
278A ALA* 3.7 28.9 - - + -
280A TRP* 3.8 23.8 - - + -
152B ARG* 4.6 10.7 - - - -
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Residues in contact with TRP 237 (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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233A ALA 2.8 19.2 + - - +
234A GLN* 3.4 16.2 - - + +
236A LEU* 1.3 78.8 - - - +
238A ALA* 1.3 65.7 + - + +
239A GLY 3.4 0.2 + - - -
152B ARG* 3.7 28.7 - - + +
155B LEU* 3.5 37.7 - - + -
156B ASP* 2.9 28.3 + - - +
159B LYS* 4.0 16.2 - - + -
201B ALA 5.7 0.2 - - - -
202B PHE* 3.6 43.1 - + - -
205B ARG* 3.0 74.5 + - + +
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Residues in contact with ALA 238 (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* 4.9 9.9 - - + -
234A GLN* 3.0 16.6 + - + +
235A ALA 3.9 3.4 - - - +
237A TRP* 1.3 79.2 - - + +
239A GLY* 1.3 64.5 + - - +
240A LYS* 3.7 22.5 - - + +
205B ARG* 4.1 23.2 - - + +
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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