Contacts of the helix formed by residues 227 - 239 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A GLY* 6.4 0.6 - - - -
190A ASP* 3.1 39.4 + - + +
221B GLU* 5.6 0.2 - - - +
226B LEU* 1.3 73.8 - - - +
228B PHE* 1.3 62.8 + - - +
229B PRO* 3.1 14.7 - - - +
230B HIS* 2.8 59.1 + - + +
231B GLY* 3.1 17.3 + - - -
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ILE* 4.3 0.9 - - + -
216B PRO* 3.7 21.5 - - + -
217B GLU 3.3 19.3 - - - -
218B VAL* 3.4 45.5 - - + +
221B GLU* 3.6 25.1 - - + -
222B GLN* 4.6 16.0 + - + +
226B LEU 3.3 5.8 + - - -
227B ASN* 1.3 68.5 - - - +
229B PRO* 1.3 76.5 - - + +
231B GLY* 3.1 4.0 + - - +
232B ILE* 2.9 46.3 + - + +
244B ILE* 3.8 11.9 - - + -
267B ALA* 5.4 1.9 - - + +
271B LEU* 3.5 27.6 - - + -
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Residues in contact with PRO 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 5.5 0.2 - - - -
227B ASN* 3.1 12.8 - - - +
228B PHE* 1.3 96.1 - - + +
230B HIS* 1.3 60.1 + - + +
232B ILE* 3.4 5.3 + - + -
233B ALA* 3.0 25.3 + - - +
267B ALA* 3.4 36.3 - - + +
270B TRP* 4.1 17.7 - - + +
271B LEU* 3.8 23.6 - - + +
274B LEU* 3.3 15.1 - - + +
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 5.3 0.2 - - - -
143A ALA* 4.9 16.7 - - + +
145A SER 5.5 3.2 + - - -
146A GLY* 5.7 5.0 + - - -
149A LYS* 5.2 5.7 + - + +
151A VAL* 3.5 35.6 - - + +
190A ASP* 3.7 26.9 + - + +
191A ILE 5.2 3.2 + - - -
192A LEU* 4.2 20.1 - - + +
194A PRO* 6.5 1.1 - - + -
227B ASN* 2.8 51.7 + - + +
228B PHE 3.1 0.2 - - - -
229B PRO* 1.3 75.6 - - + +
231B GLY* 1.3 64.4 + - - +
233B ALA* 3.1 13.2 + - - +
234B GLN* 3.1 12.1 + - - +
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Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A HIS* 4.7 16.6 - - - -
196B ILE* 3.8 28.3 - - - +
221B GLU* 5.6 0.9 - - - -
227B ASN 3.1 7.3 + - - -
228B PHE* 3.1 7.1 + - - -
230B HIS* 1.3 79.5 - - - +
232B ILE* 1.3 61.3 + - - +
234B GLN* 3.2 8.8 + - - +
235B ALA 3.1 16.6 + - - -
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ILE* 4.3 0.4 - - + -
216B PRO* 3.8 26.0 - - + -
228B PHE* 2.9 54.7 + - + +
229B PRO 3.7 4.7 - - - +
231B GLY* 1.3 71.7 - - - +
233B ALA* 1.3 56.7 + - - +
235B ALA* 2.9 4.0 + - - +
236B LEU* 2.7 38.8 + - + +
241B LEU* 3.8 27.8 - - + -
244B ILE* 3.8 10.5 - - + -
271B LEU* 3.8 8.5 - - + -
274B LEU* 3.9 14.6 - - + -
275B LEU* 4.1 10.3 - - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.4 30.3 - - + -
152A ARG* 3.6 13.7 - - + +
155A LEU* 4.5 0.9 - - - -
229B PRO 3.0 13.6 + - - +
230B HIS 3.2 10.1 - - - +
232B ILE* 1.3 77.5 - - - +
234B GLN* 1.3 56.5 + - - +
236B LEU* 3.3 6.2 + - - +
237B TRP* 2.8 30.6 + - - +
274B LEU* 3.6 15.9 - - + +
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Residues in contact with GLN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 5.4 0.4 - - + -
155A LEU* 3.7 25.0 - - + +
193A LEU* 3.9 18.1 + - - +
194A PRO* 4.9 0.3 - - - +
198A HIS* 3.0 59.5 + - + +
201A ALA* 3.8 16.4 - - - +
202A PHE* 3.9 8.1 - - - +
196B ILE* 5.6 0.2 - - + -
200B LEU* 4.4 10.7 - - + +
230B HIS 3.1 11.9 + - - +
231B GLY* 3.2 9.6 + - - +
233B ALA* 1.3 72.8 - - - +
235B ALA* 1.3 64.4 + - - +
237B TRP* 3.5 9.4 + - + +
238B ALA* 3.2 22.7 + - + +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ILE* 4.3 7.4 - - + -
200B LEU* 4.2 12.5 - - + +
214B VAL* 4.1 25.8 - - + -
216B PRO* 5.1 0.9 - - + -
231B GLY 3.1 10.5 + - - +
232B ILE* 2.9 13.3 + - - +
234B GLN* 1.3 74.0 - - - +
236B LEU* 1.3 61.2 + - - +
238B ALA* 3.3 3.0 + - - +
239B GLY 3.0 7.1 + - - -
240B LYS 2.8 27.8 + - - -
241B LEU* 4.2 15.9 - - + +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 4.1 17.8 + - - +
232B ILE* 2.7 24.1 + - + +
233B ALA* 3.6 4.3 - - - +
235B ALA* 1.3 79.7 - - - +
237B TRP* 1.3 57.2 + - - +
239B GLY* 2.9 20.6 + - - +
241B LEU* 3.7 28.9 - - + +
274B LEU* 3.8 32.3 - - + +
275B LEU* 4.6 5.4 - - + -
278B ALA* 4.0 22.2 - - + -
280B TRP* 3.8 22.2 - - + -
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 3.5 37.8 + - + +
155A LEU* 3.4 40.1 - - + +
156A ASP* 2.8 25.5 + - - -
159A LYS* 3.9 16.8 - - + -
202A PHE* 3.7 38.1 - + - -
205A ARG* 3.4 71.4 + - + -
233B ALA 2.8 18.6 + - - +
234B GLN* 3.6 13.5 - - + +
235B ALA 3.3 0.2 - - - -
236B LEU* 1.3 76.7 - - - +
238B ALA* 1.3 60.1 + - + +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG* 3.5 31.0 + - - +
200B LEU* 4.8 8.5 - - + -
234B GLN 3.2 16.4 + - - +
235B ALA* 3.7 5.6 - - - +
236B LEU 3.1 0.6 - - - -
237B TRP* 1.3 77.4 - - + +
239B GLY* 1.3 61.4 + - - +
240B LYS* 3.5 22.1 + - + +
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Residues in contact with GLY 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ALA 3.0 0.4 + - - -
236B LEU* 2.9 17.8 + - - -
237B TRP 3.3 0.6 + - - -
238B ALA* 1.3 79.6 - - - +
240B LYS* 1.3 61.1 + - - +
241B LEU 3.6 2.6 + - - -
242B PHE* 3.6 15.4 - - - -
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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