Contacts of the helix formed by residues 227 - 239 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226E LEU* 1.3 74.5 - - - +
228E PHE* 1.3 63.9 + - - +
229E PRO* 2.9 33.3 - - - +
230E HIS* 3.0 42.9 + - + +
231E GLY* 3.1 18.2 + - - -
190F ASP* 3.1 37.4 + - - +
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Residues in contact with PHE 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ILE* 5.6 0.7 - - + -
216E PRO* 3.6 26.9 - - + -
217E GLU 3.2 23.1 - - - -
218E VAL* 3.4 40.6 - - + +
221E GLU* 3.3 28.9 - - + -
222E GLN* 4.6 15.8 + - + +
226E LEU 3.4 5.4 + - - -
227E ASN* 1.3 68.6 - - - +
229E PRO* 1.3 75.3 - - + +
231E GLY* 3.1 2.5 + - - +
232E ILE* 2.9 51.9 + - + +
244E ILE* 4.0 7.0 - - + -
267E ALA* 5.6 1.5 - - + +
271E LEU* 3.8 25.8 - - + -
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Residues in contact with PRO 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E ASN* 2.9 18.4 - - - +
228E PHE* 1.3 91.6 - - + +
230E HIS* 1.3 63.8 + - + +
232E ILE* 4.3 6.7 - - + -
233E ALA* 3.0 19.4 + - - +
267E ALA* 3.5 35.4 - - + +
270E TRP* 3.9 20.2 - - + +
271E LEU* 3.6 19.5 - - + +
274E LEU* 3.1 16.7 - - + +
151F VAL* 5.0 0.6 - - - +
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Residues in contact with HIS 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E ASN* 3.0 37.2 + - + +
229E PRO* 1.3 79.7 - - + +
231E GLY* 1.3 63.6 - - - +
233E ALA* 3.1 4.7 + - - +
234E GLN* 3.0 21.7 + - - +
142F GLY 5.3 0.2 - - - -
143F ALA* 4.9 16.1 - - + +
145F SER 5.6 2.4 + - - -
146F GLY* 6.1 2.2 - - - -
149F LYS* 5.4 5.1 + - + +
151F VAL* 3.5 30.1 - - + +
190F ASP* 3.5 38.5 - - + +
191F ILE 5.1 3.6 + - - -
192F LEU* 4.2 21.2 - - + +
194F PRO* 6.4 3.4 - - + -
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Residues in contact with GLY 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ILE* 3.9 24.2 - - - +
221E GLU* 5.6 1.6 - - - -
227E ASN 3.1 11.1 + - - -
228E PHE* 3.7 3.1 - - - -
230E HIS* 1.3 79.1 - - - +
232E ILE* 1.3 62.5 + - - +
234E GLN* 3.4 7.3 + - - +
235E ALA* 3.1 21.7 + - - +
198F HIS* 4.8 14.4 - - - -
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Residues in contact with ILE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ILE* 5.6 0.2 - - + -
216E PRO* 3.7 23.8 - - + -
228E PHE* 2.9 58.1 + - + +
229E PRO 3.7 5.2 - - - +
231E GLY* 1.3 74.0 - - - +
233E ALA* 1.3 62.1 + - - +
235E ALA* 3.4 5.2 + - - +
236E LEU* 2.9 38.5 + - + +
241E LEU* 4.0 16.6 - - + +
244E ILE* 4.0 9.6 - - + -
271E LEU* 3.7 10.5 - - + -
274E LEU* 3.8 14.8 - - + -
275E LEU* 4.2 11.2 - - + -
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Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E PRO 3.0 13.3 + - - +
230E HIS 3.4 9.2 - - - +
232E ILE* 1.3 78.3 - - - +
234E GLN* 1.3 51.5 + - - +
236E LEU* 3.1 7.0 + - - +
237E TRP* 2.7 37.3 + - - +
274E LEU* 3.6 18.5 - - + +
151F VAL* 3.4 28.9 - - + -
152F ARG* 3.6 12.7 - - + +
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Residues in contact with GLN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ILE* 5.9 0.2 - - + -
200E LEU* 4.1 16.1 - - + +
230E HIS 3.0 12.7 + - - +
231E GLY* 3.8 8.7 - - - +
232E ILE 3.3 0.2 - - - -
233E ALA* 1.3 77.8 - - - +
235E ALA* 1.3 60.6 + - - +
237E TRP* 3.3 8.5 - - + +
238E ALA* 3.2 21.1 + - - +
151F VAL* 5.1 0.7 - - + -
155F LEU* 3.6 29.4 - - + +
193F LEU* 4.3 11.3 + - - +
194F PRO* 5.1 0.2 - - - +
198F HIS* 3.1 55.2 + - + +
201F ALA* 4.1 6.1 - - - +
202F PHE* 4.0 18.6 - - - +
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Residues in contact with ALA 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ILE* 4.2 6.7 - - + -
200E LEU* 4.3 14.1 - - + -
214E VAL* 4.0 27.1 - - + -
216E PRO* 5.2 0.7 - - + -
231E GLY 3.1 14.0 + - - +
232E ILE* 3.7 10.1 - - - +
234E GLN* 1.3 76.7 - - - +
236E LEU* 1.3 58.0 + - - +
238E ALA* 3.0 4.4 + - - +
239E GLY 2.9 22.0 + - - -
240E LYS 2.9 11.6 + - - -
241E LEU* 4.4 14.1 - - + +
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Residues in contact with LEU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E ILE* 2.9 39.2 + - + +
233E ALA* 3.4 5.6 - - - +
235E ALA* 1.3 79.1 - - - +
237E TRP* 1.3 58.0 + - - +
239E GLY* 2.9 19.4 + - - +
241E LEU* 3.4 31.4 - - + -
274E LEU* 4.0 21.3 - - + -
275E LEU* 4.6 5.6 - - + -
278E ALA* 4.1 21.3 - - + -
280E TRP* 3.9 17.7 - - + -
152F ARG* 4.1 19.4 + - - +
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Residues in contact with TRP 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ALA 2.7 20.2 + - - +
234E GLN* 3.3 15.0 - - - +
236E LEU* 1.3 73.5 - - - +
238E ALA* 1.3 59.1 + - + +
152F ARG* 3.6 33.5 + - + +
155F LEU* 3.5 41.3 - - + +
156F ASP* 2.6 29.6 + - - -
159F LYS* 4.0 17.9 - - + -
201F ALA 5.5 0.4 - - - -
202F PHE* 3.7 39.5 - + - -
205F ARG* 3.0 71.3 + - + +
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Residues in contact with ALA 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E LEU* 5.1 6.5 - - + -
234E GLN* 3.2 8.4 + - + +
235E ALA* 3.0 10.5 + - - +
237E TRP* 1.3 79.8 - - + +
239E GLY* 1.3 61.5 + - - +
240E LYS* 3.5 21.5 + - + +
205F ARG* 3.8 31.0 + - - +
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Residues in contact with GLY 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ALA 2.9 3.2 + - - -
236E LEU* 2.9 16.4 + - - -
237E TRP 3.3 0.4 + - - -
238E ALA* 1.3 80.9 - - - +
240E LYS* 1.3 64.2 + - - +
241E LEU 3.6 2.9 + - - -
242E PHE* 3.9 9.9 - - - -
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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