Contacts of the helix formed by residues 227 - 238 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C GLU* 5.4 0.2 - - - -
226C LEU* 1.3 72.3 - - - +
228C PHE* 1.3 62.5 + - - +
229C PRO* 3.1 18.8 - - - +
230C HIS* 2.8 55.8 + - + +
231C GLY* 3.1 18.2 + - - -
267C ALA* 6.4 0.2 - - - -
190D ASP* 3.1 39.2 + - + +
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Residues in contact with PHE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ILE* 4.4 0.7 - - + -
216C PRO* 3.6 26.0 - - + -
217C GLU 3.2 22.2 - - - -
218C VAL* 3.5 44.0 - - + +
221C GLU* 3.4 30.5 - - + -
222C GLN* 4.8 11.8 + - + +
226C LEU 3.3 5.7 + - - -
227C ASN* 1.3 71.1 - - - +
229C PRO* 1.3 75.5 - - + +
231C GLY* 3.0 3.9 + - - -
232C ILE* 2.8 54.7 + - + +
244C ILE* 4.1 6.3 - - + -
267C ALA* 5.7 0.8 - - + +
271C LEU* 3.8 22.2 - - + -
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Residues in contact with PRO 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ASN* 3.1 13.9 - - - +
228C PHE* 1.3 95.9 - - + +
230C HIS* 1.3 59.5 + - + +
232C ILE* 3.2 7.8 + - + -
233C ALA* 2.9 26.4 + - - +
267C ALA* 3.5 37.0 - - + +
270C TRP* 4.0 22.7 - - + +
271C LEU* 3.9 13.7 - - + +
274C LEU* 3.3 16.0 - - + +
151D VAL* 5.4 0.4 - - - -
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Residues in contact with HIS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C ASN* 2.8 39.7 + - + +
229C PRO* 1.3 75.5 - - + +
231C GLY* 1.3 64.5 + - - +
233C ALA* 3.1 5.5 + - - +
234C GLN* 3.0 19.8 + - - +
142D GLY 5.2 0.2 - - - -
143D ALA* 4.8 16.7 - - + +
145D SER 5.6 2.0 + - - -
146D GLY* 5.8 4.0 + - - -
149D LYS* 5.1 5.2 + - + +
151D VAL* 3.3 35.0 - - + +
190D ASP* 3.6 36.6 - - + +
191D ILE 5.2 2.2 + - - -
192D LEU* 4.1 23.1 - - + +
194D PRO* 6.4 2.7 - - + -
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Residues in contact with GLY 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 3.8 23.8 - - - +
227C ASN 3.1 7.0 + - - -
228C PHE* 3.0 7.1 + - - -
230C HIS* 1.3 78.2 - - - +
232C ILE* 1.3 61.2 + - - +
234C GLN* 3.3 8.7 + - - +
235C ALA* 3.0 21.8 + - - +
198D HIS* 4.7 16.4 - - - -
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.1 0.2 - - - +
216C PRO* 3.8 22.4 - - + -
228C PHE* 2.8 56.5 + - + +
229C PRO* 3.5 8.1 - - + +
231C GLY* 1.3 75.1 - - - +
233C ALA* 1.3 56.8 + - - +
235C ALA* 3.1 6.6 + - - +
236C LEU* 2.9 29.3 + - + +
241C LEU* 3.9 22.7 - - + -
244C ILE* 3.8 12.8 - - + -
271C LEU* 3.9 7.2 - - + -
274C LEU* 3.5 18.2 - - + -
275C LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C PRO 2.9 13.0 + - - +
230C HIS 3.1 10.1 + - - +
232C ILE* 1.3 76.9 - - - +
234C GLN* 1.3 51.8 + - - +
236C LEU* 3.2 6.8 + - - +
237C TRP* 2.7 36.8 + - - +
274C LEU* 3.6 17.4 - - + +
151D VAL* 3.5 28.7 - - + +
152D ARG* 3.7 14.6 - - + +
155D LEU* 4.7 0.7 - - - -
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Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 6.0 0.2 - - + -
200C LEU* 4.3 13.2 - - + +
230C HIS 3.0 11.3 + - - +
231C GLY* 3.3 9.6 + - - +
233C ALA* 1.3 75.8 - - - +
235C ALA* 1.3 65.1 + - - +
237C TRP* 3.3 9.5 - - + +
238C ALA* 3.2 20.1 + - + +
151D VAL* 5.4 0.9 - - + -
155D LEU* 3.8 28.5 - - + +
193D LEU* 3.9 18.5 + - - +
194D PRO* 5.0 0.2 - - - +
198D HIS* 3.2 52.9 + - + +
201D ALA* 3.7 18.6 - - - +
202D PHE* 3.8 8.7 - - - +
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.4 5.8 - - + -
200C LEU* 4.4 13.1 - - + +
214C VAL* 4.1 25.6 - - + -
216C PRO* 5.1 0.4 - - + -
231C GLY 3.0 13.5 + - - +
232C ILE* 3.1 11.4 + - - +
234C GLN* 1.3 77.3 - - - +
236C LEU* 1.3 57.8 + - - +
238C ALA* 3.1 5.4 + - - +
239C GLY 2.9 20.8 + - - -
240C LYS* 3.0 11.8 + - - -
241C LEU* 4.2 18.2 - - + +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ILE* 2.9 24.1 + - + +
233C ALA 3.6 5.8 - - - +
235C ALA* 1.3 72.5 - - - +
237C TRP* 1.3 59.9 + - - +
239C GLY* 2.8 24.5 + - - +
241C LEU* 3.5 33.4 - - + -
274C LEU* 4.0 26.0 - - + +
275C LEU* 4.7 5.2 - - + -
278C ALA* 3.9 26.7 - - + -
280C TRP* 3.6 20.9 - - + -
152D ARG* 4.3 16.0 + - - +
344H ALA* 4.7 4.0 - - - +
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Residues in contact with TRP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ALA 2.7 20.4 + - - +
234C GLN* 3.3 21.3 - - + +
236C LEU* 1.3 73.3 - - - +
238C ALA* 1.3 59.3 + - + +
239C GLY 3.3 0.4 + - - -
152D ARG* 3.7 29.8 - - + +
155D LEU* 3.6 38.5 - - + +
156D ASP* 2.7 28.2 + - - -
159D LYS* 4.1 15.7 - - + -
201D ALA 5.5 0.2 - - - -
202D PHE* 3.6 40.4 - + - -
205D ARG* 3.5 68.6 + - + +
344H ALA* 4.0 8.3 - - - +
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 5.4 6.1 - - + -
234C GLN* 3.2 8.4 + - + +
235C ALA* 3.1 8.5 + - - +
236C LEU 3.1 0.4 - - - -
237C TRP* 1.3 80.1 - - + +
239C GLY* 1.3 63.0 + - - +
240C LYS* 3.5 23.7 + - + +
205D ARG* 3.6 29.8 + - - +
344H ALA 3.7 16.5 - - - +
345H ASP* 3.8 5.0 - - - -
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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