Contacts of the helix formed by residues 227 - 238 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C GLY* 6.4 0.2 - - - -
190C ASP* 2.6 39.4 + - + +
221D GLU* 5.6 0.2 - - - -
226D LEU* 1.3 75.9 - - - +
228D PHE* 1.3 63.2 + - - +
229D PRO* 2.9 29.0 - - - +
230D HIS* 3.0 41.5 + - + +
231D GLY* 3.0 19.4 + - - -
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Residues in contact with PHE 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ILE* 4.4 0.7 - - + -
216D PRO* 3.8 17.9 - - + -
217D GLU 3.5 18.6 - - - -
218D VAL* 3.5 33.9 - - + -
221D GLU* 3.8 22.4 - - + -
222D GLN* 4.4 21.0 - - + +
226D LEU 3.5 5.8 + - - -
227D ASN* 1.3 69.1 - - - +
229D PRO* 1.3 68.6 - - + +
231D GLY* 3.0 2.9 + - - -
232D ILE* 2.8 49.4 + - + +
244D ILE* 3.8 14.1 - - + -
267D ALA* 5.5 2.8 - - + +
271D LEU* 3.4 46.0 - - + -
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Residues in contact with PRO 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 5.3 0.2 - - - -
227D ASN* 2.9 23.3 - - - +
228D PHE* 1.3 92.1 - - + +
230D HIS* 1.3 59.3 + - + -
232D ILE* 4.2 7.6 - - + -
233D ALA* 2.7 28.5 + - - +
267D ALA* 4.2 20.4 - - + +
270D TRP* 4.0 26.9 - - + +
271D LEU* 4.1 23.1 - - + +
274D LEU* 3.3 11.7 - - + +
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Residues in contact with HIS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ALA* 4.8 18.2 - - + +
145C SER 5.5 2.8 + - - -
146C GLY* 5.8 5.3 + - - -
149C LYS* 5.3 4.4 + - + +
151C VAL* 3.5 30.4 - - + +
190C ASP* 3.5 29.9 + - + +
191C ILE 5.1 3.4 + - - -
192C LEU* 4.5 14.3 - - + +
194C PRO* 6.5 1.6 - - + -
227D ASN* 3.0 48.9 + - + +
229D PRO* 1.3 77.7 - - + +
231D GLY* 1.3 67.5 + - - +
233D ALA* 3.0 8.0 + - - +
234D GLN* 3.0 21.5 + - - +
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Residues in contact with GLY 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C HIS* 4.7 17.5 - - - -
196D ILE* 3.9 23.2 - - - +
221D GLU* 5.4 1.8 - - - -
227D ASN 3.0 13.2 + - - -
228D PHE* 3.0 3.3 + - - -
230D HIS* 1.3 77.5 - - - +
232D ILE* 1.3 55.9 + - - +
234D GLN* 2.9 23.1 + - - +
235D ALA* 3.1 10.9 + - - +
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Residues in contact with ILE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ILE* 4.0 0.4 - - + +
216D PRO* 3.6 37.5 - - + -
228D PHE* 2.8 45.1 + - + +
229D PRO* 3.8 4.7 - - + +
231D GLY* 1.3 71.4 - - - +
233D ALA* 1.3 65.9 + - - +
235D ALA* 3.0 6.3 + - + +
236D LEU* 3.0 31.5 + - + +
241D LEU* 4.0 19.3 - - + -
244D ILE* 3.9 11.2 - - + -
271D LEU* 4.1 6.1 - - + -
274D LEU* 3.5 18.4 - - + -
275D LEU* 4.4 9.9 - - + -
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 3.2 36.3 - - + +
152C ARG* 3.7 10.4 - - + +
229D PRO 2.7 22.6 + - - +
230D HIS 3.0 3.8 + - - +
232D ILE* 1.3 73.0 - - - +
234D GLN* 1.3 59.3 + - - +
236D LEU* 3.3 4.7 + - - +
237D TRP* 2.9 29.8 + - - +
274D LEU* 3.8 19.7 - - + -
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Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 5.4 0.7 - - + -
155C LEU* 3.8 25.3 - - + +
193C LEU* 3.9 17.2 + - - +
194C PRO* 4.9 0.3 - - - +
198C HIS* 3.1 58.9 + - + +
201C ALA* 3.8 15.8 - - - +
202C PHE* 4.0 7.1 - - - +
196D ILE* 5.6 0.2 - - + -
200D LEU* 4.3 11.8 - - + +
230D HIS 3.0 8.9 + - - +
231D GLY* 2.9 12.1 + - - +
233D ALA* 1.3 78.9 - - - +
235D ALA* 1.3 60.2 + - - +
237D TRP* 3.5 8.9 + - + +
238D ALA* 3.3 21.0 + - + +
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Residues in contact with ALA 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ILE* 4.3 7.2 - - + -
200D LEU* 4.3 11.2 - - - +
214D VAL* 3.9 27.1 - - + -
216D PRO* 5.1 0.9 - - + -
231D GLY 3.1 9.6 + - - +
232D ILE* 3.0 14.2 + - - +
234D GLN* 1.3 74.6 - - - +
236D LEU* 1.3 64.7 + - - +
238D ALA* 3.4 1.7 + - - -
239D GLY 3.1 2.4 + - - -
240D LYS* 2.8 29.1 + - - +
241D LEU* 3.6 16.2 + - + -
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ARG* 4.3 11.2 - - - +
232D ILE* 3.0 22.9 + - + +
233D ALA* 3.7 6.1 - - - +
235D ALA* 1.3 71.4 - - - +
237D TRP* 1.3 67.5 + - - +
238D ALA 3.0 2.5 - - - -
239D GLY* 2.9 16.7 + - - +
241D LEU* 3.8 27.8 - - + -
274D LEU* 3.9 31.2 - - + +
275D LEU* 4.9 4.5 - - + -
278D ALA* 3.9 23.3 - - + -
280D TRP* 3.8 18.6 - - + -
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Residues in contact with TRP 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ARG* 3.7 28.2 - - + +
155C LEU* 3.6 39.7 - - + -
156C ASP* 2.7 31.6 + - - +
159C LYS* 4.0 21.3 - - + -
201C ALA 5.8 0.2 - - - -
202C PHE* 3.4 39.9 - + - -
205C ARG* 3.8 38.3 + - + -
233D ALA 2.9 16.4 + - - +
234D GLN* 3.6 13.2 - - + +
235D ALA 3.3 0.2 - - - -
236D LEU* 1.3 79.3 - - - +
238D ALA* 1.3 62.2 + - + +
239D GLY 3.7 0.2 + - - -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ARG* 2.9 52.6 + - + +
200D LEU* 5.0 7.6 - - + -
234D GLN* 3.3 14.0 + - + +
235D ALA* 3.4 4.0 + - - +
236D LEU 3.0 0.6 - - - -
237D TRP* 1.3 83.1 - - + +
239D GLY* 1.3 63.8 + - - +
240D LYS* 3.2 12.4 + - + +
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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