Contacts of the helix formed by residues 217 - 223 (chain H) 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 GLU 217 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H GLU* 4.1 2.2 - - - +
182H PRO* 5.3 0.8 + - - +
215H ASN 3.9 0.4 + - - -
216H PRO* 1.3 74.7 - - - +
218H VAL* 1.3 71.1 + - - +
219H ALA* 3.6 3.7 - - - +
220H HIS* 3.0 38.7 + - + +
221H GLU* 3.4 16.8 + - - +
228H PHE* 3.2 12.7 - - - -
245H ASP* 3.3 19.4 - - + +
247H ASN* 2.8 24.0 + - - +
255H ASP* 3.5 1.2 - - - +
287H ASP* 2.8 11.0 - - - +
2001H CO 2.3 25.2 + - - -
2002H MG 2.4 30.0 - - - -
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Residues in contact with VAL 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H GLU* 1.3 72.3 - - - +
219H ALA* 1.3 65.9 + - - +
221H GLU 3.7 0.5 + - - -
222H GLN* 3.3 46.7 + - - +
228H PHE* 3.4 38.2 - - + -
245H ASP 3.2 13.3 + - - +
246H LEU* 4.2 3.6 - - + -
247H ASN* 3.2 36.6 - - - +
248H GLY* 4.6 2.5 - - - -
260H PHE* 4.5 4.9 - - + -
264H ASP 6.1 0.7 - - - +
267H ALA* 6.1 1.3 - - + -
268H ALA* 6.5 1.1 - - - -
271H LEU* 4.0 11.4 - - + -
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H GLU* 3.4 6.2 - - - +
218H VAL* 1.3 76.4 - - - +
220H HIS* 1.3 63.9 + - - +
222H GLN* 3.1 4.0 + - - +
223H MET* 2.9 26.9 + - - +
247H ASN* 2.9 31.8 + - - +
248H GLY 4.2 0.9 - - - +
249H GLN* 3.6 36.9 - - + +
255H ASP* 3.8 10.8 - - - +
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Residues in contact with HIS 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H TRP* 4.1 9.1 - + - -
181H GLU* 2.7 32.1 + - + +
182H PRO 2.7 29.6 + - - +
183H LYS* 3.6 38.3 + - + +
184H PRO* 3.2 23.2 - - - +
217H GLU* 3.0 41.0 + - + +
219H ALA* 1.3 74.4 - - - +
221H GLU* 1.3 68.2 + - - +
223H MET* 3.1 15.5 + - - -
224H ALA* 4.7 0.3 - - - +
255H ASP* 3.6 7.7 + - - -
2001H CO 3.4 6.7 + - - -
2002H MG 4.0 0.4 - - - -
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Residues in contact with GLU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G HIS* 4.6 3.5 + - - -
182H PRO* 3.8 9.0 - - - +
184H PRO* 5.4 0.2 - - - -
194H PRO 4.2 3.0 - - - +
195H THR* 3.4 19.8 - - - -
196H ILE* 3.2 52.7 + - + +
216H PRO* 5.1 1.0 - - + +
217H GLU 3.4 6.6 + - - +
220H HIS* 1.3 80.3 - - - +
222H GLN* 1.3 57.6 + - - +
224H ALA* 3.0 18.6 + - - +
226H LEU* 3.2 37.8 + - + +
228H PHE* 3.6 38.1 - - + -
231H GLY* 5.7 1.0 - - - -
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Residues in contact with GLN 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H VAL* 3.3 35.5 + - - +
219H ALA 3.1 6.3 + - - +
221H GLU* 1.3 73.7 - - - +
223H MET* 1.3 56.4 + - - +
224H ALA 2.9 5.6 - - - -
225H GLY* 2.9 20.2 + - - +
226H LEU 4.0 16.6 - - - +
228H PHE* 4.6 8.7 + - + +
249H GLN* 3.1 44.5 + - + +
251H GLY* 3.9 10.7 - - - +
252H ILE* 3.7 8.7 - - - +
264H ASP* 3.7 24.0 - - - +
267H ALA* 3.8 13.2 - - - +
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Residues in contact with MET 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ILE 4.9 0.3 - - - +
224G ALA 4.5 1.9 - - - +
225G GLY* 5.8 0.9 - - - -
183H LYS* 3.8 17.5 - - - -
184H PRO* 3.6 12.2 - - + +
185H ASN* 3.6 41.1 + - - +
186H GLU* 3.5 23.3 - - + +
219H ALA 2.9 21.3 + - - +
220H HIS* 3.1 16.3 + - - +
222H GLN* 1.3 77.0 - - - +
224H ALA* 1.3 56.2 + - - +
225H GLY 3.4 1.1 - - - -
249H GLN* 4.4 10.3 - - - +
251H GLY 4.6 0.2 - - - -
252H ILE* 3.4 29.1 - - - +
253H LYS 3.5 25.4 - - - +
254H TYR* 4.1 1.3 - - - -
255H ASP* 3.6 16.2 - - - +
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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