Contacts of the helix formed by residues 217 - 223 (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 GLU 217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D GLU* 2.9 14.5 - - - +
182D PRO 5.3 0.6 + - - -
215D ASN 3.7 0.4 + - - -
216D PRO* 1.3 74.6 - - - +
218D VAL* 1.3 73.3 + - - +
219D ALA* 3.5 4.6 - - - +
220D HIS* 3.0 37.0 + - + +
221D GLU* 3.3 10.1 + - - +
228D PHE* 3.5 8.1 - - - -
245D ASP* 3.3 19.0 - - + +
247D ASN* 2.6 26.9 + - - +
255D ASP* 3.4 0.9 - - - +
257D ASP* 3.1 0.3 - - - +
287D ASP* 3.6 3.2 - - - +
2001D CO 2.2 26.9 + - - -
2002D MG 2.3 31.4 - - - -
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Residues in contact with VAL 218 (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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217D GLU* 1.3 72.1 - - - +
219D ALA* 1.3 64.9 + - - +
221D GLU* 3.5 1.0 + - - -
222D GLN* 3.2 50.6 + - - +
228D PHE* 3.5 36.9 - - + -
245D ASP 3.2 9.1 + - - +
246D LEU* 3.9 4.9 - - + -
247D ASN* 3.2 43.1 - - - +
248D GLY* 4.6 2.0 - - - -
260D PHE* 4.8 3.1 - - + -
267D ALA* 6.2 0.7 - - + -
268D ALA* 6.4 3.1 - - + -
271D LEU* 4.1 11.2 - - + -
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Residues in contact with ALA 219 (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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217D GLU* 3.3 14.3 - - - +
218D VAL* 1.3 72.8 - - - +
220D HIS* 1.3 64.0 + - - +
222D GLN* 3.1 3.5 + - - +
223D MET* 3.0 28.0 + - - +
247D ASN* 2.9 25.1 + - - +
248D GLY 4.2 1.8 - - - +
249D GLN* 3.4 35.7 - - + +
255D ASP* 3.8 11.2 - - - +
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Residues in contact with HIS 220 (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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137D TRP* 3.9 10.3 - + - -
181D GLU* 2.9 32.5 + - + +
182D PRO 2.9 27.6 + - - +
183D LYS* 3.4 32.4 + - + +
184D PRO* 3.2 22.3 - - - +
217D GLU* 3.0 42.8 + - + +
219D ALA* 1.3 75.5 - - - +
221D GLU* 1.3 65.3 + - - +
223D MET* 3.0 16.9 + - - +
255D ASP* 3.2 13.2 + - - -
2001D CO 3.2 8.5 + - - -
2002D MG 4.1 1.5 - - - -
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Residues in contact with GLU 221 (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 2.8 + - - -
182D PRO* 4.0 12.8 - - - +
184D PRO* 5.2 0.9 - - - -
194D PRO 4.3 2.0 - - - +
195D THR* 3.5 19.3 - - - -
196D ILE* 3.0 63.4 + - + +
216D PRO* 4.9 1.6 - - + +
217D GLU 3.3 6.7 + - - +
220D HIS* 1.3 75.7 - - - +
222D GLN* 1.3 62.7 + - - +
224D ALA* 3.1 13.6 + - - +
226D LEU* 3.3 37.0 + - + +
228D PHE* 3.8 28.7 - - + -
231D GLY* 5.4 1.6 - - - -
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Residues in contact with GLN 222 (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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218D VAL* 3.2 35.8 + - - +
219D ALA 3.1 6.1 + - - +
221D GLU* 1.3 72.9 - - - +
223D MET* 1.3 57.4 + - - +
224D ALA 3.0 5.4 - - - -
225D GLY* 2.9 19.2 + - - +
226D LEU 4.2 16.2 - - - +
228D PHE* 4.4 11.4 - - + +
249D GLN* 3.2 43.2 + - + +
251D GLY* 4.1 10.1 - - - +
252D ILE* 3.8 9.0 - - - +
264D ASP* 3.9 23.5 - - - +
267D ALA* 3.9 13.3 - - - +
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Residues in contact with MET 223 (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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252A ILE 5.0 0.5 - - - +
253A LYS* 6.2 0.4 - - + -
224C ALA 4.8 0.9 - - - +
183D LYS* 4.0 13.0 - - - -
184D PRO* 3.6 12.1 - - + +
185D ASN* 3.5 43.0 + - - +
186D GLU* 3.9 7.2 - - + +
219D ALA 3.0 20.1 + - - +
220D HIS* 3.0 15.6 + - - +
222D GLN* 1.3 76.2 - - - +
224D ALA* 1.3 57.0 + - - +
225D GLY 3.4 0.9 - - - -
249D GLN* 4.0 8.5 - - - +
252D ILE* 3.4 26.5 - - - +
253D LYS 3.5 26.0 - - - +
254D TYR* 4.2 2.7 - - - -
255D ASP* 3.6 32.5 - - - +
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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