Contacts of the helix formed by residues 217 - 223 (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 GLU 217 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E GLU* 3.4 4.4 - - - +
182E PRO* 5.4 0.8 + - - +
215E ASN 3.7 0.8 + - - -
216E PRO* 1.3 74.3 - - - +
218E VAL* 1.3 70.0 + - - +
219E ALA* 3.5 5.4 - - - +
220E HIS* 3.2 40.7 + - + +
221E GLU* 3.4 9.0 + - - +
228E PHE* 3.2 10.9 - - - -
245E ASP* 3.3 20.3 - - + +
247E ASN* 2.7 28.9 + - - +
255E ASP* 3.3 1.4 - - - +
257E ASP* 3.1 0.7 - - - +
287E ASP* 3.4 4.6 - - - +
2001E CO 2.2 29.3 + - - -
2002E MG 2.3 31.5 - - - -
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Residues in contact with VAL 218 (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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217E GLU* 1.3 74.1 - - - +
219E ALA* 1.3 65.0 + - - +
221E GLU* 3.5 2.6 + - - +
222E GLN* 3.2 53.4 + - - +
228E PHE* 3.4 34.5 - - + -
245E ASP 3.4 4.9 + - - +
246E LEU* 4.2 2.5 - - - -
247E ASN* 3.2 41.1 - - - +
248E GLY* 4.6 1.6 - - - -
260E PHE* 4.3 4.0 - - + -
267E ALA* 6.0 1.6 - - + -
268E ALA* 6.4 1.3 - - - -
271E LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 219 (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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217E GLU* 3.4 17.0 - - - +
218E VAL* 1.3 75.5 - - - +
220E HIS* 1.3 57.4 + - - +
222E GLN* 3.3 1.9 + - - +
223E MET* 2.9 35.0 + - - +
247E ASN* 3.0 19.8 + - - +
248E GLY 4.1 1.8 - - - +
249E GLN* 3.6 38.4 - - + +
255E ASP* 3.7 10.3 - - - +
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Residues in contact with HIS 220 (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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137E TRP* 4.2 7.6 - + - -
181E GLU* 3.0 29.2 + - + -
182E PRO 2.8 27.8 + - - +
183E LYS* 3.4 39.9 + - + +
184E PRO* 3.2 15.7 - - - +
217E GLU* 3.2 32.4 + - + +
219E ALA* 1.3 76.7 - - - +
221E GLU* 1.3 63.0 + - - +
223E MET* 3.0 28.7 + - - +
224E ALA 3.8 0.2 + - - -
255E ASP* 3.3 13.2 + - - -
2001E CO 3.1 17.4 + - - -
2002E MG 4.1 0.7 - - - -
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Residues in contact with GLU 221 (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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182E PRO* 4.0 6.9 - - - +
184E PRO* 5.4 0.4 - - - -
194E PRO 4.4 2.2 - - - +
195E THR* 3.7 17.5 - - - -
196E ILE* 3.1 50.1 + - + +
217E GLU 3.4 3.9 + - - +
218E VAL 4.1 0.2 - - - +
220E HIS* 1.3 81.2 - - - +
222E GLN* 1.3 60.5 + - - +
224E ALA* 3.2 9.4 + - - +
226E LEU* 3.0 45.0 + - + +
228E PHE* 3.3 46.4 - - + -
231E GLY* 5.6 1.7 - - - -
198F HIS* 4.8 1.4 + - - -
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Residues in contact with GLN 222 (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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218E VAL* 3.2 38.0 + - - +
219E ALA 3.7 4.0 - - - +
220E HIS 3.2 0.8 - - - -
221E GLU* 1.3 73.1 - - - +
223E MET* 1.3 57.5 + - - +
224E ALA 2.9 5.8 - - - -
225E GLY* 2.9 20.9 + - - +
226E LEU 4.1 15.7 - - - +
228E PHE* 4.6 8.3 + - + +
249E GLN* 3.2 45.2 + - + +
251E GLY* 3.8 10.4 - - - +
252E ILE* 3.5 10.2 - - - +
264E ASP* 3.9 14.3 - - - +
267E ALA* 3.8 22.7 - - - +
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Residues in contact with MET 223 (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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183E LYS* 3.8 14.1 - - - -
184E PRO* 3.7 11.9 - - + +
185E ASN* 3.8 39.4 + - - +
186E GLU* 3.5 12.8 - - + +
219E ALA 2.9 23.6 + - - +
220E HIS* 3.0 17.2 + - - +
222E GLN* 1.3 76.1 - - - +
224E ALA* 1.3 57.8 + - - +
249E GLN* 4.1 10.8 - - - +
251E GLY 4.5 5.2 - - - -
252E ILE* 3.6 21.9 - - - +
253E LYS 3.4 26.5 - - - +
254E TYR* 4.3 1.1 - - - -
255E ASP* 3.5 30.5 - - - +
224F ALA 4.9 0.7 - - - +
252H ILE 4.9 0.3 - - - +
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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