Contacts of the helix formed by residues 217 - 223 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F GLU* 2.9 15.7 - - - +
182F PRO 5.3 0.6 + - - -
215F ASN 3.7 1.4 + - - -
216F PRO* 1.3 71.3 - - - +
218F VAL* 1.3 71.7 + - - +
219F ALA* 3.6 2.5 - - - +
220F HIS* 2.9 48.3 + - + +
221F GLU* 3.3 6.2 + - - +
228F PHE* 3.4 6.7 - - - -
245F ASP* 3.2 21.1 - - + +
247F ASN* 3.0 23.0 + - - +
255F ASP* 3.5 0.2 - - - +
287F ASP* 3.1 7.0 - - - +
2001F CO 2.0 30.8 + - - -
2002F MG 2.3 31.0 - - - -
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Residues in contact with VAL 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F GLU* 1.3 72.8 - - - +
219F ALA* 1.3 63.2 + - - +
221F GLU 3.6 0.5 + - - -
222F GLN* 3.2 48.7 + - - +
228F PHE* 3.2 40.3 - - + -
245F ASP 3.1 7.4 + - - +
246F LEU* 4.0 3.4 - - + -
247F ASN* 3.2 40.8 - - - +
248F GLY* 4.8 2.2 - - - -
260F PHE* 4.8 2.9 - - + -
267F ALA* 6.1 1.3 - - + -
268F ALA* 6.5 0.4 - - - -
271F LEU* 3.9 13.2 - - + -
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F GLU* 3.3 7.3 - - - +
218F VAL* 1.3 73.7 - - - +
220F HIS* 1.3 61.8 + - - +
222F GLN* 3.3 2.4 + - - +
223F MET* 3.1 28.4 + - - +
247F ASN* 3.0 33.9 + - - +
248F GLY 4.1 1.1 - - - +
249F GLN* 3.6 35.9 - - + +
255F ASP* 3.7 11.2 - - - +
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Residues in contact with HIS 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F TRP* 4.1 7.4 - + - -
181F GLU* 3.1 30.9 + - + +
182F PRO 2.6 29.3 + - - +
183F LYS* 3.5 34.7 + - + +
184F PRO* 3.2 22.5 - - - +
217F GLU* 2.9 47.1 + - + +
219F ALA* 1.3 76.2 - - - +
221F GLU* 1.3 66.4 + - - +
223F MET* 3.1 16.1 + - - +
255F ASP* 3.5 13.5 + - - -
2001F CO 3.5 4.8 + - - -
2002F MG 4.3 0.4 - - - -
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Residues in contact with GLU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E HIS* 4.8 2.6 + - - -
182F PRO* 4.1 10.6 - - - +
184F PRO* 5.3 0.7 - - - -
194F PRO 4.4 1.6 - - - +
195F THR* 3.6 17.6 - - - -
196F ILE* 3.2 48.3 + - + +
216F PRO* 5.1 1.9 - - + +
217F GLU 3.3 4.0 + - - +
220F HIS* 1.3 82.3 - - - +
222F GLN* 1.3 59.4 + - - +
224F ALA* 2.9 21.9 + - - +
226F LEU* 3.2 35.2 + - + +
227F ASN 5.5 0.2 - - - +
228F PHE* 3.5 43.1 - - + -
231F GLY* 5.6 1.3 - - - -
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Residues in contact with GLN 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F VAL* 3.2 36.4 + - - +
219F ALA 3.8 4.0 - - - +
220F HIS 3.2 1.0 - - - -
221F GLU* 1.3 71.9 - - - +
223F MET* 1.3 56.2 + - - +
224F ALA 3.0 5.8 - - - -
225F GLY* 3.0 19.5 + - - +
226F LEU 4.0 18.6 - - - +
228F PHE* 4.2 10.3 + - + +
249F GLN* 3.3 42.8 + - + +
251F GLY* 3.7 16.1 - - - +
252F ILE* 3.8 4.5 - - - +
264F ASP* 4.1 14.4 - - - +
267F ALA* 4.0 21.7 - - - +
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Residues in contact with MET 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E ALA 4.8 0.9 - - - +
183F LYS* 3.8 15.3 - - - -
184F PRO* 3.7 10.8 - - + +
185F ASN* 3.5 46.6 + - - +
186F GLU* 4.1 4.5 - - + +
219F ALA 3.1 22.6 + - - +
220F HIS* 3.2 17.0 - - - +
221F GLU 3.1 0.8 - - - -
222F GLN* 1.3 76.8 - - - +
224F ALA* 1.3 55.3 + - - +
225F GLY 3.3 1.3 - - - -
249F GLN* 4.1 9.0 - - - +
251F GLY 4.5 4.3 - - - -
252F ILE* 3.3 24.2 - - - +
253F LYS 3.6 25.4 - - - +
254F TYR* 4.3 1.6 - - - -
255F ASP* 3.7 32.8 - - - +
252G ILE 4.7 0.3 - - - +
253G LYS* 6.0 0.2 - - + -
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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