Contacts of the helix formed by residues 217 - 222 (chain F) in PDB entry 3M4D
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 SER 217 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ASP* 4.3 10.6 + - - -
152F ASP* 3.7 25.8 + - - +
153F PHE* 3.6 21.7 - - - -
174F MET* 3.5 12.5 - - - +
213F PRO 4.6 0.9 - - - +
216F ALA* 1.3 74.8 - - - +
218F SER* 1.3 64.0 + - - +
219F LEU* 3.5 16.5 + - - +
220F LEU* 2.9 34.8 + - - +
221F SER* 4.1 2.9 + - - -
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Residues in contact with SER 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ASN* 3.4 34.1 + - - +
106E SER 4.2 6.8 + - - -
108E ASP* 4.5 6.5 + - - -
154E LYS* 5.0 6.1 - - - +
156E ILE* 4.2 26.7 - - - -
213F PRO 5.3 1.1 - - - -
216F ALA 3.2 6.3 + - - -
217F SER* 1.3 71.9 + - - +
219F LEU* 1.3 67.3 + - - +
221F SER* 3.4 6.7 + - - -
222F SER* 3.1 24.4 + - - -
223F GLY 3.2 4.5 + - - -
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Residues in contact with LEU 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ASN* 4.3 11.2 - - + +
106E SER 4.0 22.2 - - - +
107E ILE* 3.8 20.0 - - + -
63F GLY* 3.4 7.1 - - - -
84F PHE* 3.3 26.2 - - + -
153F PHE* 3.8 36.8 - - + -
169F VAL* 4.3 2.2 - - + -
217F SER* 3.1 14.7 + - - +
218F SER* 1.3 83.4 - - - +
220F LEU* 1.3 62.7 + - - +
221F SER 3.3 0.3 + - - -
223F GLY 3.5 18.3 + - - +
224F PHE* 3.8 31.4 - - + -
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Residues in contact with LEU 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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63F GLY* 3.2 11.3 - - - -
65F TYR* 3.1 36.4 + - + +
80F TRP* 3.6 33.7 - - + -
81F PRO* 3.2 21.8 - - + +
153F PHE* 3.9 12.3 - - + -
171F PHE* 4.4 2.7 - - + -
174F MET* 3.8 11.4 - - - -
196F PHE* 3.6 28.0 - - + -
213F PRO* 6.5 0.4 - - + -
216F ALA* 3.7 23.3 - - + -
217F SER* 2.9 18.6 + - - +
219F LEU* 1.3 78.8 - - - +
221F SER* 1.3 57.7 + - - +
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Residues in contact with SER 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ILE* 6.2 0.3 - - - +
159E SER* 3.8 4.2 + - - -
168E LYS* 5.9 0.7 + - - -
62F ALA* 4.7 0.3 - - - +
63F GLY* 2.8 22.9 + - - -
64F GLN* 3.2 6.8 + - - +
65F TYR* 4.0 13.7 - - - +
213F PRO* 3.9 31.7 + - - +
217F SER 4.5 0.7 + - - -
218F SER* 3.4 10.4 + - - -
219F LEU 3.2 0.2 - - - -
220F LEU* 1.3 79.3 - - - +
222F SER* 1.3 68.7 + - - +
223F GLY 3.2 1.1 - - - -
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Residues in contact with SER 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ASN* 3.5 10.7 + - - -
156E ILE* 3.3 20.1 - - - +
157E LEU 3.2 24.8 + - - +
158E GLU* 4.1 10.1 + - - -
159E SER* 2.6 33.7 + - - +
168E LYS* 4.5 10.4 + - - -
60F THR* 4.3 4.2 - - - +
62F ALA* 3.9 1.4 - - - -
218F SER 3.1 5.7 + - - -
221F SER* 1.3 84.3 + - - +
223F GLY* 1.3 57.5 - - - +
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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