Contacts of the helix formed by residues 212 - 220 (chain H) in PDB entry 4MNE
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 212 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H ILE* 3.9 14.8 - - - -
114H GLU* 2.4 43.5 + - - +
115H LEU* 4.4 9.4 - - - -
210H GLY 4.3 0.4 - - - -
211H VAL* 1.3 72.7 - - - +
213H GLY* 1.3 62.2 + - - +
214H GLN 3.4 0.2 + - - -
215H LEU* 3.2 21.7 + - - +
216H ILE* 3.2 11.5 + - - +
903H 573 2.9 36.8 + - - -
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Residues in contact with GLY 213 (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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114H GLU* 2.9 8.1 + - - -
210H GLY 5.3 0.2 - - - -
211H VAL 3.5 4.8 + - - -
212H SER* 1.3 72.1 - - - +
214H GLN* 1.3 59.5 + - - +
216H ILE* 3.3 14.3 + - - +
217H ASP* 3.1 33.7 + - - +
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Residues in contact with GLN 214 (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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107H ILE* 3.8 37.4 - - + +
110H GLN* 3.4 40.2 + - + +
111H ILE* 3.9 14.6 - - + -
114H GLU* 3.0 12.3 + - - +
213H GLY* 1.3 73.9 - - - +
215H LEU* 1.3 60.9 + - - +
217H ASP* 3.4 21.8 + - - +
218H SER* 2.9 30.7 + - - -
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Residues in contact with LEU 215 (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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99H ILE* 4.3 16.8 - - + -
101H LEU* 4.0 27.8 - - + -
111H ILE* 3.8 19.4 - - + +
115H LEU* 4.6 6.7 - - + -
139H ILE* 5.2 2.9 - - + -
141H ILE* 4.5 7.6 - - + -
212H SER* 3.2 23.7 + - - +
213H GLY 3.2 0.4 - - - -
214H GLN* 1.3 74.0 - - - +
216H ILE* 1.3 66.3 + - - +
218H SER* 3.2 1.0 + - - -
219H MET* 2.9 44.4 + - + +
903H 573 3.4 44.2 - - + +
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Residues in contact with ILE 216 (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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660G ASN* 3.6 24.5 - - + +
662G ARG* 5.9 0.3 - - - -
189H ARG* 3.3 56.3 - - - +
210H GLY* 3.9 14.8 - - - +
212H SER 3.2 12.8 - - - +
213H GLY* 3.3 13.8 + - - +
215H LEU* 1.3 76.3 - - - +
217H ASP* 1.3 64.0 + - - +
219H MET* 3.2 15.3 + - - +
220H ALA 3.6 7.3 + - - -
903H 573 3.0 22.2 - - - -
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Residues in contact with ASP 217 (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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660G ASN* 3.2 31.8 + - - -
213H GLY 3.1 14.7 + - - +
214H GLN* 3.4 25.3 + - - +
216H ILE* 1.3 75.2 - - - +
218H SER* 1.3 60.7 + - - +
220H ALA* 3.5 16.8 + - - +
221H ASN 4.9 0.7 + - - -
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Residues in contact with SER 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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101H LEU* 3.8 20.7 - - - +
103H ILE* 3.6 20.9 - - - +
107H ILE* 3.7 15.6 - - - +
111H ILE* 4.4 11.2 - - - -
214H GLN* 2.9 21.4 + - - -
215H LEU* 3.8 4.0 - - - -
216H ILE 3.1 0.2 - - - -
217H ASP* 1.3 80.4 - - - +
219H MET* 1.3 59.4 + - - +
220H ALA 3.3 0.7 + - - -
221H ASN* 4.4 10.7 + - - +
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Residues in contact with MET 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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662G ARG* 3.4 41.7 + - - +
99H ILE* 5.1 6.1 - - + -
101H LEU* 4.6 9.6 - - + -
190H ASP* 6.2 0.2 - - - +
215H LEU* 2.9 45.9 + - + +
216H ILE* 3.2 6.8 + - - +
218H SER* 1.3 78.9 - - - +
220H ALA* 1.3 62.7 + - - +
221H ASN 3.4 3.2 - - - +
222H SER* 3.4 17.0 - - - -
903H 573 3.5 53.4 - - + +
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Residues in contact with ALA 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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617G ILE* 3.7 9.4 - - - +
618G LEU* 5.2 2.9 - - + -
659G ILE 4.2 6.7 - - - +
660G ASN* 3.9 30.5 - - + +
662G ARG* 3.3 15.9 - - + +
665G ILE* 5.0 6.9 - - + +
216H ILE 3.6 2.8 + - - -
217H ASP 3.5 15.4 + - - +
218H SER 3.3 2.0 - - - -
219H MET* 1.3 72.7 - - - +
221H ASN* 1.3 55.4 + - - +
222H SER* 2.6 27.0 + - - -
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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