Contacts of the helix formed by residues 104 - 116 (chain E) 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 LYS 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E ILE* 1.3 75.5 - - - +
105E PRO* 1.3 70.6 - - + +
106E ALA* 4.2 13.0 - - + +
107E ILE* 3.1 33.5 + - + +
108E ARG* 2.8 25.5 + - - +
542F HIS 3.4 24.2 - - - +
543F ILE* 3.6 19.3 - - - +
545F GLU* 3.3 29.7 + - + +
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Residues in contact with PRO 105 (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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103E ILE 3.6 1.3 - - - +
104E LYS* 1.3 85.8 - - + +
106E ALA* 1.3 57.8 + - + +
108E ARG* 3.4 39.1 - - - +
109E ASN* 2.9 40.0 + - - +
543F ILE* 4.8 12.3 - - + +
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Residues in contact with ALA 106 (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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104E LYS* 3.2 12.5 - - + +
105E PRO* 1.3 81.9 - - + +
107E ILE* 1.3 59.7 + - + +
109E ASN* 3.6 7.1 + - - +
110E GLN* 3.3 23.6 + - - +
113E ARG* 4.3 4.2 + - - -
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Residues in contact with ILE 107 (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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103E ILE* 4.1 17.9 - - + -
104E LYS* 3.1 36.3 + - + +
106E ALA* 1.3 79.5 - - + +
108E ARG* 1.3 67.5 + - - +
109E ASN 3.2 1.3 - - - -
110E GLN* 3.9 11.2 - - - +
111E ILE* 3.1 23.6 + - + +
214E GLN* 3.7 39.7 - - + +
218E SER* 3.7 11.7 - - - +
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Residues in contact with ARG 108 (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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103E ILE* 3.9 25.7 + - + +
104E LYS 2.8 13.9 + - - +
105E PRO* 3.4 40.4 - - - +
107E ILE* 1.3 76.9 - - - +
109E ASN* 1.3 78.4 + - - +
111E ILE* 3.4 4.2 + - - +
112E ILE* 3.2 23.6 + - + +
134E TYR* 3.4 66.4 + - + -
139E ILE* 4.3 3.6 - - + +
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Residues in contact with ASN 109 (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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105E PRO* 2.9 22.1 + - - +
106E ALA* 3.8 7.4 - - - +
107E ILE 3.2 0.2 - - - -
108E ARG* 1.3 91.8 + - - +
110E GLN* 1.3 57.7 + - - +
112E ILE* 3.1 9.8 + - - +
113E ARG* 2.9 46.7 + - - +
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Residues in contact with GLN 110 (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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106E ALA 3.3 13.3 + - - +
107E ILE* 3.9 13.1 - - - +
108E ARG 3.4 0.2 - - - -
109E ASN* 1.3 75.0 - - - +
111E ILE* 1.3 61.0 + - - +
113E ARG* 3.1 23.9 - - + +
114E GLU* 2.9 53.9 + - + +
214E GLN* 3.5 30.1 + - + +
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Residues in contact with ILE 111 (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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101E LEU* 4.4 2.0 - - + -
103E ILE* 4.0 20.9 - - + -
107E ILE 3.1 21.2 + - - +
108E ARG* 3.6 4.5 - - - +
109E ASN 3.2 0.2 - - - -
110E GLN* 1.3 76.3 - - - +
112E ILE* 1.3 63.7 + - - +
114E GLU* 3.3 1.4 + - - -
115E LEU* 3.1 36.4 + - + +
139E ILE* 4.2 19.3 - - + -
212E SER* 3.8 7.1 + - - +
214E GLN* 3.5 16.4 - - + -
215E LEU* 3.7 44.6 - - + +
218E SER* 4.0 17.3 - - - +
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Residues in contact with ILE 112 (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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108E ARG* 3.2 13.2 + - + +
109E ASN* 3.1 11.2 + - - +
111E ILE* 1.3 72.9 - - + +
113E ARG* 1.3 69.0 + - - +
115E LEU* 3.5 10.7 + - + +
116E GLN* 3.2 23.6 + - + +
132E ALA* 3.8 35.4 - - + +
133E PHE* 3.7 21.3 - - - +
134E TYR* 5.1 3.8 - - + -
139E ILE* 3.6 32.5 - - + -
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Residues in contact with ARG 113 (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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106E ALA 4.3 4.2 + - - -
109E ASN* 2.9 25.0 + - - +
110E GLN* 3.1 41.1 - - + +
112E ILE* 1.3 75.1 - - - +
114E GLU* 1.3 55.7 + - + +
115E LEU 2.8 0.2 + - - -
116E GLN* 2.6 44.1 + - + +
117E VAL* 4.4 0.9 + - - +
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Residues in contact with GLU 114 (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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110E GLN* 2.9 42.1 + - + +
113E ARG* 1.3 77.9 - - + +
115E LEU* 1.3 60.8 + - - +
116E GLN 3.2 0.6 + - - -
117E VAL* 3.5 24.5 - - - +
211E VAL* 3.7 10.2 - - - +
212E SER* 2.7 39.2 + - - +
213E GLY* 4.0 7.5 + - - -
214E GLN* 3.0 25.8 + - - +
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Residues in contact with LEU 115 (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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111E ILE* 3.1 27.6 + - + +
112E ILE* 3.7 17.0 - - + +
113E ARG 2.8 1.0 + - - -
114E GLU* 1.3 72.3 - - - +
116E GLN* 1.3 65.7 + - - +
117E VAL 3.0 3.1 - - - -
118E LEU* 2.9 35.1 + - + +
129E PHE* 3.7 5.5 - - + -
132E ALA* 3.8 21.8 - - + -
139E ILE* 4.4 2.0 - - + -
141E ILE* 3.7 31.2 - - + -
211E VAL* 4.0 7.9 - - + -
212E SER* 3.7 20.0 - - - -
215E LEU* 4.3 3.4 - - + -
903E 573 3.8 22.7 - - + +
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Residues in contact with GLN 116 (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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62E GLU* 5.1 6.3 - - - +
112E ILE* 3.2 28.2 + - + +
113E ARG* 2.6 29.6 + - + +
115E LEU* 1.3 73.2 - - - +
117E VAL* 1.3 57.5 + - + +
118E LEU 2.9 6.1 + - - -
119E HIS* 3.0 53.1 + - - +
120E GLU* 4.2 2.3 + - - +
129E PHE* 4.7 1.2 - - - -
132E ALA* 4.6 16.8 + - - +
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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