Contacts of the helix formed by residues 104 - 116 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541C LEU 5.1 0.4 + - - -
542C HIS* 2.9 39.9 + - - +
543C ILE* 3.7 15.2 - - - +
545C GLU* 3.1 37.4 + - - +
103D ILE* 1.3 75.7 - - - +
105D PRO* 1.3 70.8 - - + +
106D ALA* 4.3 8.5 - - + +
107D ILE* 2.9 42.2 + - + +
108D ARG* 3.0 12.1 + - - +
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Residues in contact with PRO 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ILE* 4.6 12.8 - - + +
103D ILE 3.6 0.4 - - - +
104D LYS* 1.3 87.8 - - + +
106D ALA* 1.3 61.4 + - - +
108D ARG* 3.2 51.5 - - - +
109D ASN* 3.2 20.7 + - - +
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Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LYS* 3.3 5.4 - - + +
105D PRO* 1.3 79.7 - - - +
107D ILE* 1.3 62.8 + - + +
109D ASN* 3.6 8.1 + - - +
110D GLN* 3.1 26.7 + - - +
113D ARG* 5.6 0.2 + - - -
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ILE* 3.9 18.8 - - + -
104D LYS* 2.9 33.3 + - + +
106D ALA* 1.3 82.4 - - + +
108D ARG* 1.3 59.9 + - - +
109D ASN 3.2 0.4 - - - -
110D GLN* 3.7 11.0 - - - +
111D ILE* 3.0 29.3 + - + +
214D GLN* 3.6 34.3 - - + +
218D SER* 3.8 13.0 - - - +
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Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ILE* 5.3 4.4 - - - +
103D ILE* 2.8 52.5 + - + +
104D LYS 3.0 6.9 + - - -
105D PRO* 3.2 52.6 - - + +
107D ILE* 1.3 74.3 - - - +
109D ASN* 1.3 68.6 + - - +
111D ILE* 3.5 4.7 + - - +
112D ILE* 3.0 33.9 + - - +
134D TYR* 3.1 69.0 + - + -
139D ILE* 4.5 2.5 - - + -
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Residues in contact with ASN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D PRO* 3.2 24.0 + - - +
106D ALA* 3.9 7.8 - - - +
108D ARG* 1.3 85.3 - - - +
110D GLN* 1.3 56.0 + - - +
112D ILE* 3.3 9.8 + - - +
113D ARG* 2.9 36.4 + - - +
134D TYR* 6.0 0.3 - - - +
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Residues in contact with GLN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ALA 3.1 19.0 + - - +
107D ILE* 3.7 13.4 - - - +
108D ARG 3.3 0.2 - - - -
109D ASN* 1.3 77.6 - - - +
111D ILE* 1.3 56.8 + - - +
113D ARG* 3.3 34.5 + - - +
114D GLU* 2.9 56.3 + - - +
214D GLN* 3.6 31.1 + - + +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.0 21.5 - - + -
103D ILE* 4.3 8.7 - - + -
107D ILE 3.0 17.6 + - - +
108D ARG* 3.8 4.9 - - - +
110D GLN* 1.3 74.6 - - - +
112D ILE* 1.3 66.0 + - - +
114D GLU* 3.2 3.2 + - - +
115D LEU* 2.9 38.5 + - + +
139D ILE* 4.2 13.2 - - + -
212D SER* 4.0 7.1 + - - +
214D GLN* 3.6 15.3 - - + -
215D LEU* 3.8 40.8 - - + +
218D SER* 3.9 17.3 - - - +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ARG 3.0 22.8 + - - +
109D ASN* 3.9 9.4 - - - +
111D ILE* 1.3 76.3 - - + +
113D ARG* 1.3 63.6 + - - +
115D LEU* 3.2 14.6 + - + +
116D GLN* 3.3 22.6 + - + +
132D ALA* 3.8 20.9 - - + +
133D PHE* 3.5 12.8 - - - +
134D TYR* 3.3 41.3 - - + +
139D ILE* 4.0 14.1 - - + -
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ALA 5.6 0.4 + - - -
109D ASN* 2.9 20.9 + - - +
110D GLN* 3.3 48.5 + - - +
112D ILE* 1.3 78.0 - - - +
114D GLU* 1.3 70.2 + - - +
116D GLN* 3.1 27.9 + - + +
117D VAL* 4.3 2.8 + - - +
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D GLN* 2.9 49.5 + - + +
111D ILE 3.2 0.6 + - - +
113D ARG* 1.3 84.6 + - - +
115D LEU* 1.3 64.2 + - - +
117D VAL* 3.1 25.1 + - + +
211D VAL* 4.2 11.5 - - - +
212D SER* 2.6 39.4 + - - +
213D GLY* 3.2 7.8 + - - -
214D GLN* 3.0 21.9 + - - +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 2.9 35.3 + - + +
112D ILE* 3.6 7.6 - - - +
113D ARG 3.2 0.4 - - - -
114D GLU* 1.3 77.1 - - - +
116D GLN* 1.3 59.3 + - - +
118D LEU* 2.9 46.2 + - + +
129D PHE* 3.8 4.1 - - + -
132D ALA* 3.7 29.8 - - + -
139D ILE* 4.2 7.6 - - + -
141D ILE* 3.8 24.2 - - + -
211D VAL* 3.9 24.5 - - + -
212D SER* 4.3 6.5 - - - -
215D LEU* 4.6 2.2 - - + -
903D 573 4.0 14.8 - - + -
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ILE* 3.3 22.0 + - + +
113D ARG* 3.1 23.1 - - + +
114D GLU 3.1 0.8 - - - -
115D LEU* 1.3 77.3 - - - +
117D VAL* 1.3 60.5 + - - +
118D LEU 3.0 0.9 - - - -
119D HIS* 3.0 53.6 + - + +
120D GLU* 4.4 1.4 + - - +
129D PHE* 4.5 2.4 - - - -
131D GLY* 5.4 0.4 - - - -
132D ALA* 4.1 29.5 + - - +
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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