Contacts of the helix formed by residues 114 - 127 (chain D) in PDB entry 3E4U
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 MET 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D CYS* 3.4 23.3 - - + +
54D SER* 4.2 0.9 - - - -
86D LEU* 3.7 19.1 - - + +
89D PHE* 3.5 37.2 - - + -
90D MET* 4.0 26.2 - - + -
109D ALA* 2.8 13.4 + - + +
110D MET* 5.0 0.2 - - - +
112D LEU* 3.6 38.4 - - + +
113D GLN* 1.3 74.7 - - - +
115D GLU* 1.3 65.5 + - - +
116D HIS 3.5 1.6 - - - -
117D VAL* 3.3 14.9 + - + +
118D VAL* 3.2 25.2 + - - +
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Residues in contact with GLU 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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113D GLN 3.3 8.3 + - - +
114D MET* 1.3 72.5 - - - +
116D HIS* 1.3 78.0 + - + +
118D VAL* 3.2 6.5 + - - +
119D ASP* 2.7 48.6 + - - +
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Residues in contact with HIS 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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11C PHE* 4.0 20.2 - + + -
13C ARG* 3.6 29.2 + - - +
17C ASP* 4.7 11.5 + - - -
89D PHE* 6.4 0.2 - - + -
114D MET 3.5 0.2 - - - -
115D GLU* 1.3 90.6 + - + +
117D VAL* 1.3 60.5 + - + +
119D ASP* 3.9 6.6 - - - +
120D THR* 2.7 37.2 + - - -
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Residues in contact with VAL 117 (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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11C PHE* 4.4 9.2 - - + -
86D LEU* 3.7 12.8 - - + -
89D PHE* 3.7 37.9 - - + -
95D LEU* 3.9 17.7 - - + +
105D VAL* 4.5 0.9 - - + -
109D ALA* 3.6 22.0 - - + -
114D MET* 3.5 25.8 - - + +
115D GLU 3.2 0.4 - - - -
116D HIS* 1.3 79.4 - - + +
118D VAL* 1.3 55.7 + - - +
120D THR* 3.8 1.2 - - - -
121D CYS* 2.8 36.3 + - - +
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Residues in contact with VAL 118 (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 MET* 3.8 11.7 - - + +
109D ALA* 3.6 8.1 - - + -
110D MET* 3.2 58.3 - - + +
114D MET 3.2 14.6 + - - +
115D GLU* 3.7 6.7 - - - +
117D VAL* 1.3 73.7 - - - +
119D ASP* 1.3 65.4 + - - +
121D CYS* 3.4 6.3 + - - +
122D ARG* 3.1 50.6 + - - +
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Residues in contact with ASP 119 (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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115D GLU* 2.7 44.4 + - - +
116D HIS* 4.1 6.5 - - - +
118D VAL* 1.3 75.9 - - - +
120D THR* 1.3 63.3 + - - +
122D ARG* 2.6 42.3 + - - +
123D LYS* 3.8 20.8 + - - +
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Residues in contact with THR 120 (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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9C ILE* 4.7 17.9 - - + -
11C PHE* 3.3 30.9 - - + -
95D LEU* 4.8 7.4 - - + -
97D LEU* 5.2 1.1 - - + -
116D HIS* 2.7 26.1 + - - +
117D VAL 3.8 3.4 - - - -
118D VAL 3.2 0.2 - - - -
119D ASP* 1.3 73.6 - - - +
121D CYS* 1.3 57.5 + - - +
122D ARG 3.1 1.8 - - - -
123D LYS* 2.7 39.4 + - + +
124D PHE* 3.4 5.5 + - + +
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Residues in contact with CYS 121 (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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95D LEU* 4.4 6.1 - - - -
97D LEU* 3.7 33.9 - - - -
102D ILE* 4.0 8.1 - - + +
105D VAL* 4.4 5.6 - - - -
106D MET* 3.9 40.6 - - + -
117D VAL* 2.8 25.6 + - - +
118D VAL 3.9 4.0 - - - +
120D THR* 1.3 74.6 - - - +
122D ARG* 1.3 60.8 + - - +
124D PHE* 3.5 8.1 + - - +
125D ILE* 3.2 27.2 + - - +
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Residues in contact with ARG 122 (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 MET* 4.6 13.6 - - - -
110D MET* 4.9 8.5 - - - +
118D VAL* 3.1 36.6 + - + +
119D ASP* 2.6 47.1 + - - +
120D THR 3.0 0.2 + - - -
121D CYS* 1.3 77.2 - - - +
123D LYS* 1.3 60.4 + - + +
125D ILE* 3.5 6.6 + - - +
126D LYS* 3.1 37.0 + - + +
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Residues in contact with LYS 123 (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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119D ASP* 3.8 20.1 + - - +
120D THR* 2.7 19.3 + - + +
122D ARG* 1.3 71.9 - - + +
124D PHE* 1.3 63.3 + - - +
126D LYS* 3.6 26.3 - - - +
127D ALA* 3.5 22.5 + - - +
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Residues in contact with PHE 124 (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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9C ILE* 4.1 24.9 - - + -
97D LEU* 4.1 34.8 - - + -
98D ARG 5.4 3.4 - - - -
99D GLU* 5.0 20.4 - - + -
102D ILE* 3.3 23.6 - - + -
120D THR* 3.4 7.1 + - + +
121D CYS 3.9 8.1 - - - +
122D ARG 3.4 0.4 - - - -
123D LYS* 1.3 77.3 - - - +
125D ILE* 1.3 67.9 + - - +
127D ALA* 3.5 13.7 + - - +
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Residues in contact with ILE 125 (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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102D ILE* 3.4 28.7 - - + +
103D MET* 3.4 32.3 - - + -
106D MET* 3.5 24.5 - - + -
121D CYS 3.2 10.2 + - - +
122D ARG* 3.7 5.8 - - - +
124D PHE* 1.3 80.9 - - - +
126D LYS* 1.3 65.3 + - + +
127D ALA 2.8 13.5 + - - -
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Residues in contact with LYS 126 (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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122D ARG* 3.1 21.6 + - + +
123D LYS* 3.6 33.4 - - - +
125D ILE* 1.3 83.3 - - + +
127D ALA* 1.3 59.6 + - + +
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Residues in contact with ALA 127 (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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123D LYS 3.5 17.2 + - - +
124D PHE* 3.9 9.2 - - - +
125D ILE 2.8 13.5 + - - -
126D LYS* 1.3 77.1 - - + +
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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