Contacts of the helix formed by residues 110 - 124 (chain D) in PDB entry 4KEU
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D ASN 3.6 1.1 + - - -
109D ARG* 1.3 75.2 - - - +
111D ILE* 1.3 64.4 + - - +
112D ASP* 3.4 12.3 + - - +
113D GLU* 3.0 42.3 + - - +
114D ILE* 3.2 18.4 + - - +
151D LYS* 6.0 0.7 - - - -
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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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110D SER* 1.3 74.5 - - - +
112D ASP* 1.4 58.8 + - - +
114D ILE* 3.2 11.2 + - - +
115D ALA* 2.9 26.9 + - - +
151D LYS* 3.6 33.2 - - + +
154D ARG* 3.9 32.8 - - + -
155D ALA* 3.5 30.5 - - - +
158D ILE* 3.9 11.7 - - + -
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Residues in contact with ASP 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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110D SER* 3.1 10.8 + - - +
111D ILE* 1.4 78.6 - - - +
113D GLU* 1.3 57.1 - - + +
115D ALA* 3.4 7.0 + - - +
116D ASP* 2.9 39.3 + - - +
158D ILE* 3.5 21.7 - - - +
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Residues in contact with GLU 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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267B LYS* 3.7 18.7 + - - -
106D PHE* 5.8 0.9 - - + -
109D ARG* 3.1 46.5 + - + +
110D SER* 3.0 38.0 + - - +
112D ASP* 1.3 79.0 - - + +
114D ILE* 1.3 62.7 + - - +
116D ASP* 3.4 13.3 + - - +
117D LEU* 3.4 23.6 + - - +
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Residues in contact with ILE 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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96D ILE* 3.9 15.0 - - + -
102D LEU* 3.9 29.2 - - + -
106D PHE* 3.7 21.3 - - + -
109D ARG 5.4 2.5 - - - +
110D SER 3.4 15.5 - - - +
111D ILE* 3.2 9.6 + - - +
113D GLU* 1.3 75.2 - - + +
115D ALA* 1.3 60.3 + - - +
117D LEU* 2.9 34.5 + - + +
118D PHE* 3.3 29.5 + - + -
151D LYS* 4.2 24.9 - - + -
152D VAL* 4.9 3.6 - - + +
155D ALA* 3.7 9.2 - - + -
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Residues in contact with ALA 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 16.7 + - - +
112D ASP* 3.4 5.6 + - - +
114D ILE* 1.3 75.5 - - - +
116D ASP* 1.4 52.3 + - - +
118D PHE* 3.0 8.9 + - - +
119D ILE* 2.8 39.7 + - + +
155D ALA* 3.4 29.3 - - - +
158D ILE* 3.8 28.5 - - + -
159D ALA* 4.5 1.7 - - - +
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Residues in contact with ASP 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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38B HIS* 6.0 0.4 - - - -
112D ASP* 2.9 31.7 + - - +
113D GLU* 3.5 12.7 - - - +
114D ILE 3.1 0.2 - - - -
115D ALA* 1.4 73.3 - - - +
117D LEU* 1.3 59.2 + - + +
119D ILE* 3.8 17.7 - - - +
120D HIS* 2.9 30.5 + - - +
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Residues in contact with LEU 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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36B TRP* 3.4 45.5 + - + +
38B HIS* 3.9 19.3 - - + +
39B LEU* 3.7 33.0 - - + -
105D TYR* 4.9 3.1 - - + +
106D PHE* 3.6 37.7 - - + -
113D GLU 3.4 13.7 + - - +
114D ILE* 2.9 14.3 + - + +
116D ASP* 1.3 78.4 - - + +
118D PHE* 1.3 61.2 + - + +
120D HIS* 3.5 6.2 + - - +
121D ASP* 3.3 16.3 + - - -
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Residues in contact with PHE 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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36B TRP* 4.3 5.8 - + - -
94D THR* 3.6 29.6 - - + +
95D GLY* 3.3 29.6 - - - -
96D ILE* 3.8 20.2 - - + -
114D ILE* 3.7 24.2 - - + -
115D ALA* 3.0 5.3 + - - +
117D LEU* 1.3 77.7 - - + +
119D ILE* 1.3 60.1 + - - +
121D ASP* 3.1 4.7 + - - +
122D ILE* 2.9 33.6 + - - +
136D VAL* 4.0 17.0 - - + -
152D VAL* 4.2 10.8 - - + -
155D ALA* 3.8 38.8 - - + -
156D ALA* 3.9 7.4 - - + -
159D ALA* 3.7 12.8 - - + -
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Residues in contact with ILE 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 ALA 2.8 24.4 + - - +
116D ASP* 3.8 21.3 - - - +
117D LEU 3.4 0.2 - - - -
118D PHE* 1.3 72.5 - - - +
120D HIS* 1.3 57.4 + - - +
122D ILE* 4.3 6.3 - - - -
123D LYS* 2.8 60.4 + - + +
158D ILE* 4.6 9.0 - - + -
159D ALA* 4.2 19.1 - - - -
162D GLU* 3.9 29.6 - - + -
163D THR* 4.7 3.6 - - + -
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Residues in contact with HIS 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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36B TRP* 4.7 0.9 - + - -
38B HIS* 3.5 54.1 + + + +
116D ASP 2.9 18.8 + - - +
117D LEU 3.5 6.1 - - - +
119D ILE* 1.3 76.5 - - - +
121D ASP* 1.4 66.2 + - - +
124D GLU* 2.7 59.7 + - + +
125D GLY 3.0 25.7 + - - -
127D GLN 5.5 1.3 + - - -
128D GLY* 5.5 6.3 + - - -
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Residues in contact with ASP 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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35B GLN 4.4 1.0 - - - +
36B TRP* 2.9 30.1 + - - -
74D ARG* 3.0 23.3 + - - -
94D THR* 2.7 37.7 + - - +
117D LEU 3.3 1.5 + - - -
118D PHE 3.1 3.2 + - - +
120D HIS* 1.4 88.1 - - - +
122D ILE* 1.3 60.5 + - - +
125D GLY* 3.3 23.2 + - - +
126D ILE* 3.9 13.7 - - + -
127D GLN 4.5 0.7 + - - -
132D LYS* 3.5 8.0 - - - -
133D ALA* 3.0 19.0 + - + -
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Residues in contact with ILE 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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94D THR* 4.0 2.5 - - + -
118D PHE 2.9 27.6 + - - +
119D ILE 3.8 3.6 - - - +
121D ASP* 1.3 77.7 - - - +
123D LYS* 1.3 61.3 + - + +
132D LYS* 3.4 23.0 - - - +
133D ALA* 3.8 26.9 - - + +
136D VAL* 4.2 7.0 - - + -
159D ALA* 4.1 14.8 - - + -
163D THR* 3.4 46.7 - - + +
165D VAL* 3.6 30.1 - - + -
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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 ILE* 2.8 38.8 + - + +
122D ILE* 1.3 75.8 - - + +
124D GLU* 1.3 72.2 + - + +
132D LYS* 3.1 21.3 - - - +
162D GLU* 4.3 23.4 + - - +
163D THR* 3.8 26.9 - - + -
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Residues in contact with GLU 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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120D HIS* 2.7 52.1 + - + +
123D LYS* 1.3 85.1 - - + +
125D GLY* 1.3 56.7 - - - +
129D THR 4.0 4.0 - - - +
130D LEU* 4.2 10.2 - - - +
132D LYS* 3.5 17.5 + - - -
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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