Contacts of the helix formed by residues 96 - 108 (chain D) in PDB entry 1WNT
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 THR 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B TRP* 4.1 7.4 - - - -
90D GLN* 2.9 31.3 - - - +
94D GLU 3.5 8.5 - - - +
95D VAL* 1.3 82.5 - - - +
97D LYS* 1.3 63.1 + - - +
98D GLU* 3.2 19.5 + - - +
99D ALA* 2.8 25.3 + - - +
100D PHE* 3.2 17.3 + - - +
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Residues in contact with LYS 97 (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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64B TRP* 3.6 45.9 - - + +
65B GLU* 3.6 26.3 + - - +
105B GLU* 5.7 1.0 + - - -
109B ARG* 3.0 33.3 - - - +
96D THR* 1.3 75.8 - - - +
98D GLU* 1.3 60.4 + - + +
100D PHE* 3.6 3.8 - - - +
101D ASP* 2.8 48.1 + - - +
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Residues in contact with GLU 98 (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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88D LEU* 5.3 6.1 - - - +
90D GLN* 5.9 0.2 - - - -
96D THR* 3.2 18.5 + - - +
97D LYS* 1.3 78.7 - - + +
99D ALA* 1.3 70.4 + - - +
100D PHE 3.2 0.7 - - - -
101D ASP* 2.7 10.6 + - - -
102D ARG* 2.5 39.2 + - + +
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Residues in contact with ALA 99 (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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88D LEU* 3.9 25.8 - - + +
90D GLN* 3.2 28.9 - - - +
95D VAL* 5.2 1.8 - - + -
96D THR* 2.8 20.3 + - - +
98D GLU* 1.3 85.9 + - - +
100D PHE* 1.3 61.2 + - - +
103D SER* 2.5 31.3 + - - -
148D VAL* 4.8 4.3 - - + -
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Residues in contact with PHE 100 (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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64B TRP* 5.9 0.4 - - + -
104B PHE* 3.9 14.8 - - + -
105B GLU* 5.3 1.3 - - + -
108B LEU* 3.4 30.3 - - + -
109B ARG* 3.8 40.4 - - + -
112B ILE* 3.3 34.8 - - + -
95D VAL* 4.8 1.1 - - + -
96D THR 3.2 17.0 + - - +
97D LYS 3.6 5.4 - - - +
98D GLU 3.2 0.4 - - - -
99D ALA* 1.3 79.4 - - - +
101D ASP* 1.3 69.4 + - - +
104D PHE* 2.9 69.3 + + + -
148D VAL* 3.7 14.8 - - + +
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Residues in contact with ASP 101 (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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105B GLU* 5.0 5.3 - - - +
109B ARG* 3.3 24.6 + - - -
97D LYS* 2.8 53.2 + - - +
98D GLU* 2.7 14.5 + - - +
100D PHE* 1.3 76.3 - - - +
102D ARG* 1.3 67.5 + - - +
104D PHE* 4.2 2.3 - - - +
105D GLU* 3.2 35.9 + - - +
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Residues in contact with ARG 102 (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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39D ARG* 3.1 23.4 - - - +
60D ASP* 2.8 40.4 + - - -
62D GLY* 4.5 2.0 - - - -
86D VAL* 4.2 19.2 - - - +
88D LEU* 3.9 13.5 - - + -
98D GLU* 2.5 19.2 + - + +
101D ASP* 1.3 70.6 - - - +
103D SER* 1.3 66.6 + - - +
105D GLU* 2.8 26.0 + - - +
106D VAL* 3.0 37.6 + - - +
3245D NAP 3.1 19.0 + - - -
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Residues in contact with SER 103 (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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86D VAL* 4.3 12.5 - - - +
88D LEU* 3.1 24.0 + - - +
99D ALA 2.5 23.1 + - - -
100D PHE 3.7 0.2 - - - -
102D ARG* 1.3 76.6 - - - +
104D PHE* 1.3 57.9 + - - +
107D ASN* 3.0 40.5 + - - +
148D VAL* 3.3 27.4 - - - +
149D TYR* 5.5 1.3 - - - -
152D THR* 3.9 7.9 - - - -
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Residues in contact with PHE 104 (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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100B PHE* 3.7 14.4 - - + -
104B PHE* 3.3 35.4 - + + -
108B LEU* 3.3 33.9 - - + -
155B ALA* 4.7 0.2 - - + -
100D PHE* 2.9 48.9 + + + +
101D ASP* 4.4 2.7 - - - +
102D ARG 3.2 0.2 - - - -
103D SER* 1.3 80.8 - - - +
105D GLU* 1.3 62.5 + - - +
108D LEU* 3.3 13.2 + - + +
109D ARG 3.0 20.4 + - - -
148D VAL* 3.3 28.3 - - + -
151D SER* 3.9 19.3 - - - -
152D THR* 3.8 22.0 - - + -
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Residues in contact with GLU 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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100B PHE* 5.1 1.3 - - + -
101B ASP* 5.3 3.9 - - - +
61D LEU 4.3 0.3 - - - +
62D GLY* 4.1 21.2 - - - +
101D ASP* 3.2 28.9 + - - +
102D ARG* 2.8 20.0 + - - +
104D PHE* 1.3 78.7 - - - +
106D VAL* 1.3 58.0 + - + +
109D ARG* 3.3 43.0 + - - +
110D ALA* 3.1 27.2 + - - +
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Residues in contact with VAL 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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61D LEU* 5.1 0.9 - - + -
62D GLY* 4.0 9.9 - - - +
84D ALA* 4.1 18.4 - - + +
85D ALA* 4.1 1.3 - - - -
86D VAL* 4.4 4.9 - - + +
102D ARG* 3.0 44.2 + - - +
103D SER 4.3 0.2 - - - +
105D GLU* 1.3 74.7 - - + +
107D ASN* 1.3 69.6 + - - +
108D LEU* 3.0 10.6 + - - -
110D ALA* 3.2 26.9 - - + +
111D VAL* 4.3 2.9 + - - +
3245D NAP 3.2 41.5 - - + +
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Residues in contact with ASN 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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84D ALA 4.6 6.5 - - - -
85D ALA* 3.1 12.3 - - + -
86D VAL* 2.7 48.2 + - - +
103D SER* 3.0 25.0 + - - +
106D VAL* 1.3 77.0 - - - +
108D LEU* 1.3 60.6 + - - +
111D VAL* 3.8 12.4 - - - +
149D TYR* 3.9 12.3 - - - -
152D THR* 3.4 33.2 + - - +
153D LYS* 4.9 5.9 - - - +
156D LEU* 4.2 16.8 - - - +
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Residues in contact with LEU 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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100B PHE* 3.6 15.3 - - + -
104B PHE* 3.3 36.8 - - + -
151B SER* 4.4 2.9 - - - +
104D PHE* 3.3 17.9 + - + +
106D VAL 3.0 2.0 + - - -
107D ASN* 1.3 80.3 - - + +
109D ARG* 1.3 67.7 + - - +
110D ALA 3.3 1.3 - - - -
111D VAL* 3.3 20.7 + - - +
112D ILE* 3.3 11.1 + - - +
152D THR* 5.3 3.8 - - - +
155D ALA* 3.6 17.9 - - + -
156D LEU* 4.1 20.9 - - + +
159D LEU* 3.1 42.6 - - + -
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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