Contacts of the helix formed by residues 108 - 126 (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 LEU 108 (chain D).
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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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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS* 3.6 25.0 - - - +
100B PHE* 3.5 48.0 - - + -
101B ASP* 3.3 29.3 + - - -
61D LEU 5.6 0.8 + - - -
62D GLY 3.4 25.3 + - - -
63D ASP* 4.6 0.2 - - - +
64D TRP* 3.6 44.1 - - + +
104D PHE 3.0 7.3 + - - +
105D GLU* 3.3 33.8 + - - +
108D LEU* 1.3 73.4 - - - +
110D ALA* 1.3 67.8 + - - +
112D ILE* 3.0 15.7 + - + +
113D GLN* 3.0 12.2 + - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LEU* 3.4 47.3 + - + +
84D ALA* 6.4 0.4 - - + -
105D GLU 3.1 8.7 + - - +
106D VAL* 3.2 19.7 - - + +
109D ARG* 1.3 75.4 - - - +
111D VAL* 1.3 64.1 + - + +
113D GLN* 2.9 8.8 + - - +
114D VAL* 2.9 30.2 + - + +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ASN* 3.6 37.7 - - + +
84D ALA 5.6 4.0 - - - +
106D VAL 4.4 2.7 - - - +
107D ASN 3.8 25.4 - - - +
108D LEU* 3.3 11.2 - - - +
109D ARG 3.2 0.2 - - - -
110D ALA* 1.3 76.3 - - + +
112D ILE* 1.3 58.0 + - - +
115D SER* 2.5 39.3 + - - +
133D ASN* 3.9 19.5 - - - +
156D LEU* 4.2 16.8 - - + -
159D LEU* 4.2 9.4 - - + -
163D MET* 4.8 3.4 - - - -
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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
----------------------------------------------------------
92B PHE* 3.3 28.0 - - + -
95B VAL* 4.1 24.5 - - + +
100B PHE* 3.8 32.1 - - + -
147B SER* 5.6 0.9 - - - -
148B VAL* 4.4 7.0 - - + -
151B SER* 5.7 0.4 - - - +
64D TRP* 5.9 2.5 - - + -
108D LEU* 3.5 11.7 - - + +
109D ARG* 3.0 6.7 + - + +
111D VAL* 1.3 74.1 - - - +
113D GLN* 1.3 65.7 + - - +
116D GLN* 2.8 47.6 + - + +
159D LEU* 3.7 31.6 - - + -
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Residues in contact with GLN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LEU 4.6 4.3 - - - +
63D ASP 4.5 0.3 - - - -
64D TRP* 2.9 68.7 + - + -
67D THR* 3.0 27.2 - - + +
68D GLU* 2.9 29.3 - - - +
109D ARG 3.0 10.2 + - - +
110D ALA* 2.9 10.9 + - - +
112D ILE* 1.3 81.8 - - - +
114D VAL* 1.3 64.7 + - - +
116D GLN* 3.0 19.8 + - - +
117D ILE* 3.1 15.4 + - + +
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Residues in contact with VAL 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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11D LEU* 4.2 19.3 - - + -
13D THR* 4.3 6.5 - - + -
61D LEU* 3.5 29.6 - - + -
67D THR* 4.6 2.9 - - + -
71D LEU* 4.4 13.5 - - + -
80D LEU* 3.9 25.4 - - + -
82D ASN* 4.0 9.0 - - - +
110D ALA* 2.9 20.5 + - + +
113D GLN* 1.3 70.7 - - - +
115D SER* 1.3 64.1 + - - +
117D ILE* 2.8 25.4 + - + +
118D VAL* 3.0 18.1 + - + +
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 3.9 6.9 - - - -
80D LEU* 3.3 14.5 - - - +
82D ASN* 2.8 21.1 + - - -
111D VAL* 2.5 26.6 + - - +
114D VAL* 1.3 77.0 - - - +
116D GLN* 1.3 57.4 + - - +
118D VAL* 4.0 1.7 - - - +
119D ALA* 3.0 33.5 + - - +
131D ILE* 4.2 4.3 - - - +
163D MET* 3.5 31.5 - - - +
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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
----------------------------------------------------------
92B PHE* 2.7 37.8 + - + +
93B LEU* 3.0 29.7 + - - +
94B GLU 3.7 0.6 - - - -
95B VAL 3.3 27.6 + - - +
64D TRP* 4.0 15.2 - - - -
112D ILE* 2.8 34.7 + - + +
113D GLN* 3.1 7.3 - - - +
115D SER* 1.3 74.4 - - - +
117D ILE* 1.3 68.3 + - + +
120D ARG* 3.1 46.8 + - - +
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D THR* 4.8 5.2 - - + +
68D GLU* 5.1 8.7 - - - +
71D LEU* 3.7 48.0 - - + +
72D GLY* 5.6 2.5 - - - +
74D VAL* 4.7 13.5 - - + -
75D GLY 5.9 0.7 - - - +
113D GLN* 3.7 17.9 - - + +
114D VAL* 2.8 16.0 + - + +
116D GLN* 1.3 78.1 - - - +
118D VAL* 1.3 70.7 + - + +
120D ARG* 2.9 28.9 + - - +
121D GLY* 3.5 4.3 + - - -
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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
----------------------------------------------------------
11D LEU* 4.7 5.8 - - + -
74D VAL* 5.8 0.4 - - + -
77D VAL* 3.5 39.4 - - + +
78D ASP 5.3 0.2 - - - -
79D LEU 5.2 3.4 - - - +
80D LEU* 4.2 36.8 - - + -
114D VAL* 3.0 19.9 + - + +
115D SER* 4.0 5.8 - - - +
117D ILE* 1.3 84.9 - - + +
119D ALA* 1.3 62.3 + - - +
121D GLY* 3.5 2.1 + - - -
122D LEU* 3.2 36.4 + - + +
130D ALA 6.0 0.4 - - - +
131D ILE* 5.4 4.5 - - + -
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 5.3 0.2 - - + -
93B LEU* 4.0 14.6 - - + -
115D SER 3.0 20.9 + - - +
116D GLN 3.9 2.7 - - - +
118D VAL* 1.3 75.2 - - - +
120D ARG* 1.3 56.2 + - - +
122D LEU* 3.1 13.0 + - + +
123D ILE* 2.7 38.1 + - - +
131D ILE* 5.1 4.7 - - + -
167D LEU* 4.2 27.8 - - + -
172D ILE* 4.7 3.1 - - + +
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Residues in contact with ARG 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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93B LEU* 2.8 38.0 + - + +
116D GLN* 3.1 64.1 + - - +
117D ILE* 2.9 15.3 + - - +
119D ALA* 1.3 75.2 - - - +
121D GLY* 1.3 52.0 + - - +
123D ILE* 3.5 8.7 - - - +
124D ALA* 2.5 38.5 + - - +
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Residues in contact with GLY 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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76D PRO* 6.2 2.0 - - - -
117D ILE 3.5 7.0 + - - -
118D VAL 4.0 2.9 - - - -
119D ALA 3.2 0.4 - - - -
120D ARG* 1.3 76.2 - - - +
122D LEU* 1.3 56.2 + - - +
124D ALA* 3.3 8.2 - - - +
125D ARG* 2.5 51.3 + - - +
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Residues in contact with LEU 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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77D VAL 4.1 11.0 - - - +
78D ASP* 4.0 22.7 - - - +
118D VAL* 3.2 29.3 + - + +
119D ALA* 3.1 12.7 + - - +
121D GLY* 1.3 76.2 - - - +
123D ILE* 1.3 60.3 + - - +
125D ARG* 3.4 5.2 + - - +
126D GLY 3.1 1.4 + - - -
127D VAL* 2.8 50.8 + - + +
128D PRO 3.4 24.7 - - - +
129D GLY* 4.0 11.4 - - - -
130D ALA 4.6 2.7 - - - +
131D ILE* 5.7 2.2 - - + -
172D ILE* 4.0 28.3 - - + -
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Residues in contact with ILE 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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93B LEU* 3.3 34.3 - - + -
119D ALA 2.7 20.5 + - - +
120D ARG* 3.6 6.1 - - - +
122D LEU* 1.3 73.1 - - - +
124D ALA* 1.3 66.4 + - - +
126D GLY* 3.0 14.5 + - - +
127D VAL 5.0 0.4 - - - -
167D LEU* 4.0 11.0 - - + -
170D HIS* 3.3 54.7 - - + +
172D ILE* 4.2 2.9 - - + +
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ARG 2.5 23.5 + - - +
121D GLY* 2.9 11.0 + - - +
123D ILE* 1.3 77.9 - - - +
125D ARG* 1.3 62.8 + - + +
126D GLY* 3.2 0.9 + - - -
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PRO* 3.4 33.8 - - - +
77D VAL 3.4 23.8 + - - -
78D ASP* 2.5 30.5 + - - -
121D GLY* 2.5 24.8 + - - +
122D LEU* 4.2 10.9 - - - +
124D ALA* 1.3 74.8 - - + +
126D GLY* 1.3 63.0 + - - +
127D VAL* 3.8 30.5 - - + +
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Residues in contact with GLY 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 LEU 3.1 0.4 + - - -
123D ILE* 3.0 17.6 + - - -
124D ALA 3.1 1.4 + - - -
125D ARG* 1.3 77.9 - - - +
127D VAL* 1.3 61.1 + - - +
128D PRO* 4.4 2.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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