Contacts of the helix formed by residues 108 - 125 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 3.6 15.3 - - + -
104A PHE* 4.9 4.7 - - + -
151A SER* 5.2 3.8 - - - -
104C PHE* 3.5 20.9 + - + +
106C VAL 3.1 0.6 + - - -
107C ASN* 1.3 78.8 - - + +
109C ARG* 1.3 63.4 - - - +
110C ALA 3.2 2.2 - - - -
111C VAL* 3.0 23.1 - - - +
112C ILE* 3.1 29.3 + - + +
152C THR* 3.7 9.4 - - - +
155C ALA* 4.1 11.4 - - + -
156C LEU* 3.5 50.3 - - + +
159C LEU* 3.9 14.4 - - + -
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 3.4 32.9 - - - +
100A PHE* 3.7 35.4 - - + -
101A ASP* 3.4 22.2 + - - -
61C LEU 5.8 0.4 + - - -
62C GLY 2.8 29.3 + - - -
64C TRP* 3.6 38.1 - - + +
104C PHE 3.1 11.5 + - - +
105C GLU* 3.0 41.9 + - - +
108C LEU* 1.3 76.2 - - - +
110C ALA* 1.3 51.7 + - - +
112C ILE* 3.0 11.1 + - + +
113C GLN* 2.8 29.7 + - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 3.5 41.3 - - + +
67C THR* 6.2 0.9 - - + -
82C ASN* 4.6 0.4 - - - +
84C ALA* 6.1 1.8 - - + -
105C GLU 3.3 4.5 + - - +
106C VAL 3.4 17.7 - - - +
108C LEU 3.2 0.2 - - - -
109C ARG* 1.3 73.8 - - - +
111C VAL* 1.3 56.2 - - + +
112C ILE 3.0 1.6 - - - -
113C GLN* 2.5 28.1 + - - +
114C VAL* 2.7 28.8 + - + +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASN* 3.5 29.0 - - + +
84C ALA 5.2 4.9 - - - +
106C VAL 4.7 1.3 - - - +
107C ASN 3.1 26.0 - - - +
108C LEU* 3.0 11.2 - - - +
110C ALA* 1.3 75.1 - - + +
112C ILE* 1.3 47.9 + - - +
115C SER* 2.4 46.0 + - - +
133C ASN* 3.7 23.3 - - - +
156C LEU* 4.1 14.6 - - + -
159C LEU* 3.3 26.9 - - + -
163C MET* 4.7 0.9 - - - -
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.4 14.6 - - + -
95A VAL* 3.8 25.1 - - + -
100A PHE* 3.3 42.2 - - + -
148A VAL* 4.8 8.5 - - + -
151A SER* 6.4 0.4 - - - -
64C TRP* 5.0 4.0 - - + -
108C LEU* 3.1 17.2 + - + +
109C ARG* 3.0 10.3 + - + +
110C ALA 3.0 0.6 - - - -
111C VAL* 1.3 75.9 - - - +
113C GLN* 1.3 59.7 + - - +
116C GLN* 2.8 47.3 + - + +
159C LEU* 3.8 26.9 - - + -
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Residues in contact with GLN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU 5.2 2.3 - - - +
63C ASP 4.5 0.2 - - - -
64C TRP* 2.8 85.7 + - + +
67C THR* 3.6 21.0 - - + -
68C GLU* 3.0 21.4 - - - +
109C ARG 2.8 7.0 + - - +
110C ALA* 2.5 18.7 + - - +
112C ILE* 1.3 71.0 - - - +
114C VAL* 1.3 66.2 + - - +
115C SER 3.3 0.3 + - - -
116C GLN* 3.4 16.7 + - - +
117C ILE* 3.5 20.3 + - + +
120C ARG* 5.1 0.8 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.7 29.8 - - + -
13C THR* 4.2 11.9 - - + -
61C LEU* 4.6 11.9 - - + -
67C THR* 4.8 4.9 - - + -
71C LEU* 3.9 24.5 - - + -
80C LEU* 4.1 12.1 - - + -
82C ASN* 3.9 14.8 - - - +
110C ALA* 2.7 25.0 + - + +
113C GLN* 1.3 72.6 - - - +
115C SER* 1.3 60.2 + - - +
117C ILE* 3.2 19.3 + - + +
118C VAL* 3.2 19.1 + - + +
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.5 23.0 - - - -
80C LEU* 3.7 12.0 - - - +
82C ASN* 3.0 18.9 + - - -
111C VAL* 2.4 27.2 + - - +
114C VAL* 1.3 73.9 - - - +
116C GLN* 1.3 65.5 + - - +
118C VAL* 4.3 0.7 - - - +
119C ALA* 3.2 24.4 + - - +
131C ILE* 3.8 6.0 - - - +
163C MET* 3.6 19.3 - - - +
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.4 31.5 + - + +
93A LEU* 3.6 26.0 + - + +
95A VAL 3.2 23.2 + - - +
64C TRP* 3.6 20.0 - - - -
112C ILE* 2.8 32.9 + - + +
113C GLN* 3.6 14.0 - - - +
114C VAL 3.2 1.2 - - - -
115C SER* 1.3 79.0 - - - +
117C ILE* 1.3 54.0 + - - +
120C ARG* 2.7 63.9 + - - +
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR* 5.6 1.1 - - + -
68C GLU* 5.0 11.9 - - + +
71C LEU* 4.1 41.7 - - + +
72C GLY* 4.7 8.1 - - - +
74C VAL* 4.7 11.4 - - + -
113C GLN* 3.5 24.6 + - + +
114C VAL* 3.2 11.1 + - + +
116C GLN* 1.3 79.4 - - - +
118C VAL* 1.3 65.5 + - + +
120C ARG* 3.2 19.3 - - - +
121C GLY* 2.8 27.0 + - - -
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 5.0 5.8 - - + -
74C VAL* 5.6 1.8 - - + -
77C VAL* 4.0 39.2 - - + +
79C LEU 4.8 2.5 - - - +
80C LEU* 3.8 32.5 - - + -
114C VAL* 3.2 24.1 + - + +
115C SER 4.3 1.1 - - - +
117C ILE* 1.3 80.3 - - + +
119C ALA* 1.3 51.0 + - - +
121C GLY* 3.0 3.5 + - - -
122C LEU* 2.5 60.7 + - + +
131C ILE* 5.2 2.9 - - + -
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 5.0 0.9 - - + -
93A LEU* 3.8 14.8 - - + -
115C SER 3.2 19.5 + - - +
116C GLN 3.6 2.5 - - - +
118C VAL* 1.3 76.5 - - - +
120C ARG* 1.3 54.1 + - - +
122C LEU* 2.8 12.6 + - - +
123C ILE* 2.5 43.1 + - + +
131C ILE* 5.6 3.1 - - + +
167C LEU* 4.2 16.4 - - + -
172C ILE* 4.0 17.0 - - + -
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.0 45.3 + - + +
113C GLN* 5.1 1.0 + - - +
116C GLN* 2.7 51.5 + - - +
117C ILE* 3.2 23.3 - - - +
119C ALA* 1.3 72.4 - - - +
121C GLY* 1.3 58.4 + - - +
123C ILE* 3.3 6.1 + - - +
124C ALA* 3.0 29.7 + - - +
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Residues in contact with GLY 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 6.2 2.7 - - - -
77C VAL 5.7 0.2 - - - -
117C ILE 2.8 17.0 + - - -
118C VAL* 3.4 3.8 - - - -
120C ARG* 1.3 71.0 - - - +
122C LEU* 1.3 64.6 + - - +
124C ALA* 3.4 5.3 + - - +
125C ARG* 3.2 38.2 + - - +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C VAL 4.0 14.3 + - - +
78C ASP* 3.8 24.2 - - - +
118C VAL* 2.5 42.1 + - + +
119C ALA* 3.1 10.3 - - - +
121C GLY* 1.3 75.0 - - - +
123C ILE* 1.3 60.4 + - - +
125C ARG* 3.6 10.0 + - - +
126C GLY 3.4 2.6 + - - -
127C VAL* 3.2 32.4 + - + +
128C PRO 3.1 28.7 - - - +
129C GLY* 3.8 10.8 - - - -
130C ALA 5.0 3.1 - - - +
131C ILE* 5.6 2.7 - - + -
172C ILE* 3.8 26.7 - - + -
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.7 28.9 - - + -
119C ALA* 2.5 24.5 + - + +
120C ARG* 3.8 4.7 - - - +
122C LEU* 1.3 72.6 - - - +
124C ALA* 1.3 61.9 + - - +
126C GLY* 2.9 20.2 + - - -
127C VAL 5.1 0.9 - - - +
167C LEU* 5.1 2.5 - - + -
170C HIS* 3.5 58.3 - - + +
172C ILE* 4.2 8.1 - - + -
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ARG 3.0 16.5 + - - +
121C GLY* 3.4 7.2 + - - +
122C LEU 3.4 0.2 - - - -
123C ILE* 1.3 79.0 - - - +
125C ARG* 1.3 61.5 + - + +
126C GLY 3.1 0.7 + - - -
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 3.1 49.1 + - - +
77C VAL 3.3 12.7 + - - -
78C ASP* 2.9 31.6 + - - -
121C GLY* 3.2 21.4 + - - +
122C LEU* 4.0 8.7 - - - +
123C ILE 3.2 0.6 - - - -
124C ALA* 1.3 79.1 - - + +
126C GLY* 1.3 65.0 + - - +
127C VAL* 2.9 33.8 - - + +
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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