Contacts of the helix formed by residues 120 - 134 (chain C) in PDB entry 1WZN
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 ASP 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C TYR 4.3 0.2 + - - -
119C PHE* 1.3 72.5 - - - +
121C GLU* 1.3 64.2 + - - +
122C GLU* 3.2 20.4 + - - +
123C ASP* 2.9 35.4 + - - +
124C LEU* 2.9 19.1 + - - +
182C LYS* 4.0 11.4 + - - +
208C ASN* 3.4 20.8 - - - +
210C TYR* 2.9 10.0 + - - -
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Residues in contact with GLU 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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120C ASP* 1.3 73.8 - - - +
122C GLU* 1.3 81.1 + - - +
124C LEU* 3.2 6.1 + - - +
125C ARG* 3.1 62.4 + - - +
210C TYR* 3.0 15.7 + - + +
218C LEU* 3.8 22.6 - - + +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ASP* 3.2 22.1 - - - +
121C GLU* 1.3 96.2 + - - +
123C ASP* 1.3 66.5 + - - +
125C ARG* 3.3 16.4 + - - +
126C LYS* 3.2 18.7 + - - +
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Residues in contact with ASP 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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98C LEU* 3.5 35.1 - - + +
119C PHE* 3.9 19.7 - - + -
120C ASP* 2.9 27.4 + - - +
122C GLU* 1.3 77.0 - - - +
124C LEU* 1.3 59.7 + - - +
126C LYS* 3.3 14.0 + - - +
127C LEU* 2.9 24.6 + - - +
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Residues in contact with LEU 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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116C ILE* 4.0 33.4 - - + +
119C PHE* 4.1 8.7 - - + +
120C ASP 2.9 16.2 + - - +
121C GLU* 3.5 5.8 - - - +
123C ASP* 1.3 74.8 - - - +
125C ARG* 1.3 61.4 + - - +
127C LEU* 3.4 12.2 + - + +
128C PHE* 3.0 69.9 + - + -
210C TYR* 3.6 39.3 - - + +
215C VAL* 5.3 4.0 - - + -
218C LEU* 4.1 11.0 - - + -
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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
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121C GLU* 3.1 45.9 + - - +
122C GLU* 3.5 13.2 + - - +
124C LEU* 1.3 75.4 - - + +
126C LYS* 1.3 59.5 + - - +
128C PHE* 3.3 2.9 + - - -
129C SER* 2.9 30.7 + - - -
218C LEU* 3.7 27.8 - - + +
221C LYS* 5.1 15.2 - - + +
222C TYR* 3.4 35.1 - - + +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.1 41.1 + - + +
99C GLU* 5.4 4.2 - - - +
122C GLU 3.2 9.5 + - - +
123C ASP* 3.5 23.6 + - - +
125C ARG* 1.3 78.6 - - - +
127C LEU* 1.3 62.2 + - - +
129C SER* 3.3 7.6 + - - -
130C LYS* 3.0 41.8 + - + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 4.1 17.7 - - + -
97C VAL* 3.9 37.2 - - + +
98C LEU* 3.9 8.7 - - + +
100C ILE* 5.3 1.8 - - + -
111C MET* 3.8 29.6 - - + -
116C ILE* 5.1 0.7 - - + -
119C PHE* 4.1 16.6 - - + -
123C ASP 2.9 18.0 + - - +
124C LEU* 3.6 15.7 - - + +
125C ARG 3.2 0.2 - - - -
126C LYS* 1.3 76.5 - - - +
128C PHE* 1.3 66.7 + - + +
130C LYS* 3.1 7.2 + - - +
131C VAL* 2.8 37.9 + - + +
141C PHE* 5.2 3.4 - - + -
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Residues in contact with PHE 128 (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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116C ILE* 5.0 5.8 - - + -
124C LEU* 3.0 57.9 + - + +
125C ARG* 3.8 2.5 - - - +
127C LEU* 1.3 81.7 - - + +
129C SER* 1.3 62.6 + - - +
131C VAL* 3.4 6.5 + - + +
132C ALA* 3.0 24.1 + - - +
141C PHE* 3.3 41.1 - + - -
143C THR* 5.5 0.9 - - + -
215C VAL* 4.2 19.3 - - + -
218C LEU* 4.0 23.8 - - + -
219C ALA* 4.0 20.6 - - + -
222C TYR* 3.7 22.1 - - + +
223C PHE* 4.1 11.4 - + + -
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Residues in contact with SER 129 (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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125C ARG 2.9 18.9 + - - -
126C LYS* 3.5 7.9 - - - -
128C PHE* 1.3 77.4 - - - +
130C LYS* 1.3 63.1 + - - +
132C ALA* 3.3 5.0 + - - +
133C GLU* 3.1 31.4 + - - +
222C TYR* 3.5 27.8 - - - -
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Residues in contact with LYS 130 (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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97C VAL 4.9 0.7 - - - +
98C LEU 3.6 24.9 + - - +
99C GLU* 4.9 3.0 - - - +
100C ILE* 3.3 46.5 + - + +
101C ALA* 5.3 3.0 - - - +
102C PHE 4.7 1.2 - - - +
126C LYS* 3.0 34.9 + - - +
127C LEU* 3.5 8.7 - - + +
129C SER* 1.3 73.9 - - - +
131C VAL* 1.3 66.2 + - - +
133C GLU* 3.2 22.0 + - - +
134C ALA* 3.0 23.4 + - - +
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Residues in contact with VAL 131 (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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48C LEU* 3.7 29.6 - - + -
100C ILE* 4.6 3.1 - - + -
109C VAL* 3.8 15.3 - - + -
127C LEU* 2.8 29.1 + - + +
128C PHE* 3.7 7.9 - - - +
130C LYS* 1.3 75.8 - - - +
132C ALA* 1.3 64.5 + - - +
134C ALA* 3.2 8.0 + - - +
135C LEU* 3.1 23.9 + - + +
141C PHE* 3.5 45.8 - - + -
223C PHE* 3.9 4.9 - - + -
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Residues in contact with ALA 132 (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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128C PHE 3.0 17.4 + - - +
129C SER* 3.5 6.3 - - - +
130C LYS 3.2 0.2 - - - -
131C VAL* 1.3 77.2 - - - +
133C GLU* 1.3 63.8 + - + +
135C LEU* 3.3 20.1 + - - +
222C TYR* 3.7 28.5 - - + +
223C PHE* 4.1 14.3 - - + -
249C ALA* 5.5 3.4 - - + +
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Residues in contact with GLU 133 (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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102C PHE 3.8 9.9 - - - +
103C LYS* 3.2 19.3 - - + +
104C ASN* 2.8 22.0 + - - -
129C SER* 3.1 24.0 + - - +
130C LYS* 3.2 29.1 + - - +
132C ALA* 1.3 80.0 - - + +
134C ALA* 1.3 57.4 + - - +
135C LEU 3.5 1.9 + - - +
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Residues in contact with ALA 134 (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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46C LEU* 4.7 5.4 - - + -
100C ILE* 4.7 4.3 - - + -
102C PHE* 3.6 33.2 + - + +
104C ASN 3.8 0.4 - - - -
105C GLU* 3.0 23.4 + - - -
106C PHE* 3.0 17.0 + - + -
109C VAL* 4.4 11.4 - - + -
130C LYS 3.0 15.7 + - - +
131C VAL* 3.2 9.4 + - - +
133C GLU* 1.3 75.6 - - - +
135C LEU* 1.3 60.0 + - - +
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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