Contacts of the helix formed by residues 124 - 140 (chain B) in PDB entry 1WZ9
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 LYS 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ASP* 3.1 24.1 + - + +
123B ASP* 1.3 78.7 - - - +
125B LEU* 1.3 56.5 + - - +
126B GLU 3.4 2.5 - - - -
127B GLU* 4.0 16.4 - - + +
128B THR* 2.7 35.6 + - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASP 3.6 2.2 + - - -
121B PHE* 3.3 26.2 + - + +
122B LYS 5.2 1.6 - - - +
123B ASP 3.6 4.0 + - - -
124B LYS* 1.3 76.6 - - - +
126B GLU* 1.3 64.1 + - - +
128B THR* 3.8 2.3 - - - -
129B LYS* 3.1 42.2 + - + +
153B VAL* 4.4 3.6 - - + +
154B ASN* 3.6 35.0 - - + +
155B ASP* 3.9 25.8 - - + +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS 3.4 0.4 - - - -
125B LEU* 1.3 81.4 - - - +
127B GLU* 1.3 61.2 + - - +
129B LYS* 3.6 5.6 + - - +
130B GLY* 3.4 17.5 + - - -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS* 3.5 19.1 + - + +
125B LEU 3.4 0.2 - - - -
126B GLU* 1.3 75.9 - - - +
128B THR* 1.3 60.6 + - - +
130B GLY* 3.4 2.2 + - - +
131B GLN* 2.9 29.6 + - - +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 3.6 28.8 - - + +
120B ASP* 2.7 23.4 + - - +
121B PHE* 3.7 17.9 - - + -
124B LYS* 2.7 23.2 + - - +
125B LEU* 3.8 4.9 - - - -
127B GLU* 1.3 74.0 - - - +
129B LYS* 1.3 54.5 + - - +
131B GLN* 3.0 7.8 + - - +
132B ILE* 2.7 51.8 + - + +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PHE* 5.9 2.2 - - + -
125B LEU* 3.1 33.3 + - + +
126B GLU* 3.8 6.7 - - - +
128B THR* 1.3 75.5 - - + +
130B GLY* 1.3 56.6 + - - +
133B ASN* 2.9 40.7 + - - +
148B LEU* 3.5 33.2 + - + +
152B SER* 4.0 20.2 + - - -
153B VAL* 3.1 41.2 + - + +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU 3.4 11.2 + - - -
127B GLU* 3.8 2.9 - - - -
128B THR 3.3 0.4 - - - -
129B LYS* 1.3 74.7 - - - +
131B GLN* 1.3 60.3 + - - +
133B ASN* 3.7 7.1 - - - +
134B ASN* 2.8 43.6 + - - -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 6.0 4.5 - - + -
127B GLU 2.9 18.3 + - - +
128B THR* 3.0 10.1 + - + +
130B GLY* 1.3 75.0 - - - +
132B ILE* 1.3 58.7 + - + +
134B ASN* 4.2 3.9 - - - +
135B SER* 3.1 30.0 + - - -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TYR* 3.6 50.9 - - + +
119B VAL* 5.1 2.9 - - + -
121B PHE* 3.7 35.9 - - + -
128B THR* 2.7 31.3 + - + +
131B GLN* 1.3 71.9 - - + +
133B ASN* 1.3 65.6 + - - +
135B SER* 3.9 0.6 - - - -
136B ILE* 3.1 36.8 + - + +
147B ILE* 4.5 3.6 - - + -
148B LEU* 3.8 31.4 - - + -
160B LEU* 4.2 4.9 - - + -
162B VAL* 4.8 1.8 - - + -
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Residues in contact with ASN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LYS* 2.9 29.3 + - - +
130B GLY* 3.7 7.8 - - - +
132B ILE* 1.3 76.1 - - - +
134B ASN* 1.3 59.1 + - - +
136B ILE* 4.1 1.2 - - - +
137B LYS* 3.1 28.2 + - - +
144B PHE 4.4 0.5 - - - +
145B GLU 3.6 14.1 - - - +
146B ASN* 4.1 16.0 - - - +
147B ILE* 3.4 9.2 + - - +
148B LEU* 3.2 40.3 + - - +
149B ALA 5.5 0.2 - - - +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY* 2.8 31.7 + - - +
131B GLN* 4.2 4.3 - - - +
133B ASN* 1.3 72.5 - - - +
135B SER* 1.3 65.2 + - - +
137B LYS* 3.3 20.9 + - - +
138B ASP* 3.0 24.5 + - - +
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 5.2 0.2 + - - -
93B TYR* 4.4 9.5 + - - -
117B GLU* 4.7 12.3 + - - -
131B GLN 3.1 18.9 + - - -
132B ILE* 3.9 5.4 - - - -
134B ASN* 1.3 77.2 - - - +
136B ILE* 1.3 57.2 + - - +
138B ASP* 3.3 7.5 + - - +
139B LEU* 2.9 46.2 + - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.0 24.2 - - + -
91B ARG* 4.0 7.9 - - + -
93B TYR* 3.4 22.2 - - - +
132B ILE* 3.1 21.5 + - + +
133B ASN 4.2 1.1 - - - +
135B SER* 1.3 71.7 - - - +
137B LYS* 1.3 65.3 + - - +
139B LEU* 3.3 6.6 + - + +
140B THR* 3.0 31.8 + - + +
144B PHE* 4.4 5.6 - - + +
147B ILE* 3.9 44.2 - - + -
162B VAL* 4.1 14.6 - - + -
164B ALA* 3.9 13.0 - - + -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN 3.1 20.3 + - - +
134B ASN* 3.4 20.6 + - - +
136B ILE* 1.3 77.5 - - - +
138B ASP* 1.3 57.8 + - - +
140B THR* 3.5 1.6 + - - -
141B ASP 3.3 3.8 + - - -
142B GLY* 2.7 50.5 + - - +
144B PHE 3.2 20.3 + - - +
145B GLU* 4.1 12.8 - - - +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ASN 3.0 13.2 + - - +
135B SER* 3.5 10.8 - - - +
137B LYS* 1.3 78.3 - - - +
139B LEU* 1.3 61.8 + - + +
141B ASP* 3.0 24.5 + - - +
142B GLY 4.8 0.9 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 3.4 28.2 + - - +
89B ILE* 3.8 31.8 - - + +
91B ARG* 3.4 38.6 - - - +
135B SER* 2.9 38.3 + - - +
136B ILE* 3.3 9.4 + - + +
138B ASP* 1.3 81.0 - - + +
140B THR* 1.3 59.0 + - - +
141B ASP* 3.3 1.6 - - - -
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 4.5 1.6 - - + -
89B ILE* 3.9 19.5 - - + -
136B ILE* 3.0 17.9 + - + +
137B LYS 3.6 2.3 + - - -
138B ASP 3.2 0.2 - - - -
139B LEU* 1.3 78.6 - - - +
141B ASP* 1.3 71.2 + - - +
142B GLY 3.3 0.2 - - - -
143B HIS* 3.1 9.5 + - - +
144B PHE* 3.1 49.5 + - + +
164B ALA* 3.9 16.4 - - + +
166B TYR* 3.2 27.7 - - + -
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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