Contacts of the helix formed by residues 115 - 132 (chain A) in PDB entry 5W4A
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLY* 1.3 72.9 - - - +
116A GLU* 1.3 67.4 + - - +
117A ASP* 3.7 6.4 + - - +
118A ALA* 3.1 32.4 + - + +
119A ALA* 3.1 17.2 + - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS* 5.9 0.9 + - - -
111A LEU* 4.1 21.8 - - + +
113A GLN 4.1 12.5 - - - +
114A GLY* 4.0 2.2 - - - -
115A ASP* 1.3 76.8 + - - +
117A ASP* 1.3 61.9 + - - +
119A ALA* 3.3 6.3 + - - +
120A LYS* 2.9 44.8 + - + +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.3 5.9 + - - +
116A GLU* 1.3 82.4 - - - +
118A ALA* 1.3 62.7 + - - +
120A LYS* 3.1 12.8 + - - +
121A LYS* 3.0 35.4 + - + +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 3.1 33.4 + - + +
117A ASP* 1.3 78.8 - - - +
119A ALA* 1.3 64.0 + - - +
121A LYS* 3.3 8.7 + - - +
122A LYS* 3.1 22.7 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 3.8 41.1 - - + +
111A LEU* 4.6 6.7 - - + +
114A GLY 4.7 0.7 - - - +
115A ASP 3.1 13.0 + - - +
116A GLU* 3.6 9.9 - - - +
118A ALA* 1.3 76.4 - - - +
120A LYS* 1.3 58.1 + - - +
122A LYS* 3.3 7.5 + - - +
123A LEU* 2.8 35.1 + - - +
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 6.3 1.8 - - - +
111A LEU* 4.0 16.8 - - + -
116A GLU* 2.9 28.9 + - - +
117A ASP* 3.1 11.3 + - - +
119A ALA* 1.3 74.8 - - - +
121A LYS* 1.3 62.3 + - + +
123A LEU* 4.3 4.0 - - - -
124A ASN* 2.8 27.4 + - - +
148A ILE* 3.8 31.7 + - - -
149A ASN* 3.0 32.6 + - - +
151A GLU* 6.1 3.2 - - - +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 3.0 27.2 + - + +
118A ALA* 3.7 8.7 - - - +
120A LYS* 1.3 79.5 - - - +
122A LYS* 1.3 61.5 + - - +
124A ASN* 3.3 11.6 + - + +
125A LEU* 3.3 26.4 + - - +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 3.5 31.1 - - + +
118A ALA 3.1 14.9 + - - +
119A ALA* 3.6 9.2 - - - +
121A LYS* 1.3 76.2 - - - +
123A LEU* 1.3 61.8 + - - +
125A LEU* 3.3 9.9 + - - +
126A MSE 3.1 42.0 + - + +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.7 19.1 - - + -
110A ILE* 3.7 26.7 - - + -
111A LEU* 3.5 45.1 - - + -
119A ALA 2.8 21.8 + - - +
120A LYS* 3.8 5.8 - - + +
122A LYS* 1.3 69.2 - - - +
124A ASN* 1.3 61.0 + - - +
126A MSE 3.1 33.8 + - + +
127A GLY 2.8 27.0 + - - -
145A ILE* 3.3 24.1 - - + +
148A ILE* 5.5 2.7 - - + -
149A ASN* 4.6 1.8 - - - +
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS 2.8 21.8 + - - +
121A LYS* 3.5 13.0 + - + +
122A LYS 3.2 0.4 - - - -
123A LEU* 1.3 73.2 - - - +
125A LEU* 1.3 77.9 + - - +
127A GLY* 3.2 1.4 + - - -
128A ARG* 3.1 44.4 + - - +
145A ILE* 4.2 3.5 - - - +
146A LYS* 5.0 8.0 + - - +
149A ASN* 3.7 16.2 + - - +
154C TYR* 4.9 3.4 + - - -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS 3.3 12.1 + - - +
122A LYS* 3.3 9.3 + - - +
123A LEU 3.3 0.4 - - - -
124A ASN* 1.3 90.7 - - - +
126A MSE 1.3 62.1 + - - +
128A ARG* 3.3 14.8 + - - +
129A LYS* 3.2 34.7 + - - +
154C TYR* 5.0 5.8 - - - +
185C ASP 5.7 3.8 - - - +
189C GLU* 4.8 7.6 - - - +
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Residues in contact with MSE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASP 5.8 2.7 - - - +
108A LEU* 4.3 10.3 - - + -
110A ILE* 5.3 0.4 - - + -
122A LYS* 3.1 39.7 + - + +
123A LEU* 3.1 31.6 + - + +
125A LEU* 1.3 76.4 - - - +
127A GLY* 1.3 57.3 + - - +
129A LYS* 3.3 11.3 + - - +
130A ALA* 2.9 28.3 + - + +
141A LEU* 4.6 14.6 - - + -
145A ILE* 4.0 11.7 - - + -
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU 2.8 19.2 + - - -
124A ASN 3.8 1.6 - - - -
126A MSE 1.3 74.8 - - - +
128A ARG* 1.3 62.6 + - - +
130A ALA* 4.2 4.7 - - - -
131A LYS* 3.1 20.8 + - - +
142A ALA* 3.3 19.3 - - - +
145A ILE* 3.8 21.1 - - - +
146A LYS* 4.4 5.6 - - - -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASN* 3.1 36.8 + - - +
125A LEU* 3.7 7.9 - - - +
126A MSE 3.3 0.4 - - - -
127A GLY* 1.3 76.8 - - - +
129A LYS* 1.3 61.1 + - - +
131A LYS* 3.6 8.8 + - - +
132A LEU* 3.6 21.6 + - - +
146A LYS* 3.8 22.0 - - - +
154C TYR* 3.0 37.1 + - - -
157C PHE* 4.2 7.9 - - - -
158C THR* 2.9 44.5 + - - +
161C SER* 5.6 0.6 + - - -
189C GLU* 2.9 46.3 + - - +
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.2 25.2 + - - +
126A MSE 3.8 9.4 - - - +
127A GLY 3.2 0.2 - - - -
128A ARG* 1.3 74.3 - - - +
130A ALA* 1.3 66.8 + - - +
132A LEU* 3.2 22.6 + - - +
133A GLN* 3.7 14.0 + - - +
188C ASP* 4.2 30.6 + - + +
189C GLU* 4.2 18.2 - - + +
192C VAL* 4.8 19.6 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MSE 2.9 18.8 + - + +
127A GLY* 3.3 8.7 + - - +
129A LYS* 1.3 76.8 - - - +
131A LYS* 1.3 60.6 + - - +
133A GLN* 3.0 26.6 + - - +
138A ALA* 3.3 38.5 - - + +
139A LYS 4.4 0.2 + - - -
141A LEU* 4.4 18.8 - - + -
142A ALA* 4.2 3.6 - - + +
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY 3.1 15.9 + - - +
128A ARG* 3.9 7.0 - - - +
129A LYS 3.2 0.4 - - - -
130A ALA* 1.3 76.7 - - - +
132A LEU* 1.3 60.9 + - + +
133A GLN 3.3 0.2 - - - +
139A LYS* 3.1 39.0 + - + +
142A ALA* 3.6 15.2 - - + +
143A ILE* 5.7 6.5 - - + +
146A LYS* 4.0 26.2 - - + +
159A GLU* 5.5 1.0 + - - -
162A GLU* 3.5 27.8 + - - +
162C GLU* 2.6 42.7 + - - +
164C CYS* 5.9 1.0 - - - +
165C GLY* 6.0 0.2 - - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG 3.6 16.4 - - - +
129A LYS* 3.2 9.6 + - - +
130A ALA 3.1 1.0 - - - -
131A LYS* 1.3 77.4 - - + +
133A GLN* 1.3 63.0 + - - +
134A LYS* 4.4 4.2 + - - +
139A LYS* 4.9 0.4 - - - -
161C SER* 4.1 20.4 - - - +
164C CYS* 4.0 34.4 - - + +
189C GLU* 3.8 42.8 - - + +
192C VAL* 3.6 21.3 - - + +
193C ILE* 4.2 7.9 - - + -
196C ASN* 3.0 26.5 + - - +
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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