Contacts of the helix formed by residues 125 - 146 (chain A) in PDB entry 3P8W
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 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASN* 4.1 13.7 - - - +
122A ASN* 3.1 26.6 + - + +
124A ALA* 1.3 80.3 - - - +
126A ASN* 1.3 63.9 + - - +
127A ASP 3.4 1.1 - - - -
128A ASN* 3.6 28.7 + - + +
129A LEU* 3.2 35.9 + - + +
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Residues in contact with ASN 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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117A TYR* 3.6 25.3 + - - +
120A ASN* 3.9 15.0 + - - +
122A ASN 3.4 3.0 + - - +
123A PRO* 3.3 15.9 + - + +
125A LEU* 1.3 77.9 - - - +
127A ASP* 1.3 73.7 + - - +
129A LEU* 3.3 3.9 + - - +
130A GLU* 3.0 32.4 + - - +
195A ARG* 4.0 5.5 + - - -
240A LEU* 3.4 27.2 - - + +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO 4.7 2.6 + - - -
124A ALA 4.6 4.1 + - - +
125A LEU 3.4 0.2 - - - -
126A ASN* 1.3 88.9 + - - +
128A ASN* 1.3 66.2 + - - +
130A GLU* 3.5 11.9 + - - +
131A LYS* 3.1 24.1 + - - +
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Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA 4.9 3.6 + - - +
125A LEU* 3.6 31.6 + - + +
126A ASN 3.4 0.2 - - - -
127A ASP* 1.3 79.4 - - - +
129A LEU* 1.3 70.6 + - - +
131A LYS* 3.3 15.5 + - - +
132A GLY* 3.0 24.1 + - - -
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Residues in contact with LEU 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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113A LYS* 4.6 3.4 - - - +
116A ALA* 3.6 32.1 - - + +
117A TYR* 3.9 20.0 - - + +
120A ASN* 3.3 43.1 - - + +
125A LEU* 3.2 31.5 + - + +
126A ASN 3.7 4.0 - - - +
127A ASP 3.3 0.2 - - - -
128A ASN* 1.3 84.4 - - - +
130A GLU* 1.3 65.2 + - - +
132A GLY* 3.3 2.4 + - - +
133A LEU* 3.1 24.3 + - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 3.8 20.5 - - + +
126A ASN* 3.0 21.6 + - - +
127A ASP* 3.9 15.5 - - - +
129A LEU* 1.3 72.6 - - - +
131A LYS* 1.3 57.2 + - - +
133A LEU* 3.3 6.8 + - - +
134A LEU* 2.8 40.5 + - + +
197A PHE* 3.3 39.0 - - + -
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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 ASP 3.1 14.3 + - - +
128A ASN* 3.4 16.2 - - - +
130A GLU* 1.3 77.6 - - - +
132A GLY* 1.3 58.6 + - - +
134A LEU* 3.7 10.1 - - + +
135A LYS* 2.8 38.7 + - + +
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Residues in contact with GLY 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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113A LYS* 3.9 20.0 - - - +
128A ASN* 3.0 14.5 + - - -
129A LEU* 3.3 3.9 + - - -
131A LYS* 1.3 76.6 - - - +
133A LEU* 1.3 61.7 + - - +
135A LYS* 3.4 6.5 + - - +
136A ALA* 3.1 23.6 + - - +
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Residues in contact with LEU 133 (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 37.7 - - + +
113A LYS* 3.8 14.7 - - + +
114A PHE* 4.1 14.8 - - + +
117A TYR* 3.8 26.9 - - + -
129A LEU 3.1 13.3 + - - +
130A GLU* 3.5 7.6 - - - +
132A GLY* 1.3 76.1 - - - +
134A LEU* 1.3 62.0 + - - +
136A ALA* 3.3 2.1 + - - +
137A LEU* 3.0 31.6 + - + +
187A VAL* 4.5 6.3 - - + -
191A CYS* 4.2 9.9 - - - -
197A PHE* 4.0 26.0 - - + -
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Residues in contact with LEU 134 (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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130A GLU* 2.8 42.5 + - + +
131A LYS* 3.8 8.1 - - + +
133A LEU* 1.3 72.6 - - - +
135A LYS* 1.3 52.5 + - - +
137A LEU* 3.3 5.1 + - + -
138A LYS* 2.8 35.8 + - - +
197A PHE* 3.5 23.8 - - + -
200A PRO* 3.4 40.4 - - + -
203A PHE* 3.5 14.9 - - + -
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Residues in contact with LYS 135 (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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131A LYS* 2.8 27.1 + - + +
132A GLY* 3.9 5.6 - - - +
134A LEU* 1.3 76.5 - - - +
136A ALA* 1.3 55.5 + - - +
138A LYS* 3.2 8.6 + - + +
139A VAL* 3.0 52.1 + - + +
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Residues in contact with ALA 136 (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 GLY* 5.3 0.7 - - - -
109A ASP* 3.9 20.1 - - - +
110A ILE* 3.4 28.6 - - + +
113A LYS* 3.9 19.3 - - + -
132A GLY 3.1 13.9 + - - +
133A LEU* 3.5 9.0 - - - +
135A LYS* 1.3 72.6 - - - +
137A LEU* 1.3 66.3 + - - +
139A VAL* 3.3 8.0 + - - +
140A LEU 3.1 17.3 + - - -
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Residues in contact with LEU 137 (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 14.4 - - + -
133A LEU* 3.0 41.0 + - + +
134A LEU* 3.6 13.2 - - + +
136A ALA* 1.3 76.2 - - - +
138A LYS* 1.3 58.1 + - - +
140A LEU* 3.2 6.1 + - + +
141A ASP* 2.8 27.5 + - - +
184A LEU* 4.1 22.9 - - + -
187A VAL* 5.5 4.5 - - + -
197A PHE* 4.4 11.0 - - + -
199A ILE* 4.0 39.0 - - + -
203A PHE* 3.8 13.2 - - + -
206A VAL* 3.8 13.4 - - + +
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Residues in contact with LYS 138 (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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134A LEU 2.8 17.8 + - - +
135A LYS* 3.5 9.9 - - + +
136A ALA 3.2 0.2 - - - -
137A LEU* 1.3 77.6 - - - +
139A VAL* 1.3 56.7 + - + +
141A ASP* 2.9 31.7 + - - +
142A ASN* 2.8 54.7 + - - +
202A ALA* 3.9 15.2 + - - +
203A PHE* 3.7 28.1 - - + -
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Residues in contact with VAL 139 (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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106A ALA* 5.9 0.2 - - - +
107A GLY 5.8 3.4 - - - +
109A ASP* 5.8 4.9 - - - +
135A LYS* 3.0 38.0 + - + +
136A ALA* 3.3 10.0 + - - +
138A LYS* 1.3 75.3 - - + +
140A LEU* 1.3 62.3 + - - +
142A ASN* 3.4 14.5 + - + +
143A TYR* 3.1 21.5 + - - +
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Residues in contact with LEU 140 (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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106A ALA* 4.4 3.1 - - + -
107A GLY* 4.1 17.3 - - - +
110A ILE* 3.8 28.5 - - + -
136A ALA 3.1 5.9 + - - -
137A LEU* 3.4 7.6 - - + +
139A VAL* 1.3 75.6 - - - +
141A ASP* 1.3 64.9 + - - +
143A TYR* 3.1 5.1 + - + +
144A LEU* 3.0 41.3 + - + +
168A LEU* 3.8 24.0 - - + -
180A LEU* 3.8 13.7 - - + -
184A LEU* 4.0 27.6 - - + -
206A VAL* 4.0 15.5 - - + -
209A TYR* 5.1 0.7 - - + -
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Residues in contact with ASP 141 (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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137A LEU 2.8 17.1 + - - +
138A LYS* 2.9 41.3 + - + +
140A LEU* 1.3 73.4 - - - +
142A ASN* 1.3 63.7 + - - +
144A LEU* 3.2 2.7 + - - +
145A THR* 3.1 34.5 + - - +
202A ALA 4.3 0.3 - - - +
203A PHE* 3.2 19.5 - - + -
204A ARG 4.2 1.9 + - - -
205A GLY 2.8 29.1 + - - -
206A VAL* 2.9 22.9 + - + +
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Residues in contact with ASN 142 (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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138A LYS* 2.8 45.4 + - - +
139A VAL* 3.7 16.7 - - + +
141A ASP* 1.3 72.3 - - - +
143A TYR* 1.3 61.7 + - - +
145A THR* 3.6 7.3 + - - -
146A SER* 2.7 31.2 + - - +
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Residues in contact with TYR 143 (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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100A ASN* 4.0 5.4 - - - +
102A GLU* 3.5 36.9 - - + +
103A SER* 2.5 44.8 + - - -
106A ALA* 3.6 25.1 - - + -
139A VAL 3.1 13.8 + - - +
140A LEU 3.1 8.5 + - - +
142A ASN* 1.3 76.9 - - - +
144A LEU* 1.3 56.4 + - - +
146A SER* 3.3 22.1 + - - +
148A LEU* 3.8 23.7 - - + +
165A ARG* 2.7 32.7 + - - -
168A LEU* 3.3 34.5 - - + -
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Residues in contact with LEU 144 (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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140A LEU* 3.0 43.0 + - + +
141A ASP 3.2 4.2 + - - +
143A TYR* 1.3 78.8 - - - +
145A THR* 1.3 57.5 + - - +
163A SER* 3.5 9.5 + - - +
165A ARG* 3.4 26.1 + - + +
166A LYS 5.5 0.4 - - - +
167A PHE* 4.2 5.2 - - - +
168A LEU* 4.0 30.3 - - + +
205A GLY* 4.3 11.2 - - - +
206A VAL* 4.0 26.2 - - + +
208A ARG* 4.7 3.5 + - - -
209A TYR* 4.0 37.5 - - + -
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Residues in contact with THR 145 (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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141A ASP* 3.1 23.5 + - - +
142A ASN* 3.6 9.4 + - - -
143A TYR 3.3 0.2 - - - -
144A LEU* 1.3 75.2 - - - +
146A SER* 1.3 58.6 + - - +
147A PRO* 3.6 1.2 - - - +
161A GLY 3.7 1.7 - - - +
162A VAL* 3.5 20.8 - - + -
163A SER* 2.7 31.0 + - - +
204A ARG* 6.0 0.4 - - + -
205A GLY* 3.7 28.0 - - - +
208A ARG* 3.9 11.2 - - - +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 2.7 22.6 + - - +
143A TYR* 3.3 13.8 + - - +
145A THR* 1.3 75.2 - - - +
147A PRO* 1.3 71.5 - - - +
148A LEU* 3.4 5.7 + - - +
161A GLY 4.9 0.4 - - - -
165A ARG* 2.8 24.9 + - - -
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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