Contacts of the helix formed by residues 144 - 159 (chain A) in PDB entry 3V6A
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 GLU 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLN* 4.4 7.7 - - - +
107A GLN* 3.7 19.9 + - - +
139A GLN* 4.4 2.6 + - - -
143A GLY* 1.3 73.8 - - - +
145A ASP* 1.3 67.6 + - - +
146A ILE* 4.3 7.1 - - + +
147A VAL* 3.1 17.6 + - + +
148A ARG* 2.9 19.9 + - - +
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Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLY 4.7 2.5 - - - +
144A GLU* 1.3 72.4 - - - +
146A ILE* 1.3 66.5 + - + +
148A ARG* 3.2 13.6 + - - +
149A GLU* 3.0 25.3 + - - +
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Residues in contact with ILE 146 (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 GLN* 3.9 32.1 - - + +
144A GLU* 3.2 4.9 - - + +
145A ASP* 1.3 80.7 - - + +
147A VAL* 1.3 63.0 - - + +
149A GLU* 3.3 12.8 + - - +
150A ARG* 3.1 39.1 + - - +
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Residues in contact with VAL 147 (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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103A THR* 3.5 26.5 - - + +
104A GLN* 4.1 15.9 - - - +
107A GLN* 3.8 30.7 - - + +
139A GLN* 3.8 35.2 - - + +
144A GLU* 3.1 23.3 + - + +
146A ILE* 1.3 75.2 - - - +
148A ARG* 1.3 59.4 + - - +
150A ARG* 3.2 6.5 + - + +
151A ALA* 2.8 29.6 + - - +
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Residues in contact with ARG 148 (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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139A GLN 4.2 4.8 + - - +
140A ILE* 2.8 59.6 + - - +
141A LEU* 4.8 5.3 + - - +
143A GLY 4.9 2.9 - - - +
144A GLU 2.9 13.4 + - - +
145A ASP* 3.2 16.6 + - - +
147A VAL* 1.3 76.7 - - - +
149A GLU* 1.3 62.0 + - - +
151A ALA* 3.5 2.7 + - - +
152A ILE* 3.1 38.5 + - + +
182A VAL* 4.0 11.5 + - - +
185A ASP 3.2 22.0 + - - -
186A VAL* 3.7 10.9 - - - +
190A GLU* 2.7 41.5 + - - +
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Residues in contact with GLU 149 (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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145A ASP 3.0 13.2 + - - +
146A ILE* 3.6 17.1 - - - +
147A VAL 3.2 0.2 - - - -
148A ARG* 1.3 78.5 - - - +
150A ARG* 1.3 69.6 + - - +
152A ILE* 3.3 9.2 + - - +
153A LYS* 3.0 38.8 + - + +
190A GLU* 5.7 2.0 - - - +
193A LEU* 5.9 0.3 - - - +
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Residues in contact with ARG 150 (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 LEU* 2.6 62.0 + - + +
107A GLN* 3.5 15.0 + - - -
108A THR 3.0 16.2 + - - -
109A ASP* 3.3 22.8 + - - -
114A PHE* 4.1 18.1 - - + -
146A ILE* 3.1 31.1 + - + +
147A VAL* 3.7 7.0 - - - +
149A GLU* 1.3 83.5 + - - +
151A ALA* 1.3 57.4 + - - +
153A LYS* 3.4 7.4 + - - +
154A PHE* 2.9 28.1 + - - +
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Residues in contact with ALA 151 (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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103A THR* 4.2 8.5 - - + -
106A LEU* 4.1 10.7 - - - +
136A LEU* 4.1 21.4 - - + +
139A GLN* 5.0 0.2 - - + -
140A ILE* 3.5 28.5 - - + +
147A VAL 2.8 17.7 + - - +
148A ARG* 3.7 0.7 - - - +
150A ARG* 1.3 78.3 - - - +
152A ILE* 1.3 61.3 + - - +
154A PHE* 3.3 4.1 + - - +
155A LEU* 3.1 26.5 + - - +
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Residues in contact with ILE 152 (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 ILE* 3.8 21.8 - - + -
148A ARG* 3.1 40.1 + - + +
149A GLU* 3.3 6.5 + - - +
151A ALA* 1.3 73.2 - - - +
153A LYS* 1.3 61.1 + - - +
155A LEU* 3.2 7.1 + - - +
156A SER* 2.8 28.1 + - - -
190A GLU* 4.0 22.9 - - + +
193A LEU* 3.8 35.4 - - + -
194A PHE* 3.8 30.3 - - + -
197A ILE* 4.1 4.3 - - + +
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Residues in contact with LYS 153 (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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114A PHE* 6.4 2.7 - - + -
149A GLU* 3.0 33.3 + - + +
150A ARG* 3.8 7.9 - - - +
152A ILE* 1.3 78.6 - - - +
154A PHE* 1.3 54.3 + - - +
156A SER* 3.6 8.1 - - - +
157A THR* 2.6 53.6 + - + +
193A LEU* 3.8 29.4 - - + +
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Residues in contact with PHE 154 (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 LEU* 4.0 11.9 - - + -
118A ASN* 2.9 36.8 - - - +
121A LEU* 3.5 41.3 - - + -
122A LEU* 3.8 22.0 - - + -
125A PHE* 4.4 12.1 - + - -
136A LEU* 3.8 33.4 - - + -
150A ARG 2.9 14.2 + - - +
151A ALA* 3.4 8.7 - - - +
152A ILE 3.1 0.6 - - - -
153A LYS* 1.3 76.6 - - - +
155A LEU* 1.3 66.5 + - + +
157A THR* 4.0 3.4 - - - -
158A LYS* 2.8 52.9 + - + +
159A LEU* 5.6 2.0 - - + -
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Residues in contact with LEU 155 (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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133A LEU* 4.2 16.2 - - + -
136A LEU* 4.0 27.4 - - + -
137A PHE* 3.8 32.1 - - + -
140A ILE* 4.0 18.8 - - + -
151A ALA 3.1 10.2 + - - +
152A ILE* 3.2 3.3 + - - +
154A PHE* 1.3 82.8 - - + +
156A SER* 1.3 61.0 - - - +
157A THR 3.3 0.5 + - - -
159A LEU* 3.6 44.5 + - + +
175A ILE* 5.8 1.6 - - + -
194A PHE* 4.7 2.0 - - + -
197A ILE* 3.6 31.1 - - + +
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Residues in contact with SER 156 (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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152A ILE 2.8 20.9 + - - -
153A LYS* 3.5 13.3 - - - +
154A PHE 3.2 0.2 - - - -
155A LEU* 1.3 74.2 - - - +
157A THR* 1.3 63.7 + - - +
160A LYS* 4.9 2.6 + - - +
193A LEU* 3.4 29.5 - - - +
196A LYS* 3.2 36.4 + - - +
197A ILE* 3.9 15.9 - - - +
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Residues in contact with THR 157 (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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153A LYS* 2.6 42.2 + - + +
154A PHE* 4.0 0.7 - - - -
156A SER* 1.3 83.5 - - - +
158A LYS* 1.3 84.8 + - - +
159A LEU 3.9 0.9 - - - -
160A LYS* 3.4 35.4 - - - +
161A THR* 4.0 3.5 - - - +
196A LYS* 5.1 4.5 - - - +
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Residues in contact with LYS 158 (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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114A PHE* 6.1 1.8 - - - -
115A ASN* 5.9 0.8 + - - -
118A ASN* 3.8 23.7 - - - +
122A LEU* 4.1 25.2 - - + +
154A PHE* 2.8 53.9 + - + +
157A THR* 1.3 97.6 + - - +
159A LEU* 1.3 65.1 + - - +
160A LYS 3.0 2.9 - - - -
161A THR* 2.8 32.2 + - + +
162A LEU 3.7 1.6 + - - -
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Residues in contact with LEU 159 (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 PHE* 3.6 36.6 - - + -
154A PHE* 4.1 3.0 + - + -
155A LEU* 3.6 37.0 + - + +
158A LYS* 1.3 76.3 - - - +
160A LYS* 1.3 61.9 + - - +
161A THR 3.1 0.2 - - - -
162A LEU* 3.1 30.0 + - + +
167A LEU* 3.6 27.0 - - + +
175A ILE* 4.0 21.8 - - + -
197A ILE* 4.1 22.9 - - + +
201A LEU* 4.7 9.2 - - + -
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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