Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 4IJ3
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A THR* 4.9 1.3 - - - -
140A GLY 3.7 2.8 + - - -
141A ALA* 1.3 78.8 - - - +
143A VAL* 1.3 66.3 + - - +
144A GLN* 3.1 11.6 + - - +
145A THR* 2.7 43.7 + - - -
146A LEU* 3.1 17.5 + - - +
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Residues in contact with VAL 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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79A THR* 4.1 19.6 - - + +
82A ALA* 4.1 23.1 - - + -
83A LEU* 3.8 29.6 - - + +
86A ASP* 4.2 17.0 - - + +
142A ASP* 1.3 75.0 - - - +
144A GLN* 1.3 65.6 + - - +
146A LEU* 3.0 11.6 + - - +
147A ARG* 2.9 23.2 + - - +
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Residues in contact with GLN 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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142A ASP* 3.1 11.0 + - - +
143A VAL* 1.3 77.8 - - - +
145A THR* 1.3 59.4 + - - +
147A ARG* 3.1 35.7 + - - +
148A GLU* 2.9 57.9 + - - +
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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 ALA* 3.7 13.0 - - + -
142A ASP* 2.7 34.0 + - - -
144A GLN* 1.3 72.7 + - - +
146A LEU* 1.3 62.5 + - - +
148A GLU* 3.3 13.2 + - - +
149A ARG* 3.0 62.1 + - + +
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Residues in contact with LEU 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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76A PHE* 4.1 15.7 - - + -
79A THR* 3.5 32.1 - - + -
80A TRP* 4.8 1.3 - - + -
83A LEU* 3.7 25.1 - - + -
136A PHE* 3.7 8.9 - - + -
137A PRO 4.1 5.4 - - - +
138A VAL* 3.9 28.9 - - + +
141A ALA* 3.6 24.0 - - + +
142A ASP 3.1 14.9 + - - +
143A VAL* 3.0 9.3 + - - +
145A THR* 1.3 75.7 - - - +
147A ARG* 1.3 63.9 + - - +
149A ARG* 3.2 7.7 + - - +
150A LEU* 3.0 27.4 + - - +
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Residues in contact with ARG 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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83A LEU* 3.9 12.3 - - + +
86A ASP* 2.7 29.0 + - - +
87A VAL* 4.0 5.8 - - + -
90A TRP* 3.5 23.3 - - + -
143A VAL* 2.9 14.3 + - - +
144A GLN* 3.1 50.8 + - - +
146A LEU* 1.3 76.8 - - - +
148A GLU* 1.3 64.4 + - - +
150A LEU* 3.0 9.2 + - - +
151A ILE* 2.9 23.0 + - + +
202A GLU* 2.5 45.2 + - - -
256A ARG* 2.9 20.7 - - - +
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Residues in contact with GLU 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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144A GLN* 2.9 44.7 + - + +
145A THR* 3.8 13.1 + - - +
147A ARG* 1.3 80.9 + - - +
149A ARG* 1.3 59.1 + - + +
151A ILE* 3.2 2.6 + - - -
152A ASP* 2.9 34.0 + - - +
196A GLY 5.2 0.5 - - - +
198A TYR* 3.5 57.2 + - + +
202A GLU* 4.9 0.8 - - - +
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Residues in contact with ARG 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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136A PHE* 3.7 16.7 - - + -
137A PRO* 2.8 53.0 + - - +
138A VAL* 3.9 2.4 - - - +
139A ALA 4.8 5.5 + - - +
141A ALA* 3.8 16.1 - - - +
145A THR* 3.0 43.6 + - + +
146A LEU* 3.5 11.2 - - - +
147A ARG 3.1 0.4 - - - -
148A GLU* 1.3 74.8 - - + +
150A LEU* 1.3 60.9 + - - +
152A ASP* 3.3 13.3 + - - +
153A ALA* 2.8 28.1 + - - +
53B TYR* 3.6 40.0 + - - +
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Residues in contact with LEU 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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62A ALA* 4.0 25.1 - - + -
80A TRP* 5.4 0.4 - - + -
83A LEU* 4.0 32.3 - - + -
87A VAL* 4.4 11.2 - - + -
90A TRP* 4.3 3.6 - - + -
94A LEU* 3.9 29.6 - - + -
96A LEU* 4.2 8.1 - - + -
123A PHE* 4.9 6.2 - - + -
136A PHE* 3.6 22.9 - - + -
146A LEU 3.0 15.9 + - - +
147A ARG* 3.0 10.3 + - - +
149A ARG* 1.3 74.9 - - - +
151A ILE* 1.3 61.8 + - - +
153A ALA* 3.0 4.8 + - - +
154A LEU* 2.8 33.3 + - - +
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Residues in contact with ILE 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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90A TRP* 3.5 28.0 - - + -
147A ARG* 2.9 19.0 + - + +
148A GLU* 3.2 8.7 + - - +
150A LEU* 1.3 76.2 - - - +
152A ASP* 1.3 61.8 + - - +
154A LEU* 3.3 9.7 + - - +
155A GLU* 3.0 27.5 + - - +
168A LEU* 4.8 7.0 - - + -
198A TYR* 3.8 30.3 - - + -
201A ARG* 3.9 30.3 - - + -
202A GLU* 3.8 23.3 - - + +
205A LEU* 3.9 9.9 - - + -
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Residues in contact with ASP 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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148A GLU* 2.9 14.6 + - - +
149A ARG* 3.5 15.8 - - - +
150A LEU 3.2 0.2 - - - -
151A ILE* 1.3 75.6 - - - +
153A ALA* 1.3 64.0 + - - +
155A GLU* 3.0 22.8 + - - +
156A SER* 3.0 12.7 + - - -
198A TYR* 2.6 36.2 + - - -
201A ARG* 4.7 0.9 + - - -
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Residues in contact with ALA 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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123A PHE* 3.5 43.9 - - + -
136A PHE* 4.5 7.6 - - + -
149A ARG 2.8 14.5 + - - +
150A LEU* 3.0 11.9 + - - +
152A ASP* 1.3 76.7 - - - +
154A LEU* 1.3 62.1 + - - +
156A SER* 2.6 30.0 + - - -
157A HIS* 3.9 0.7 + - - -
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Residues in contact with LEU 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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60A ALA* 3.9 28.0 - - + -
90A TRP* 4.4 11.7 - - + -
93A ALA* 4.3 6.1 - - + +
94A LEU* 4.3 20.2 - - + -
123A PHE* 4.4 3.4 - - + -
150A LEU 2.8 20.6 + - - +
151A ILE* 3.6 8.7 - - - +
153A ALA* 1.3 72.4 - - - +
155A GLU* 1.3 59.1 + - - +
156A SER 3.1 2.9 + - - -
157A HIS* 2.6 34.3 + - + +
161A TRP* 3.7 7.7 - - - -
162A PRO* 4.7 5.4 - - + -
165A CYS* 4.7 11.4 - - - -
168A LEU* 4.4 10.1 - - + -
205A LEU* 4.0 39.0 - - + -
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Residues in contact with GLU 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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151A ILE* 3.0 17.5 + - - +
152A ASP* 3.0 16.0 + - - +
154A LEU* 1.3 76.4 - - - +
156A SER* 1.3 58.3 + - - +
157A HIS 3.2 8.3 + - - +
161A TRP* 3.7 16.5 - - + -
168A LEU* 3.4 38.7 - - + +
169A GLU* 4.5 1.6 + - - -
201A ARG* 2.9 39.0 + - - -
217A ARG* 4.3 2.8 + - - -
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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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123A PHE* 4.3 3.1 - - - -
125A LYS* 3.5 23.0 + - - +
152A ASP 3.0 7.8 + - - -
153A ALA* 2.6 24.9 + - - -
155A GLU* 1.3 75.7 - - - +
157A HIS* 1.3 65.6 + - - +
158A HIS* 3.2 18.0 + - - +
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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