Contacts of the helix formed by residues 143 - 162 (chain A) in PDB entry 5J1T
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 ASN 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A HIS* 2.9 5.5 + - - +
142A SER* 1.3 75.2 + - - +
144A ILE* 1.3 64.9 + - - +
145A THR* 3.3 2.7 - - - -
146A LEU* 3.0 11.8 + - + +
147A TYR* 3.0 45.1 + - + +
403A CL 3.2 23.0 - - - +
33C ASN* 3.0 28.1 + - - +
34C VAL* 4.9 0.2 - - - +
53C THR* 3.5 15.6 - - - +
54C SER* 2.9 36.3 + - - -
55C GLY 3.7 0.7 + - - +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ALA 3.2 17.9 + - - +
142A SER* 4.4 6.5 - - - +
143A ASN* 1.3 76.9 - - - +
145A THR* 1.3 65.1 + - - +
147A TYR* 3.1 13.2 + - - +
148A LYS* 2.7 36.0 + - + +
176A HIS* 3.6 39.7 - - + +
178A GLY* 3.6 26.5 - - - +
179A LEU* 3.6 12.8 - - + +
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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
----------------------------------------------------------
142A SER 5.0 1.0 + - - -
143A ASN 3.3 1.0 - - - -
144A ILE* 1.3 84.2 - - - +
146A LEU* 1.3 58.9 + - - +
148A LYS* 3.3 9.7 + - + +
149A ASP* 2.9 48.4 + - - +
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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
----------------------------------------------------------
143A ASN* 3.0 16.6 + - + +
145A THR* 1.3 79.2 - - - +
147A TYR* 1.3 65.0 + - + +
149A ASP* 4.1 5.4 - - + +
150A GLN* 3.2 55.2 + - + +
30C PHE* 4.1 12.1 - - + +
31C SER* 3.8 32.3 - - - +
32C PHE 3.8 4.9 - - - +
33C ASN* 3.6 47.8 - - - +
54C SER* 4.5 10.9 - - - +
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Residues in contact with TYR 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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137A HIS 3.5 20.2 - - - -
138A PHE* 3.5 44.9 - + + -
139A PRO* 3.3 2.8 - - - +
140A HIS 3.0 41.5 + - - -
141A ALA* 5.4 0.7 - - - -
143A ASN* 3.0 30.5 + - + +
144A ILE* 3.6 9.0 - - - +
146A LEU* 1.3 78.5 - - + +
148A LYS* 1.3 57.9 + - - +
150A GLN* 3.4 3.7 + - - +
151A LEU* 2.8 32.1 + - - +
176A HIS* 6.3 1.6 - - + -
179A LEU* 3.9 13.2 - - + -
403A CL 3.0 28.2 - - + +
33C ASN* 4.0 11.2 - - - -
103C ILE* 4.1 14.8 - - + +
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 2.7 28.0 + - + +
145A THR* 3.7 9.4 - - + +
147A TYR* 1.3 75.2 - - - +
149A ASP* 1.3 70.5 + - - +
151A LEU* 3.8 1.3 - - - +
152A GLN* 2.9 52.0 + - - +
178A GLY 4.9 6.9 + - - +
179A LEU* 3.5 16.2 - - + -
182A ALA* 3.7 26.0 - - + +
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Residues in contact with ASP 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 THR* 2.9 38.6 + - - +
146A LEU* 4.1 6.6 - - + +
148A LYS* 1.3 85.1 - - - +
150A GLN* 1.3 63.9 + - + +
152A GLN* 3.7 10.1 + - - +
153A LEU* 3.3 31.0 + - + +
30C PHE* 6.0 2.4 - - - -
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Residues in contact with GLN 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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146A LEU* 3.2 42.5 + - + +
147A TYR* 3.8 2.4 - - - +
149A ASP* 1.3 78.5 - - + +
151A LEU* 1.3 59.1 + - - +
153A LEU* 3.3 9.1 + - + +
154A TRP* 2.9 31.0 + - - +
33C ASN* 5.2 2.1 + - - +
100C ARG* 6.2 1.4 - - - +
101C ASN 4.0 18.6 + - - +
102C PRO* 4.7 2.0 - - - +
103C ILE* 3.7 39.3 - - + +
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Residues in contact with LEU 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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132A PHE* 3.6 43.1 - - + -
138A PHE* 4.2 8.3 - - + -
147A TYR 2.8 18.6 + - - +
148A LYS* 3.2 4.5 + - - +
150A GLN* 1.3 74.3 - - - +
152A GLN* 1.3 64.9 + - + +
154A TRP* 3.3 1.4 + - + +
155A ILE* 3.0 41.0 + - + +
169A PHE* 4.0 14.1 - - + -
175A MET* 4.4 0.9 - - + -
179A LEU* 4.1 26.2 - - + +
182A ALA* 5.7 1.6 - - + -
183A ILE* 3.7 24.5 - - + -
103C ILE* 3.6 9.4 - - + -
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Residues in contact with GLN 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 LYS* 2.9 52.2 + - + +
149A ASP* 4.1 10.4 - - - +
151A LEU* 1.3 76.9 - - + +
153A LEU* 1.3 64.1 + - + +
155A ILE* 4.2 0.7 - - - +
156A ARG* 3.1 26.3 + - - +
182A ALA* 3.8 27.6 + - + +
183A ILE* 6.1 0.4 - - + -
186A PHE* 4.2 20.4 - - + -
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Residues in contact with LEU 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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149A ASP* 3.3 22.2 + - + +
150A GLN* 3.7 8.1 - - + +
151A LEU 3.3 0.2 - - - -
152A GLN* 1.3 81.8 - - + +
154A TRP* 1.3 63.9 + - - +
156A ARG* 4.0 3.2 - - + +
157A GLY* 3.0 22.0 + - - -
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Residues in contact with TRP 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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130A HIS* 3.2 32.7 + + - +
132A PHE* 3.6 30.2 - + + -
150A GLN 2.9 18.1 + - - +
151A LEU* 3.7 6.7 - - - +
153A LEU* 1.3 78.5 - - - +
155A ILE* 1.3 63.2 + - - +
157A GLY* 4.0 0.3 - - - -
158A ASN* 2.9 50.0 + - - +
167A PHE* 4.6 4.9 - + - -
103C ILE* 4.6 7.6 - - + -
104C ASN* 2.9 37.0 - - + +
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Residues in contact with ILE 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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132A PHE* 4.7 1.8 - - + -
151A LEU* 3.0 45.2 + - + +
154A TRP* 1.3 75.0 - - - +
156A ARG* 1.3 64.3 + - - +
158A ASN* 3.9 0.5 - - - -
159A VAL* 2.9 25.6 + - - +
167A PHE* 4.0 35.4 - - + -
169A PHE* 4.1 10.3 - - + -
183A ILE* 3.9 12.6 - - + -
186A PHE* 3.8 33.2 - - + -
198A TYR* 3.8 22.2 - - + -
203A PHE* 4.6 8.5 - - + -
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Residues in contact with ARG 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 GLN 3.1 18.6 + - - +
153A LEU* 4.1 4.0 - - + +
155A ILE* 1.3 78.6 - - - +
157A GLY* 1.3 57.1 + - - +
159A VAL* 3.9 0.5 - - - +
160A SER* 2.8 41.0 + - - +
186A PHE* 5.0 5.6 - - + -
193A VAL 4.6 0.9 + - - -
194A ASP* 3.1 44.3 + - - +
195A GLY 5.4 0.2 - - - -
196A VAL* 3.9 14.3 - - + +
198A TYR* 3.2 22.3 + - - +
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Residues in contact with GLY 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 LEU 3.0 16.9 + - - -
154A TRP 4.0 0.4 - - - -
156A ARG* 1.3 77.6 - - - +
158A ASN* 1.3 63.0 + - - +
160A SER* 3.5 7.2 - - - -
161A ALA* 3.2 22.5 + - - +
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Residues in contact with ASN 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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127A ASP 5.0 1.4 - - - +
130A HIS* 3.3 31.9 + - - +
154A TRP* 2.9 62.0 + - - +
155A ILE 4.1 2.0 - - - +
157A GLY* 1.3 75.5 - - - +
159A VAL* 1.3 60.1 + - - +
161A ALA* 3.2 7.8 + - - +
162A CYS* 2.9 24.4 + - - +
165A SER* 3.4 9.7 + - - +
167A PHE* 4.3 9.0 - - + -
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Residues in contact with VAL 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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155A ILE 2.9 21.1 + - - +
156A ARG 4.2 1.3 - - - +
158A ASN* 1.3 72.0 - - - +
160A SER* 1.3 67.1 + - - +
161A ALA 3.2 0.5 + - - -
162A CYS 3.3 22.6 + - - +
163A ALA* 3.5 13.4 + - - +
165A SER* 4.2 5.8 - - - -
167A PHE* 3.5 27.8 - - + -
196A VAL* 3.7 11.4 - - + +
197A SER 3.5 25.4 - - - +
198A TYR* 3.5 27.8 - - + -
201A ALA* 4.5 5.4 - - + -
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Residues in contact with SER 160 (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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156A ARG* 2.8 29.2 + - - +
157A GLY* 3.5 9.0 - - - -
159A VAL* 1.3 78.8 - - - +
161A ALA* 1.3 58.9 + - - +
163A ALA 5.4 0.3 + - - -
196A VAL* 3.6 26.7 - - - +
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Residues in contact with ALA 161 (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 TYR* 5.6 3.1 - - + -
157A GLY 3.2 12.5 + - - +
158A ASN* 3.2 8.8 + - - +
159A VAL 3.1 0.6 - - - -
160A SER* 1.3 78.3 - - - +
162A CYS* 1.3 62.0 + - + +
163A ALA 4.3 0.2 - - - -
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Residues in contact with CYS 162 (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 TYR* 3.8 11.4 - - - -
128A TYR* 3.7 38.1 - - + -
158A ASN 2.9 6.4 + - - +
159A VAL* 3.3 11.6 + - - +
161A ALA* 1.3 80.0 - - + +
163A ALA* 1.3 64.3 + - - +
164A ARG* 3.2 25.5 + - - -
165A SER* 2.7 31.3 + - - +
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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