Contacts of the helix formed by residues 144 - 162 (chain A) in PDB entry 1JT0
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 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ILE* 3.1 13.8 - - - +
143A ASN* 1.3 85.8 + - - +
145A VAL* 1.3 62.0 + - - +
146A ASN* 2.9 34.1 + - - +
147A ALA* 3.1 22.6 + - + +
148A VAL* 3.4 15.9 + - - +
177C LYS* 5.5 3.6 - - - -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A HIS* 3.6 31.6 - - + +
131A PHE* 3.7 26.9 - - + -
132A LYS* 4.0 18.6 - - + +
135A ASN* 3.9 14.4 - - - +
142A ILE* 3.7 30.1 - - + +
143A ASN 3.5 2.6 + - - +
144A ASP* 1.3 72.6 + - - +
146A ASN* 1.3 55.1 + - - +
147A ALA 3.1 2.0 - - - -
148A VAL* 3.8 0.6 - - - +
149A SER* 2.4 36.6 + - - -
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Residues in contact with ASN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 4.6 1.0 - - - +
128A HIS* 4.1 21.6 - - + +
144A ASP* 2.9 25.8 + - - +
145A VAL* 1.3 78.7 - - - +
147A ALA* 1.3 62.5 + - - +
149A SER* 2.9 15.0 + - - -
150A LYS* 3.3 33.0 + - - +
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Residues in contact with ALA 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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144A ASP* 3.1 30.5 + - + +
145A VAL 3.1 0.4 - - - -
146A ASN* 1.3 78.7 - - - +
148A VAL* 1.3 59.0 + - + +
149A SER 3.0 0.9 - - - -
150A LYS* 2.7 28.1 + - - +
151A ILE* 2.7 20.4 + - + +
174C LEU* 4.2 16.6 - - + -
177C LYS* 5.2 9.6 - - + -
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Residues in contact with VAL 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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131A PHE* 3.2 28.0 - - + -
142A ILE* 3.7 16.2 - - + -
143A ASN* 4.6 0.4 - - - +
144A ASP 3.4 19.8 + - - +
145A VAL 3.5 3.0 + - - +
147A ALA* 1.3 78.3 - - + +
149A SER* 1.3 57.5 + - - +
151A ILE* 3.8 8.5 - - - +
152A ALA* 3.0 27.4 + - - +
182A PHE* 4.0 7.4 - - + -
186A LEU* 3.7 21.5 - - + -
177C LYS* 4.5 15.5 - - + +
181C ILE* 4.0 18.2 - - + -
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.4 9.8 - - - +
127A TYR* 3.6 7.4 - - - +
128A HIS* 3.5 37.2 + - - +
131A PHE* 3.6 14.6 - - - -
145A VAL 2.4 26.1 + - - -
146A ASN* 2.9 20.4 + - - -
148A VAL* 1.3 76.4 - - - +
150A LYS* 1.3 59.2 + - - +
153A ALA* 3.1 27.9 + - - +
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Residues in contact with LYS 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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121A ASN* 5.9 2.4 - - - +
124A ILE* 3.0 30.8 - - + +
146A ASN* 3.3 31.8 + - - +
147A ALA* 2.7 17.0 + - - +
149A SER* 1.3 69.4 - - - +
151A ILE* 1.3 70.5 + - - +
153A ALA* 2.9 3.1 + - - +
154A ASN* 2.9 36.1 + - - +
163C THR* 5.9 0.9 - - + -
166C GLN* 4.3 22.0 - - + +
174C LEU* 3.8 27.1 - - + -
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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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147A ALA 2.7 19.3 + - - +
148A VAL* 3.8 7.6 - - - +
150A LYS* 1.3 77.0 - - - +
152A ALA* 1.3 54.7 + - - +
154A ASN* 3.0 0.8 + - - -
155A ALA* 2.8 32.7 + - + +
182A PHE* 4.0 14.8 - - + -
159C ILE* 3.6 16.0 - - + +
174C LEU* 2.8 59.7 - - + +
175C MET* 4.9 0.4 - - - -
177C LYS* 4.5 6.1 - - + -
178C PHE* 3.5 42.6 - - + +
181C ILE* 4.9 2.7 - - + -
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Residues in contact with ALA 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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79A PHE* 4.0 6.3 - - + -
127A TYR* 4.0 12.1 - - + -
131A PHE* 3.7 20.0 - - + -
148A VAL 3.0 17.8 + - - +
149A SER 3.9 2.9 - - - +
151A ILE* 1.3 81.1 - - - +
153A ALA* 1.3 62.2 + - - +
155A ALA* 4.7 4.0 - - - +
156A VAL* 3.0 32.9 + - - +
178A PHE* 5.3 1.3 - - - -
182A PHE* 3.7 19.3 - - + -
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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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93A TYR* 5.2 1.6 + - - -
123A TYR* 4.2 3.4 - - + +
124A ILE* 4.0 23.8 - - + +
127A TYR* 3.5 26.5 - - + -
149A SER 3.1 19.1 + - - +
150A LYS 2.9 5.4 + - - +
152A ALA* 1.3 77.2 - - - +
154A ASN* 1.3 65.9 + - - +
156A VAL* 3.4 3.6 + - - +
157A ASN* 3.1 27.4 + - - +
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Residues in contact with ASN 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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124A ILE* 5.9 1.4 - - - +
150A LYS* 2.9 30.2 + - - +
151A ILE 3.8 1.6 - - - +
153A ALA* 1.3 79.7 - - - +
155A ALA* 1.3 63.8 + - - +
157A ASN* 3.2 9.4 + - - +
158A GLY 3.2 15.9 + - - -
158C GLY* 3.3 17.1 - - - +
159C ILE* 3.9 13.9 - - + +
162C PHE* 3.4 25.7 + - - +
163C THR* 2.5 37.1 - - - +
174C LEU* 5.9 0.4 - - - +
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Residues in contact with ALA 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* 2.8 22.5 + - + +
152A ALA 4.3 0.9 - - - +
154A ASN* 1.3 68.7 - - - +
156A VAL* 1.3 67.4 + - - +
157A ASN 3.0 1.8 - - - -
158A GLY 3.1 10.2 + - - -
159A ILE* 3.1 19.3 + - - +
178A PHE* 4.0 17.3 - - + -
155C ALA* 3.5 26.6 - - + -
159C ILE* 3.5 17.8 - - + +
178C PHE* 4.3 8.5 - - + -
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Residues in contact with VAL 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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79A PHE* 5.2 0.4 - - + -
83A ASN* 3.4 23.8 - - - +
86A SER* 3.8 15.9 - - - +
93A TYR* 4.8 5.2 - - - +
127A TYR* 3.5 14.8 - - + +
152A ALA* 3.0 23.6 + - - +
153A ALA 3.7 3.6 - - - +
155A ALA* 1.3 76.7 - - - +
157A ASN* 1.3 61.1 + - - +
159A ILE* 3.4 9.4 + - - +
160A VAL* 3.0 32.5 + - + +
175A MET* 3.2 20.9 - - + -
178A PHE* 3.6 24.2 - - + -
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Residues in contact with ASN 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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92A TYR* 6.2 0.4 - - - -
93A TYR* 3.7 21.7 + - - -
96A GLN* 3.5 21.3 + - - +
123A TYR* 5.9 3.8 - - - +
153A ALA* 3.1 18.8 + - - +
154A ASN* 3.3 14.2 + - - +
155A ALA 3.0 0.6 - - - -
156A VAL* 1.3 77.0 - - - +
158A GLY* 1.3 65.0 + - - +
160A VAL* 3.3 4.0 + - - +
161A THR* 3.1 30.8 + - - +
162C PHE* 3.0 40.6 - - + -
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Residues in contact with GLY 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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154A ASN 3.2 4.9 + - - -
155A ALA 3.1 5.0 + - - -
157A ASN* 1.3 77.8 - - - +
159A ILE* 1.3 63.7 + - - +
161A THR* 4.6 0.4 - - - -
162A PHE* 2.9 38.8 + - - +
154C ASN* 3.2 24.7 - - - +
158C GLY* 3.4 15.0 - - - -
162C PHE* 4.7 0.7 - - - -
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Residues in contact with ILE 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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87A LEU* 5.2 3.8 - - + +
155A ALA 3.1 14.5 + - - +
156A VAL* 3.6 6.7 - - - +
157A ASN 3.3 0.2 - - - -
158A GLY* 1.3 76.9 - - - +
160A VAL* 1.3 56.8 + - - +
163A THR* 2.7 37.3 + - + +
171A ARG* 4.6 1.6 + - - +
174A LEU* 5.4 3.6 - - + -
175A MET* 3.9 31.2 - - + +
178A PHE* 3.4 51.1 - - + -
151C ILE* 4.2 13.9 - - + +
154C ASN* 3.6 11.9 - - + +
155C ALA* 3.9 16.6 - - + +
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Residues in contact with VAL 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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86A SER* 3.8 25.6 - - - +
87A LEU* 3.6 24.5 - - + -
93A TYR* 4.5 20.9 - - + +
156A VAL* 3.0 20.0 + - + +
157A ASN* 3.8 5.8 - - - +
158A GLY 3.2 0.4 - - - -
159A ILE* 1.3 77.2 - - - +
161A THR* 1.3 70.6 + - + +
164A HIS* 4.1 4.8 + - + -
171A ARG* 2.7 31.0 + - - +
175A MET* 3.6 20.9 - - + -
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Residues in contact with THR 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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93A TYR* 5.4 0.4 - - + +
96A GLN* 3.3 39.7 - - + -
97A ASN* 5.4 7.0 - - - -
100A ILE* 5.7 1.3 - - + -
157A ASN* 3.1 20.5 + - - +
160A VAL* 1.3 80.8 - - + +
162A PHE* 1.3 88.9 + - - +
163A THR 3.3 3.4 + - - -
164A HIS* 3.1 31.8 + - + +
100C ILE* 5.9 3.7 - - - +
162C PHE* 3.6 10.0 - - + -
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Residues in contact with PHE 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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100A ILE* 6.1 1.8 - - + -
158A GLY* 2.9 18.9 + - - +
161A THR* 1.3 105.7 + - - +
163A THR* 1.3 59.2 + - - +
164A HIS 3.7 0.4 - - - -
165A GLU* 4.2 5.9 - - - +
100C ILE* 3.4 42.0 - - + -
120C GLU* 5.2 6.6 - - - +
154C ASN* 3.2 21.3 + - - +
157C ASN* 2.7 51.6 - - + -
158C GLY 4.1 1.3 - - - -
161C THR* 3.5 28.7 - - + -
162C PHE* 3.8 10.8 - + - -
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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
------------------------------------------------------------
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