Contacts of the helix formed by residues 142 - 163 (chain p) in PDB entry 3J7Y
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 TYR 142 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3746 GLU* 3.4 29.4 - - + -
3756 PRO 4.2 6.8 + - - -
3776 TYR* 5.7 0.9 - - - -
141M VAL* 5.7 0.9 - - - +
142M GLU* 3.4 43.4 + - + -
143M GLU* 3.4 40.3 + - - +
145M ALA* 4.0 21.3 - - + -
146M ASP* 4.0 6.7 - - - +
162M LEU* 3.7 23.1 - - + -
97p SER* 4.0 1.1 + - - -
140p SER* 3.4 7.2 - - - +
141p ARG* 1.3 108.1 + - + +
143p GLN* 1.3 64.2 + - - +
144p PHE 3.3 3.0 + - - +
145p ARG* 3.6 17.0 + - + +
146p ASN* 3.7 4.2 + - - +
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Residues in contact with GLN 143 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M ASP* 3.5 40.2 + - + +
242M TYR* 4.7 5.7 + - - -
80p TYR* 3.4 61.7 + - + +
82p ARG* 5.0 13.2 + - - +
97p SER* 3.8 17.0 - - - +
98p LYS 5.9 0.4 - - - +
99p ALA* 5.3 0.9 - - + -
141p ARG 3.8 2.4 + - - -
142p TYR* 1.3 71.3 - - - +
144p PHE* 1.3 67.6 + - + +
145p ARG 3.2 0.2 - - - -
146p ASN* 3.2 8.7 + - + +
147p LEU* 2.9 28.9 + - - +
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Residues in contact with PHE 144 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M ALA* 5.1 8.3 - - + -
146M ASP* 4.7 18.4 + - + -
162M LEU* 3.8 30.3 - - + -
165M ALA* 5.0 2.0 - - + -
166M ALA* 4.7 14.8 - - + -
169M LYS* 4.3 24.7 - - + -
240M TYR* 3.8 35.1 - - + -
242M TYR* 3.4 41.7 - + - -
80p TYR* 5.4 1.3 - - - -
142p TYR 3.3 1.3 - - - -
143p GLN* 1.3 92.0 - - + +
145p ARG* 1.3 57.8 + - - +
147p LEU* 3.2 8.7 + - - +
148p ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 145 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3746 GLU* 3.9 12.4 + - - -
142M GLU* 5.4 5.9 - - - +
161M GLU* 5.4 3.0 - - - +
162M LEU* 3.5 41.5 - - + +
240M TYR* 3.3 34.8 + - + -
139p SER* 5.5 2.2 - - - +
140p SER* 3.1 28.9 - - - +
142p TYR* 3.6 12.7 + - + +
143p GLN 3.2 0.2 - - - -
144p PHE* 1.3 78.7 - - - +
146p ASN* 1.3 57.9 + - - +
148p ALA* 3.2 4.7 + - + +
149p ASP* 2.9 29.0 + - - +
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Residues in contact with ASN 146 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97p SER* 3.0 33.1 + - - -
98p LYS* 3.6 4.2 - - - +
99p ALA* 3.7 13.0 - - + -
137p SER* 2.7 27.5 + - - +
138p GLU* 3.3 3.2 + - - +
139p SER* 3.1 29.6 + - - +
140p SER* 3.6 10.4 + - - -
142p TYR 3.7 3.1 + - - -
143p GLN* 3.2 13.6 + - - +
145p ARG* 1.3 79.1 - - - +
147p LEU* 1.3 59.1 + - - +
149p ASP* 3.2 8.1 + - - +
150p CYS* 2.9 32.1 + - - -
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Residues in contact with LEU 147 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M TYR 3.8 12.3 - - - +
241M GLY* 4.3 5.4 - - - -
242M TYR* 3.8 24.7 - - + +
73p LEU* 6.1 0.4 - - + -
78p ILE* 3.7 33.4 - - + -
80p TYR* 3.5 24.0 - - + +
99p ALA* 4.2 4.7 - - - +
101p VAL* 4.0 16.4 - - + -
143p GLN 2.9 12.5 + - - +
144p PHE* 3.4 11.0 - - - +
146p ASN* 1.3 75.1 - - - +
148p ALA* 1.3 58.3 + - - +
150p CYS* 3.2 7.4 + - - +
151p LEU* 2.9 48.3 + - + +
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Residues in contact with ALA 148 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M LYS* 3.3 27.8 - - + +
240M TYR* 3.6 32.3 - - + +
144p PHE 2.9 6.0 + - - +
145p ARG 3.3 9.2 - - - +
147p LEU* 1.3 77.3 - - - +
149p ASP* 1.3 56.1 - - - +
151p LEU* 3.2 6.0 + - - +
152p GLN* 2.9 29.3 + - - +
155p ARG* 5.2 0.5 + - - -
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Residues in contact with ASP 149 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137p SER* 3.6 20.7 + - - -
139p SER* 4.5 12.4 + - - +
145p ARG 2.9 13.2 + - - +
146p ASN* 3.2 12.5 + - - +
148p ALA* 1.3 76.4 - - - +
150p CYS* 1.3 57.5 + - - +
152p GLN* 3.2 10.0 + - - +
153p LYS* 2.9 43.4 + - - +
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Residues in contact with CYS 150 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99p ALA* 3.3 26.9 - - - -
101p VAL* 3.3 27.4 - - + -
135p LEU* 3.6 15.6 - - - +
137p SER* 3.3 26.9 - - - -
146p ASN 2.9 17.5 + - - -
147p LEU 3.4 5.6 - - - +
149p ASP* 1.3 76.5 - - - +
151p LEU* 1.3 63.0 + - - +
153p LYS* 3.2 21.4 + - - +
154p ILE* 3.3 14.7 + - - +
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Residues in contact with LEU 151 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M ARG 4.5 3.6 - - - +
239M LYS 3.7 9.9 - - - +
241M GLY* 3.6 35.7 - - - +
71p ILE* 4.1 12.6 - - + +
73p LEU* 3.5 27.1 - - + -
76p LEU* 4.0 15.9 - - + -
101p VAL* 5.6 1.8 - - + -
147p LEU* 2.9 35.4 + - + +
148p ALA 3.2 5.4 + - - +
150p CYS* 1.3 76.0 - - + +
152p GLN* 1.3 62.8 + - - +
154p ILE* 3.2 19.3 + - + +
155p ARG* 3.2 34.8 + - - +
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Residues in contact with GLN 152 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M LYS* 6.2 0.2 - - - +
148p ALA 2.9 13.2 + - - +
149p ASP* 3.4 14.4 - - - +
151p LEU* 1.3 77.4 - - - +
153p LYS* 1.3 57.6 + - - +
155p ARG* 3.2 31.1 + - - +
156p ASP* 2.9 62.9 + - - +
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Residues in contact with LYS 153 (chain p).
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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135p LEU* 3.6 26.0 - - + -
136p THR 4.7 4.0 - - - +
137p SER* 3.2 28.0 - - - +
149p ASP* 2.9 30.6 + - - +
150p CYS* 3.2 10.8 - - - +
152p GLN* 1.3 77.3 - - - +
154p ILE* 1.3 56.7 + - - +
156p ASP* 3.2 12.1 + - - +
157p MET* 2.9 32.5 + - + +
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Residues in contact with ILE 154 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71p ILE* 3.6 20.4 - - + -
76p LEU* 4.1 15.5 - - + -
101p VAL* 4.0 24.5 - - + -
103p PHE* 3.8 28.0 - - + -
110p TRP* 4.0 12.6 - - + -
111p ILE* 5.3 0.9 - - + -
135p LEU* 3.9 14.1 - - + -
150p CYS 3.3 11.4 + - - +
151p LEU* 3.2 13.7 + - - +
153p LYS* 1.3 73.6 - - - +
155p ARG* 1.3 58.3 + - - +
157p MET* 3.2 14.9 + - + +
158p ILE* 2.9 41.3 + - + +
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Residues in contact with ARG 155 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M ARG* 3.2 38.6 + - - +
239M LYS* 4.0 11.5 + - - +
70p ASP* 4.2 22.9 + - - +
71p ILE* 3.4 33.8 - - - +
148p ALA 5.2 0.4 + - - -
151p LEU* 3.2 33.9 + - - +
152p GLN* 3.2 35.3 + - - +
154p ILE* 1.3 79.2 - - - +
156p ASP* 1.3 56.1 + - - +
158p ILE* 3.2 11.0 + - - +
159p THR* 2.9 37.0 + - + +
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Residues in contact with ASP 156 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152p GLN* 2.9 52.5 + - - +
153p LYS* 3.2 13.3 + - - +
155p ARG* 1.3 75.9 - - - +
157p MET* 1.3 57.5 + - + +
159p THR* 2.4 28.3 + - - +
160p GLU* 2.9 16.9 + - - +
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Residues in contact with MET 157 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103p PHE* 5.4 0.4 - - + -
119p ILE* 4.4 15.6 - - + +
123p HIS* 3.7 42.0 - - + +
126p LYS* 6.1 0.4 - - - -
133p LEU* 3.8 28.0 - - + -
135p LEU* 3.6 33.0 - - + -
153p LYS* 2.9 12.7 + - + +
154p ILE* 3.4 22.0 - - + +
156p ASP* 1.3 77.0 - - + +
158p ILE* 1.3 58.9 + - + +
160p GLU* 3.2 25.7 + - - +
161p ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 158 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70p ASP* 4.4 15.7 - - - +
71p ILE* 4.5 1.1 - - + -
110p TRP* 4.0 19.1 - - + -
111p ILE* 4.8 8.7 - - + -
115p VAL* 4.4 15.0 - - + +
119p ILE* 4.5 15.0 - - + -
154p ILE* 2.9 38.8 + - + +
155p ARG* 3.2 12.5 + - + +
157p MET* 1.3 77.4 - - + +
159p THR* 1.3 58.3 + - + +
161p ALA* 3.2 8.6 + - - +
162p SER* 2.9 30.0 + - - -
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Residues in contact with THR 159 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155p ARG* 2.9 22.3 + - + +
156p ASP* 2.4 31.5 + - - +
158p ILE* 1.3 77.2 - - + +
160p GLU* 1.3 56.8 + - - +
162p SER* 3.2 9.6 + - - -
163p GLN 2.9 28.1 + - - -
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Residues in contact with GLU 160 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119p ILE* 5.5 1.8 - - + +
122p THR* 3.5 20.5 + - + +
123p HIS* 3.4 33.9 + - - -
156p ASP 2.9 12.2 + - - +
157p MET* 3.2 22.6 - - - +
159p THR* 1.3 78.2 + - - +
161p ALA* 1.3 66.8 + - + +
163p GLN* 3.2 22.3 - - - -
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Residues in contact with ALA 161 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115p VAL* 3.5 40.9 - - + +
118p LYS* 3.9 34.7 + - + +
119p ILE* 4.1 6.1 - - + +
157p MET 2.9 13.6 + - - +
158p ILE 3.3 9.0 - - - +
160p GLU* 1.3 81.0 - - + +
162p SER* 1.3 64.5 + - - +
163p GLN* 4.3 0.3 - - - -
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Residues in contact with SER 162 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115p VAL* 4.6 11.8 - - - +
158p ILE* 2.9 15.4 + - - -
159p THR* 3.3 12.6 - - - -
161p ALA* 1.3 78.8 - - - +
163p GLN* 1.3 70.4 + - - +
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Residues in contact with GLN 163 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159p THR 2.9 12.8 + - - +
160p GLU* 3.2 21.2 + - - -
161p ALA 4.3 0.7 - - - -
162p SER* 1.3 85.3 - - - +
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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