Contacts of the helix formed by residues 139 - 150 (chain B) in PDB entry 1J59
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 VAL 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ASP* 1.3 73.2 - - - +
140B THR* 1.3 75.0 + - - +
141B GLY 2.9 1.6 + - - -
142B ARG* 2.9 26.3 + - - +
143B ILE* 2.9 32.0 + - + +
176B VAL* 3.7 20.4 - - + -
178B CYS* 3.8 22.7 - - + -
182B THR* 5.4 3.1 - - + +
186B ILE* 4.7 13.0 - - + -
13D T 3.1 44.0 + - - +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ASP* 3.3 12.6 + - - -
139B VAL* 1.3 79.6 - - - +
141B GLY* 1.3 60.7 + - - +
143B ILE* 3.5 4.6 + - - +
144B ALA* 3.3 18.0 + - - +
186B ILE* 3.7 44.4 - - + +
189B MET* 6.2 2.7 - - + -
190B LEU* 4.9 14.6 - - + +
193B GLN* 5.9 2.0 - - - +
13D T 4.0 9.0 + - - -
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.0 14.1 - - - -
138B ASP* 3.1 14.6 + - - -
139B VAL 3.0 1.0 - - - -
140B THR* 1.3 78.6 - - - +
142B ARG* 1.3 65.7 + - - +
144B ALA* 3.0 16.1 + - - +
145B GLN* 3.2 15.1 + - - +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN* 3.5 35.7 - - + +
134B LEU* 3.1 40.4 + - - +
137B LEU* 3.9 15.7 - - + +
138B ASP 3.3 8.8 + - - +
139B VAL* 2.9 34.0 + - - +
141B GLY* 1.3 73.2 - - - +
143B ILE* 1.3 64.9 + - - +
145B GLN* 3.0 8.3 + - - +
146B THR* 2.9 22.3 + - - +
176B VAL* 3.1 37.5 + - + +
177B GLY 3.6 15.0 + - - -
178B CYS* 4.5 1.6 - - - +
13D T 5.4 2.6 + - - -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 2.9 28.9 + - + +
140B THR* 3.7 8.3 - - - +
141B GLY 3.1 0.2 - - - -
142B ARG* 1.3 76.2 - - - +
144B ALA* 1.3 57.3 + - - +
146B THR* 3.5 1.8 - - - -
147B LEU* 2.8 48.4 + - + +
172B ILE* 4.2 8.7 - - + -
176B VAL* 3.6 25.6 - - + -
183B VAL* 4.0 37.5 - - + +
186B ILE* 4.3 15.7 - - + -
187B LEU* 4.8 4.9 - - + +
190B LEU* 4.4 13.2 - - + -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B THR 3.3 10.0 + - - +
141B GLY* 3.0 10.7 + - - +
143B ILE* 1.3 75.7 - - - +
145B GLN* 1.3 66.9 + - + +
147B LEU* 3.6 7.1 + - - +
148B LEU* 3.1 31.6 + - + +
190B LEU* 5.4 9.2 - - + +
195B LEU* 5.1 19.3 - - + -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 3.9 12.0 + - - +
133B ASN* 3.5 35.5 + - - +
137B LEU* 4.1 12.9 - - + +
141B GLY 3.2 14.2 + - - +
142B ARG 3.0 8.4 + - - +
144B ALA* 1.3 73.9 - - + +
146B THR* 1.3 61.8 + - - +
148B LEU* 3.5 11.8 - - + +
149B ASN* 2.8 54.1 + - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ARG* 2.9 7.8 + - - +
143B ILE 3.5 7.6 - - - -
145B GLN* 1.3 76.4 - - - +
147B LEU* 1.3 61.5 + - + +
149B ASN* 4.8 3.1 - - - -
150B LEU* 2.7 64.9 + - + +
172B ILE* 4.5 8.5 - - + -
175B ILE* 4.0 26.4 - - + +
176B VAL* 3.3 26.7 - - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 2.8 34.0 + - + +
144B ALA* 4.0 7.2 - - - +
146B THR* 1.3 80.6 - - + +
148B LEU* 1.4 56.4 + - + +
150B LEU* 4.2 8.3 - - + -
151B ALA* 3.0 28.9 - - - +
165B ILE* 4.4 8.8 - - + +
167B ILE* 5.2 1.6 - - + -
172B ILE* 4.1 24.2 - - + -
187B LEU* 3.9 17.9 - - + -
190B LEU* 4.7 9.2 - - + -
195B LEU* 5.7 4.9 - - + -
196B ILE* 3.6 33.4 - - + -
202B THR* 5.2 2.0 - - + +
204B VAL* 4.2 10.4 - - + +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA* 3.1 23.0 + - + +
145B GLN* 3.2 13.9 + - + +
147B LEU* 1.4 73.0 - - + +
149B ASN* 1.3 68.1 + - - +
151B ALA* 3.1 25.2 + - - +
152B LYS* 4.0 5.1 + - - +
195B LEU* 6.2 4.7 - - + -
204B VAL* 4.6 16.4 - - + -
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 5.0 8.3 + - - +
133B ASN* 5.9 0.4 - - - +
145B GLN* 2.8 51.6 + - - +
146B THR* 4.2 3.1 - - - +
148B LEU* 1.3 74.8 - - - +
150B LEU* 1.3 63.4 + - - +
152B LYS* 4.0 7.9 + - - +
153B GLN* 3.8 18.0 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR* 3.8 31.2 - - + -
146B THR* 2.7 51.8 + - + +
147B LEU* 4.2 11.2 - - + -
149B ASN* 1.3 74.6 - - + +
151B ALA* 1.3 55.2 + - - +
152B LYS 2.6 16.5 + - - -
153B GLN* 3.3 16.2 + - - +
155B ASP* 3.8 18.8 - - - +
165B ILE* 4.2 11.4 - - + -
167B ILE* 4.7 22.2 - - + -
172B ILE* 4.7 2.2 - - + -
175B ILE* 4.3 14.4 - - + -
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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