Contacts of the helix formed by residues 142 - 157 (chain J) in PDB entry 5JGH
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 SER 142 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140J ASP 3.5 2.4 + - - -
141J LYS* 1.3 77.0 - - - +
143J GLN* 1.3 60.9 + - - +
144J LEU* 3.8 8.9 + - - +
145J ASP* 3.0 30.0 + - - -
146J LEU* 2.8 26.0 + - - +
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Residues in contact with GLN 143 (chain J).
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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1I T 5.6 1.8 - - - +
131J ARG* 2.9 34.7 + - - -
142J SER* 1.3 71.3 - - - +
144J LEU* 1.3 60.4 + - - +
146J LEU* 3.5 20.6 - - + +
147J MET* 2.7 45.3 + - - +
2K T 4.9 0.4 + - - -
21L A 3.1 29.7 + - - +
22L A 2.9 57.9 + - - +
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Residues in contact with LEU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J SER* 3.2 9.7 + - - +
143J GLN* 1.3 79.9 - - - +
145J ASP* 1.3 64.8 + - - +
147J MET* 3.1 10.7 + - - +
148J LYS* 3.1 17.4 + - - +
1K T 3.5 43.1 - - - +
2K T 3.2 51.6 + - + +
22L A 4.5 9.1 + - + -
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Residues in contact with ASP 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLN* 3.6 23.1 + - - +
141J LYS* 3.7 28.9 - - + +
142J SER* 3.0 28.9 + - - +
144J LEU* 1.3 77.4 - - - +
146J LEU* 1.3 64.0 + - - +
148J LYS* 2.9 24.4 + - - +
149J ILE* 3.0 16.9 + - + +
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Residues in contact with LEU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J ARG* 5.5 4.0 - - + +
134J VAL* 4.0 22.7 - - + +
135J PHE* 3.5 35.7 - - + +
138J HIS* 3.8 34.8 - - + +
141J LYS* 3.9 11.4 - - + +
142J SER 2.8 21.8 + - - +
143J GLN* 3.1 24.4 + - + +
145J ASP* 1.3 71.6 - - - +
147J MET* 1.3 59.0 + - + +
149J ILE* 3.1 10.4 + - + +
150J ILE* 2.8 38.5 + - + +
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Residues in contact with MET 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J PHE* 4.4 4.5 - - - -
127J ALA* 4.4 17.0 - - + -
131J ARG* 3.2 36.1 - - - +
143J GLN* 2.7 37.9 + - - +
144J LEU 3.1 6.9 + - - +
146J LEU* 1.3 71.6 - - + +
148J LYS* 1.3 58.8 + - - +
150J ILE* 4.0 8.8 - - - +
151J GLY* 2.9 23.4 + - - -
2K T 3.1 25.4 - - - +
3K T 3.5 33.3 + - - +
20L A 3.7 10.5 - - + -
21L A 3.6 15.7 - - + +
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Residues in contact with LYS 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLY 5.0 0.4 - - - -
152A ASP* 3.3 39.2 - - - +
155A GLN* 3.7 23.1 - - + +
3B T 4.5 7.3 + - - -
4B A 3.1 32.8 + - - +
144J LEU* 3.1 12.8 + - - +
145J ASP* 2.9 16.7 + - - +
147J MET* 1.3 76.8 - - - +
149J ILE* 1.3 62.5 + - - +
151J GLY* 3.2 1.7 + - - -
152J ASP* 3.0 17.8 + - - +
2K T 3.3 43.2 + - - +
3K T 4.0 6.9 + - - -
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Residues in contact with ILE 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP 4.9 0.7 - - - -
155A GLN* 4.1 25.8 - - + +
156A SER* 3.9 21.0 - - - -
134J VAL* 5.3 4.3 - - + -
138J HIS* 3.6 51.1 - - + +
141J LYS* 4.2 16.6 - - + -
145J ASP 3.0 13.0 + - - +
146J LEU* 3.1 13.4 + - + +
148J LYS* 1.3 75.3 - - - +
150J ILE* 1.3 64.3 + - + +
152J ASP* 3.0 6.2 + - - +
153J LYS* 2.9 34.2 + - + +
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Residues in contact with ILE 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J PHE* 3.8 21.3 - - + -
126J TYR* 3.8 17.9 - - + -
127J ALA* 3.9 15.7 - - + +
130J VAL* 3.9 13.0 - - + -
131J ARG* 3.8 26.5 - - + -
134J VAL* 3.6 33.9 - - + -
146J LEU* 2.8 27.7 + - + +
147J MET* 4.0 9.6 - - - +
149J ILE* 1.3 71.2 - - - +
151J GLY* 1.3 57.5 + - - +
153J LYS* 3.0 9.0 + - + +
154J TRP* 2.7 28.4 + - - +
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Residues in contact with GLY 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP* 4.8 1.3 - - - -
123J PHE* 3.8 14.5 - - - -
147J MET 2.9 16.6 + - - -
148J LYS 3.6 3.6 - - - -
149J ILE 3.1 0.2 - - - -
150J ILE* 1.3 77.3 - - - +
152J ASP* 1.3 61.5 + - - +
154J TRP* 3.2 3.8 + - - +
155J GLN* 2.9 29.4 + - - +
3K T 3.8 17.0 - - - -
4K A 4.0 4.7 + - - -
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Residues in contact with ASP 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 5.1 1.7 - - - +
152A ASP* 3.8 17.8 - - + +
153A LYS* 3.1 34.9 + - - +
156A SER* 2.5 30.9 + - - +
148J LYS 3.0 5.9 + - - +
149J ILE 3.0 8.8 + - - +
151J GLY* 1.3 74.6 - - - +
153J LYS* 1.3 57.3 + - - +
155J GLN* 3.2 10.6 + - - +
156J SER* 2.9 42.8 + - - -
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Residues in contact with LYS 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A SER* 6.0 1.8 - - - -
126J TYR* 3.1 25.0 + - - +
130J VAL* 4.0 11.4 - - - +
134J VAL* 3.8 31.3 - - + +
137J GLN* 5.4 3.6 + - - +
149J ILE* 2.9 26.4 + - + +
150J ILE* 3.3 13.9 - - - +
152J ASP* 1.3 76.1 - - + +
154J TRP* 1.3 57.3 + - - +
156J SER* 3.1 9.3 + - - -
157J LEU* 2.9 28.4 + - - +
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Residues in contact with TRP 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J PRO* 4.0 11.9 - - + -
123J PHE* 3.5 30.5 - + + -
126J TYR* 3.7 36.0 - + + -
150J ILE 2.7 9.7 + - - +
151J GLY 3.6 6.1 - - - +
153J LYS* 1.3 74.0 - - - +
155J GLN* 1.3 69.5 + - - +
157J LEU* 2.8 42.0 + - + +
162J LYS* 3.0 50.0 - - + +
165J TYR* 3.9 26.5 - + + -
166J ILE* 5.0 5.6 - - + -
4K A 2.8 36.7 + - - -
5K T 3.0 26.4 + - - -
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Residues in contact with GLN 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A HIS* 2.9 35.0 + - + +
141A LYS* 6.2 0.2 - - - +
149A ILE* 4.4 16.1 - - + +
151J GLY 2.9 15.2 + - - +
152J ASP* 3.6 14.4 - - - +
154J TRP* 1.3 78.1 - - - +
156J SER* 1.3 59.8 + - - +
157J LEU 4.0 0.3 - - - +
162J LYS* 3.2 20.6 + - - +
4K A 2.8 52.4 + - - +
5K T 4.9 1.4 + - - -
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Residues in contact with SER 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J ASP* 2.9 29.6 + - - -
153J LYS* 3.4 8.3 - - - -
155J GLN* 1.3 74.9 - - - +
157J LEU* 1.3 64.1 + - - +
158J ASP* 3.6 1.4 + - - -
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Residues in contact with LEU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J TYR* 3.8 32.5 - - + +
153J LYS 2.9 6.6 + - - +
154J TRP* 2.8 49.3 + - + +
155J GLN 4.0 0.5 - - - +
156J SER* 1.3 79.3 - - - +
158J ASP* 1.3 68.5 + - - +
159J GLN 3.4 1.2 + - - -
161J ILE* 3.5 35.9 - - + -
162J LYS* 3.2 25.5 + - + +
165J TYR* 4.7 0.2 - - + -
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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