Contacts of the helix formed by residues 142 - 157 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP 4.4 0.2 + - - -
141A LYS* 1.3 76.6 - - - +
143A GLN* 1.3 60.7 + - - +
144A LEU* 3.7 11.1 + - - +
145A ASP* 3.2 26.7 + - - +
146A LEU* 2.8 29.3 + - - +
1F T 6.6 0.4 - - - -
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Residues in contact with GLN 143 (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 ARG* 3.5 26.6 + - - +
142A SER* 1.3 74.4 - - - +
144A LEU* 1.3 62.8 + - + +
146A LEU* 3.4 6.4 + - - +
147A MET* 3.0 55.0 + - - +
2B T 4.6 0.2 - - - +
21C A 3.0 45.2 + - + +
22C A 3.0 60.5 + - + +
1F T 5.3 3.3 + - - +
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Residues in contact with LEU 144 (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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142A SER* 3.2 8.9 + - - +
143A GLN* 1.3 80.6 - - + +
145A ASP* 1.3 65.1 + - - +
147A MET* 3.3 9.5 + - - +
148A LYS* 3.3 16.8 + - - +
1B T 3.1 47.3 - - + +
2B T 3.2 50.7 + - + +
22C A 4.5 7.9 - - + +
1F T 6.1 0.2 - - - +
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Residues in contact with ASP 145 (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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141A LYS* 3.9 32.7 + - + +
142A SER* 3.2 20.7 + - - +
144A LEU* 1.3 80.3 - - - +
146A LEU* 1.3 64.2 + - - +
148A LYS* 3.0 30.0 + - - +
149A ILE* 3.1 13.9 + - - +
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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
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131A ARG* 3.4 38.6 - - + +
134A VAL* 4.0 23.1 - - + -
135A PHE* 3.5 28.0 - - + +
138A HIS* 4.0 20.9 - - + +
141A LYS* 3.9 24.9 - - + +
142A SER 2.8 20.2 + - - +
143A GLN* 3.7 8.3 - - - +
145A ASP* 1.3 71.7 - - - +
147A MET* 1.3 58.7 + - + +
149A ILE* 3.0 8.1 + - + +
150A ILE* 2.7 35.1 + - + +
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Residues in contact with MET 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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123A PHE* 3.4 27.3 - - + -
124A ILE* 4.9 0.7 - - + -
127A ALA* 3.7 22.0 - - + -
131A ARG* 5.5 2.0 - - - -
143A GLN* 3.0 41.3 + - - +
144A LEU 3.6 5.2 - - - +
145A ASP 3.1 0.4 - - - -
146A LEU* 1.3 77.9 - - - +
148A LYS* 1.3 52.1 + - - +
150A ILE* 3.6 12.5 - - - +
151A GLY* 2.7 33.3 + - - -
2B T 3.2 25.8 - - + +
3B T 3.1 41.1 - - - +
20C A 4.4 9.4 - - + +
21C A 4.5 0.7 - - + -
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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
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144A LEU 3.5 14.8 - - - +
145A ASP* 3.0 20.5 + - - +
147A MET* 1.3 77.7 - - - +
149A ILE* 1.3 63.1 + - + +
151A GLY* 3.4 0.9 + - - -
152A ASP* 3.0 31.7 + - - +
2B T 3.5 23.4 + - - +
3B T 3.4 30.0 + - - +
2K T 5.8 1.6 + - - -
3K T 3.6 33.5 + - - +
4K A 6.2 0.2 - - - +
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Residues in contact with ILE 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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134A VAL* 3.9 20.9 - - + -
138A HIS* 4.1 16.8 - - + +
141A LYS* 4.0 29.6 - - + -
145A ASP 3.1 11.7 + - - +
146A LEU* 3.0 11.0 + - + +
148A LYS* 1.3 78.7 - - + +
150A ILE* 1.3 62.9 + - - +
152A ASP* 3.0 11.9 + - + +
153A LYS* 2.9 28.9 + - + +
152J ASP* 5.6 1.3 - - - +
155J GLN* 4.4 18.2 - - + +
4K A 3.8 31.2 - - - +
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Residues in contact with ILE 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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123A PHE* 3.4 23.7 - - + -
126A TYR* 3.8 12.8 - - + -
127A ALA* 3.7 40.8 - - + +
130A VAL* 4.0 9.0 - - + -
131A ARG* 4.0 20.2 - - + -
134A VAL* 4.0 24.2 - - + -
146A LEU* 2.7 24.9 + - + +
147A MET* 3.8 12.1 - - - +
149A ILE* 1.3 71.9 - - - +
151A GLY* 1.3 57.4 + - - +
153A LYS* 3.0 8.4 + - - +
154A TRP 2.9 25.1 + - - -
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Residues in contact with GLY 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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123A PHE* 3.5 17.4 - - - -
147A MET 2.7 21.8 + - - -
148A LYS 3.4 2.2 + - - -
150A ILE* 1.3 73.4 - - - +
152A ASP* 1.3 62.1 + - - +
154A TRP* 3.5 2.9 + - - +
155A GLN* 3.1 27.4 + - - +
3B T 3.7 15.3 - - - -
4B A 3.8 7.2 + - - -
148J LYS* 4.8 0.4 - - - -
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Residues in contact with ASP 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 3.0 17.4 + - - +
149A ILE* 3.0 11.7 + - + +
151A GLY* 1.3 74.7 - - - +
153A LYS* 1.3 65.6 + - - +
155A GLN* 3.2 11.1 + - - +
156A SER* 3.3 13.9 + - - -
148J LYS* 3.3 50.2 - - - +
152J ASP* 3.8 15.3 + - + +
3K T 3.3 34.5 + - - +
4K A 3.9 7.8 + - - -
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Residues in contact with LYS 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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126A TYR* 3.4 23.9 + - - +
130A VAL* 4.1 12.2 - - - +
134A VAL* 3.6 32.6 - - + +
137A GLN* 5.9 3.2 - - - +
149A ILE* 2.9 25.7 + - + +
150A ILE* 3.0 10.5 + - - +
152A ASP* 1.3 76.6 - - - +
154A TRP* 1.3 56.5 + - - +
156A SER* 3.1 5.0 + - - -
157A LEU* 2.7 29.6 + - - +
152J ASP* 3.1 31.5 + - - +
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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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122A PRO* 3.8 22.7 - - + -
123A PHE* 3.4 36.8 - + + -
126A TYR* 3.6 41.8 - + + -
150A ILE 2.9 6.4 + - - +
151A GLY 3.9 3.1 - - - +
152A ASP 3.3 0.4 - - - -
153A LYS* 1.3 77.9 - - - +
155A GLN* 1.3 68.9 + - - +
157A LEU* 3.2 32.6 + - + +
162A LYS* 3.5 39.8 - - + +
165A TYR* 4.0 15.5 - + + -
166A ILE* 4.5 6.7 - - + -
4B A 3.0 22.3 + - - -
5B T 2.9 39.2 + - - -
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Residues in contact with GLN 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 GLY 3.1 12.9 + - - +
152A ASP 3.2 7.4 + - - +
153A LYS 3.2 1.0 - - - -
154A TRP* 1.3 82.4 - - - +
156A SER* 1.3 60.8 + - - +
157A LEU 3.6 0.5 + - - +
162A LYS* 3.7 14.9 + - - +
4B A 3.1 43.8 + - - -
5B T 4.5 6.0 + - - -
138J HIS* 5.0 2.9 + - - -
141J LYS* 4.3 18.9 - - - -
145J ASP* 3.6 23.1 + - + +
148J LYS* 3.7 23.8 - - + +
149J ILE* 4.1 26.2 - - + +
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Residues in contact with SER 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 ASP 3.3 3.7 + - - -
153A LYS 3.1 7.1 + - - -
155A GLN* 1.3 75.8 - - - +
157A LEU* 1.3 68.4 + - - +
158A ASP* 3.4 4.7 + - - +
138J HIS* 5.1 7.0 + - - -
149J ILE* 3.9 28.3 - - - -
152J ASP* 2.5 35.2 + - - -
153J LYS* 6.0 1.6 - - - -
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Residues in contact with LEU 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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126A TYR* 3.6 44.6 - - + +
153A LYS 2.7 10.6 + - - +
154A TRP* 3.2 40.2 + - + +
155A GLN 4.2 0.5 - - - +
156A SER* 1.3 80.7 - - - +
158A ASP* 1.3 71.2 + - - +
159A GLN 3.6 0.2 + - - -
161A ILE* 3.9 28.3 - - + -
162A LYS* 3.2 24.6 + - + +
165A TYR* 4.5 1.8 - - + -
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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
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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