Contacts of the helix formed by residues 144 - 155 (chain A) in PDB entry 2JG1
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
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Residue Dist Surf HB Arom Phob DC
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142A ASN* 3.3 15.5 + - - +
143A GLN* 1.3 78.7 - - + +
145A TYR* 1.3 57.5 + - - +
146A TYR 3.3 2.2 - - - -
147A ALA* 3.0 16.9 + - + +
148A GLN* 2.6 61.8 + - - +
171A THR* 4.5 7.0 - - + -
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Residues in contact with TYR 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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7A LEU* 4.0 11.0 - - + -
58A PHE* 3.8 3.6 - + - -
114A ALA* 2.6 43.5 + - + -
117A PHE* 3.3 28.6 - + - +
118A ILE* 3.6 18.5 - - + +
137A LEU* 4.0 11.2 - - + +
141A LEU* 3.6 35.4 - - + -
142A ASN 3.1 20.1 + - - +
143A GLN 3.3 2.6 + - - -
144A ASP* 1.3 80.0 + - - +
146A TYR* 1.3 58.1 + - - +
148A GLN* 3.3 22.0 + - - +
149A ILE* 3.0 49.2 + - + +
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Residues in contact with TYR 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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5A LEU* 5.3 0.6 + - + -
7A LEU* 3.7 21.0 + - + +
133A ILE* 3.2 32.8 - - + +
134A SER 3.7 9.5 + - - -
135A GLY 2.6 32.5 + - - -
136A SER 4.0 5.7 + - - -
137A LEU* 3.7 30.1 - - + +
143A GLN 4.9 1.1 + - - +
144A ASP 3.3 0.2 - - - -
145A TYR* 1.3 74.5 - - - +
147A ALA* 1.3 60.7 + - - +
149A ILE* 3.2 15.4 + - + +
150A ILE* 2.8 40.4 + - + +
162A LEU* 4.6 4.7 - - + -
164A CYS* 4.5 11.2 - - + -
168A THR* 3.7 28.3 - - + -
172A VAL* 3.9 17.0 - - + -
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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* 3.0 22.5 + - + +
146A TYR* 1.3 79.7 - - - +
148A GLN* 1.3 54.9 + - - +
150A ILE* 3.9 5.5 - - - +
151A GLU* 3.0 30.2 + - - +
171A THR* 5.1 6.9 - - + +
172A VAL* 4.7 5.5 - - + +
175A ASN* 3.6 39.4 - - + +
177A TYR* 4.3 4.9 - - - +
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Residues in contact with GLN 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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118A ILE* 4.2 21.0 - - + +
142A ASN* 4.4 10.5 - - - +
144A ASP* 2.6 49.7 + - - +
145A TYR* 3.4 23.9 - - - +
147A ALA* 1.3 74.1 - - + +
149A ILE* 1.3 63.1 + - - +
151A GLU* 3.5 6.9 - - - +
152A ARG* 2.8 50.9 + - - +
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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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5A LEU* 4.0 17.5 - - + -
7A LEU* 4.3 3.8 - - + -
117A PHE* 4.1 10.8 - - + -
118A ILE* 3.9 17.3 - - + -
121A PHE* 3.5 30.5 - - + -
133A ILE* 3.8 21.1 - - + -
145A TYR* 3.0 41.4 + - + +
146A TYR* 3.6 21.3 - - + +
148A GLN* 1.3 74.8 - - - +
150A ILE* 1.3 64.1 + - - +
152A ARG* 3.1 20.1 + - - +
153A CYS* 3.2 12.6 + - - -
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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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133A ILE* 4.4 6.3 - - + -
146A TYR* 2.8 27.8 + - + +
147A ALA* 3.9 5.2 - - - +
149A ILE* 1.3 71.6 - - - +
151A GLU* 1.3 56.9 + - - +
153A CYS* 3.2 8.4 + - - +
154A GLN* 2.9 29.3 + - - +
160A VAL* 4.0 27.4 - - + -
162A LEU* 4.4 13.7 - - + -
172A VAL* 3.7 32.1 - - + -
177A TYR* 3.5 24.7 - - + +
178A LYS 3.5 22.2 - - - +
179A PRO* 4.0 6.7 - - + -
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Residues in contact with GLU 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 3.0 18.8 + - - +
148A GLN* 3.5 10.1 - - - +
150A ILE* 1.3 76.3 - - - +
152A ARG* 1.3 71.5 + - - +
154A GLN* 3.4 1.6 + - - +
155A ASN* 2.9 47.2 + - - +
177A TYR* 3.3 55.6 + - + +
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Residues in contact with ARG 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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118A ILE* 3.5 26.9 - - + +
121A PHE* 4.0 17.7 - - + -
122A GLU* 2.8 39.6 + - + -
125A MSE 4.1 8.0 - - + +
148A GLN* 2.8 55.2 + - - +
149A ILE* 3.1 10.9 + - - +
151A GLU* 1.3 95.5 + - - +
153A CYS* 1.3 62.2 + - - +
155A ASN* 3.6 13.6 + - - +
156A LYS* 3.6 22.2 + - - +
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Residues in contact with CYS 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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121A PHE* 3.4 32.5 - - - -
125A MSE 4.1 9.6 - - - -
131A VAL* 3.9 15.3 - - - -
149A ILE* 3.2 14.8 + - - -
150A ILE 3.2 7.4 + - - +
152A ARG* 1.3 74.0 - - - +
154A GLN* 1.3 60.1 + - - +
156A LYS* 3.0 18.4 + - - -
158A VAL* 3.0 38.4 + - + +
160A VAL* 3.5 25.6 - - + -
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Residues in contact with GLN 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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150A ILE* 2.9 18.7 + - - +
151A GLU 3.8 4.0 - - - +
153A CYS* 1.3 72.8 - - - +
155A ASN* 1.3 62.8 + - - +
156A LYS 3.3 0.9 + - - -
157A GLY* 3.4 13.1 + - - +
158A VAL 4.3 3.6 + - - +
177A TYR* 4.3 22.7 - - + -
178A LYS* 3.1 37.8 + - - +
180A THR* 5.7 1.8 + - - -
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Residues in contact with ASN 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 GLU* 2.9 39.4 + - - +
152A ARG* 3.7 14.2 - - - +
153A CYS 3.2 0.4 - - - -
154A GLN* 1.3 77.5 - - - +
156A LYS* 1.3 69.5 + - + +
157A GLY 3.6 0.2 - - - -
177A TYR* 4.6 10.9 + - - -
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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