Contacts of the helix formed by residues 150 - 161 (chain A) in PDB entry 1JQE
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.7 4.3 - - - +
149A LYS* 1.3 80.1 - - + +
151A ILE* 1.3 57.3 + - - +
152A PRO* 3.5 10.2 - - - +
153A ALA* 3.0 36.1 + - + +
154A THR* 2.8 30.9 + - - +
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Residues in contact with ILE 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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145A LEU* 3.6 35.2 - - + +
148A VAL* 4.0 7.9 - - + +
149A LYS 3.8 1.8 + - - -
150A ASP* 1.3 68.8 - - - +
152A PRO* 1.3 70.6 - - + +
154A THR* 3.0 6.9 + - - -
155A LEU* 2.7 50.9 + - + +
197A GLN* 3.7 30.9 - - - +
199A ILE* 4.3 22.7 - - + -
204A LEU* 3.9 11.2 - - + -
207A MET* 3.6 24.0 - - + -
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Residues in contact with PRO 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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150A ASP* 3.5 9.6 - - - +
151A ILE* 1.3 94.0 - - + +
153A ALA* 1.3 56.0 + - - +
155A LEU* 4.5 3.1 - - + -
156A LYS* 2.9 31.1 + - - +
207A MET* 3.7 26.5 - - + -
211A LEU* 3.6 27.8 - - + +
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Residues in contact with ALA 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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124A GLN* 4.0 12.4 + - - +
150A ASP* 3.0 34.6 + - + +
152A PRO* 1.3 77.5 - - - +
154A THR* 1.3 58.2 + - - +
156A LYS* 3.8 5.4 - - - +
157A PHE* 2.9 31.5 + - - +
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Residues in contact with THR 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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120A SER* 4.3 6.3 + - - +
121A SER* 6.0 1.4 - - - -
124A GLN* 4.0 14.0 + - - +
141A MET* 3.3 33.7 - - + -
145A LEU* 4.3 9.0 - - + -
148A VAL* 3.0 21.1 - - + +
150A ASP 2.8 21.8 + - - -
151A ILE* 3.4 5.2 - - - -
153A ALA* 1.3 76.8 - - - +
155A LEU* 1.3 62.8 + - - +
157A PHE* 3.4 0.5 + - - +
158A PHE* 3.0 42.7 + - + +
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Residues in contact with LEU 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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141A MET* 4.9 3.4 - - - -
145A LEU* 4.2 15.9 - - + -
151A ILE* 2.7 41.0 + - + +
152A PRO* 4.5 0.2 - - + -
154A THR* 1.3 74.2 - - - +
156A LYS* 1.3 61.7 + - - +
158A PHE* 5.3 0.4 - - - -
159A HIS* 3.0 27.4 + - - +
168A MET* 4.0 7.5 - - + +
170A ILE* 3.2 35.7 - - + -
204A LEU* 4.7 7.0 - - + -
207A MET* 4.3 18.8 - - + -
208A LEU* 3.9 27.4 - - + -
211A LEU* 3.7 16.4 - - + -
213A LEU* 4.3 1.5 - - + +
290A ILE* 4.7 1.3 - - + -
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Residues in contact with LYS 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 PRO 2.9 18.7 + - - +
153A ALA* 3.9 5.8 - - - +
155A LEU* 1.3 76.2 - - - +
157A PHE* 1.3 63.5 + - - +
159A HIS* 3.5 7.3 + - - +
160A SER* 3.1 23.2 + - - -
211A LEU* 4.0 27.8 + - + +
213A LEU* 4.9 4.9 - - + -
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Residues in contact with PHE 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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123A TYR* 4.5 2.2 - + - -
124A GLN* 3.3 58.1 - - + +
127A MET* 4.0 15.7 - - + -
128A LEU* 3.9 28.5 - - + -
133A LEU* 5.8 1.6 - - + -
153A ALA 2.9 19.1 + - - +
154A THR 3.8 1.8 - - - +
156A LYS* 1.3 78.2 - - - +
158A PHE* 1.3 90.8 + + - +
160A SER* 2.5 30.3 + - - -
161A LEU* 3.3 37.3 + - + +
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Residues in contact with PHE 158 (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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57A LEU* 3.9 17.9 - - + -
59A ILE* 3.6 26.2 - - + -
120A SER* 3.9 28.5 - - - -
123A TYR* 3.8 19.1 - + - -
124A GLN* 4.6 2.0 - - - -
139A ILE* 3.3 28.5 - - + +
141A MET* 3.8 11.2 - - + -
154A THR* 3.0 48.7 + - + +
157A PHE* 1.3 99.3 - + - +
159A HIS* 1.3 63.3 + - - +
161A LEU* 3.0 16.7 + - + +
162A LEU* 3.6 1.6 + - - +
168A MET* 3.7 20.6 - - - -
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Residues in contact with HIS 159 (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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155A LEU 3.0 20.3 + - - +
156A LYS* 3.8 6.1 + - - +
157A PHE 3.2 0.2 - - - -
158A PHE* 1.3 77.7 - - - +
160A SER* 1.3 67.3 + - - +
161A LEU 3.1 0.2 - - - -
162A LEU* 3.1 30.5 + - + +
168A MET* 3.9 14.7 - - + +
213A LEU* 3.7 35.8 - - + +
290A ILE* 3.9 7.6 - - + -
291A GLU 3.2 20.3 + - - -
292A ALA* 2.9 28.8 + - - -
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Residues in contact with SER 160 (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 LEU* 5.4 1.4 - - - +
135A LYS* 2.6 32.9 + - - -
156A LYS* 3.1 14.3 + - - -
157A PHE* 2.5 29.1 + - - -
159A HIS* 1.3 83.0 - - - +
161A LEU* 1.3 59.2 + - - +
162A LEU 3.3 0.7 - - - -
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Residues in contact with LEU 161 (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 TYR* 4.4 9.6 - - + +
127A MET* 5.3 3.8 - - + -
133A LEU* 3.9 22.9 - - + -
134A GLN* 3.7 20.9 - - + +
135A LYS* 3.1 11.1 - - - -
136A TRP* 2.7 48.3 + - + +
139A ILE* 4.0 8.1 - - + -
157A PHE* 3.6 46.0 - - + +
158A PHE* 3.0 23.5 + - + +
160A SER* 1.3 86.7 - - - +
162A LEU* 1.3 55.2 + - - +
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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