Contacts of the helix formed by residues 121 - 132 (chain B) in PDB entry 1JUO
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B VAL* 1.3 75.6 - - - +
122B PRO* 1.3 75.4 - - + +
123B GLN* 3.0 21.8 + - - +
124B GLU* 2.9 40.6 + - - +
125B LEU* 2.9 10.6 + - - +
152B GLY 4.8 5.2 - - - +
153B LYS* 4.6 5.4 - - + +
154B ILE* 4.2 3.4 - - - -
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Residues in contact with PRO 122 (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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121B ASP* 1.3 89.0 - - + +
123B GLN* 1.3 61.1 + - - +
125B LEU* 4.3 6.1 - - + -
126B GLN* 3.3 18.7 + - - +
141B VAL* 3.7 16.0 - - + +
142B ASN* 5.0 14.1 - - - +
145B ALA* 3.9 26.7 - - + -
152B GLY 4.3 12.8 - - - +
154B ILE* 4.2 4.5 - - + -
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Residues in contact with GLN 123 (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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121B ASP* 3.0 11.7 + - - +
122B PRO* 1.3 78.9 - - - +
124B GLU* 1.3 64.9 + - - +
126B GLN* 3.5 10.3 + - - +
127B LYS* 3.4 54.1 + - - +
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Residues in contact with GLU 124 (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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112B PHE* 3.2 33.8 - - + +
113B ASP* 4.9 0.5 - - - -
114B THR* 3.4 21.4 + - + +
115B ASP* 5.2 3.1 - - - +
119B THR 4.5 1.9 - - - +
120B VAL* 3.4 16.5 - - + +
121B ASP* 2.9 45.9 + - - +
123B GLN* 1.3 80.7 - - - +
125B LEU* 1.3 62.5 + - - +
127B LYS* 3.2 22.0 + - - +
128B ALA* 3.1 21.8 + - - +
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Residues in contact with LEU 125 (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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120B VAL* 4.4 14.3 - - + +
121B ASP 2.9 14.4 + - - +
122B PRO* 3.8 5.4 - - + +
123B GLN 3.3 0.2 - - - -
124B GLU* 1.3 75.6 - - - +
126B GLN* 1.3 61.2 + - - +
128B ALA* 3.4 3.2 + - - +
129B LEU* 2.9 59.0 + - + +
141B VAL* 4.5 9.0 - - + -
144B ILE* 4.1 24.5 - - + -
145B ALA* 4.5 11.0 - - + +
154B ILE* 4.2 26.7 - - + -
159B TYR* 3.8 24.2 - - + -
162B CYS* 5.1 5.6 - - - -
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Residues in contact with GLN 126 (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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122B PRO 3.3 13.9 + - - +
123B GLN* 3.9 10.1 - - - +
124B GLU 3.3 0.2 - - - -
125B LEU* 1.3 79.3 - - - +
127B LYS* 1.3 51.4 + - - +
129B LEU* 3.8 6.2 - - + +
130B THR* 2.5 55.1 + - + +
136B LEU* 3.2 24.3 + - + +
137B SER 4.0 8.5 - - - -
138B PRO* 4.1 12.3 - - - +
141B VAL* 3.6 28.4 - - + +
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Residues in contact with LYS 127 (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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112B PHE* 3.3 37.8 - - + -
123B GLN* 3.4 48.5 + - + +
124B GLU* 3.2 17.8 + - - +
125B LEU 3.1 0.4 - - - -
126B GLN* 1.3 76.2 - - - +
128B ALA* 1.3 65.1 + - - +
130B THR* 2.6 20.3 + - - -
131B THR* 2.9 17.1 + - + +
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Residues in contact with ALA 128 (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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108B HIS* 3.7 20.8 - - - +
109B PHE* 4.7 3.6 - - + +
112B PHE* 3.6 15.1 - - + -
120B VAL* 6.5 0.7 - - + -
124B GLU 3.1 9.6 + - - +
125B LEU* 3.7 7.9 - - - +
127B LYS* 1.3 77.7 - - - +
129B LEU* 1.3 63.0 + - - +
131B THR* 3.0 14.8 + - - -
132B MET* 3.1 18.2 + - - +
159B TYR* 4.1 25.4 - - + +
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Residues in contact with LEU 129 (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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125B LEU* 2.9 48.3 + - + +
126B GLN* 3.9 5.6 - - + +
128B ALA* 1.3 79.3 - - - +
130B THR* 1.3 58.9 + - + +
132B MET* 3.3 19.4 - - - +
134B PHE* 3.0 37.3 + - + +
136B LEU* 3.8 25.4 - - + -
141B VAL* 4.9 8.5 - - + -
144B ILE* 4.1 11.9 - - + -
159B TYR* 4.0 14.8 - - + -
162B CYS* 5.1 4.9 - - - -
163B CYS* 5.1 2.9 - - - -
166B LEU* 4.1 22.7 - - + -
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Residues in contact with THR 130 (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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126B GLN* 2.5 41.6 + - + +
127B LYS* 2.6 19.2 + - - -
129B LEU* 1.3 72.7 - - + +
131B THR* 1.3 55.1 + - - +
132B MET 2.9 4.9 - - - -
133B GLY* 2.6 21.3 + - - -
134B PHE 3.0 17.9 - - - +
135B ARG* 2.7 36.5 + - - +
136B LEU 5.4 2.5 - - - +
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Residues in contact with THR 131 (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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108B HIS* 3.1 29.8 + - - -
112B PHE* 3.5 23.9 - - + -
127B LYS* 2.9 21.7 + - - +
128B ALA* 3.0 17.5 + - - -
130B THR* 1.3 74.3 - - - +
132B MET* 1.3 57.0 + - - +
133B GLY 3.1 0.6 + - - -
135B ARG* 5.7 0.4 - - - +
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Residues in contact with MET 132 (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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105B TRP* 3.6 34.1 - - + +
108B HIS* 3.3 28.9 - - + +
128B ALA 3.1 17.2 + - - +
129B LEU* 3.3 14.1 - - + +
130B THR 2.9 0.6 - - - -
131B THR* 1.3 77.6 - - - +
133B GLY* 1.3 56.8 + - - +
134B PHE* 3.5 30.9 + - + -
159B TYR* 3.7 23.8 - - - -
163B CYS* 4.3 14.8 - - + +
166B LEU* 5.9 0.4 - - + -
167B ARG* 5.9 0.9 - - - +
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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