Contacts of the helix formed by residues 128 - 139 (chain B) in PDB entry 2JJ7
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 GLN 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.7 15.6 + - - +
69B PRO 2.9 25.4 + - - -
70B ASN* 3.4 17.9 + - - +
71B PHE* 2.8 40.9 + - - +
72B LEU 4.6 0.5 + - - -
86B TYR* 4.3 8.7 - - + -
124B GLY 4.1 2.2 + - - +
125B SER* 3.1 23.7 + - - +
126B PHE 3.1 1.6 + - - -
127B GLU* 1.3 75.9 - - - +
129B LEU* 1.3 65.7 + - - +
130B LYS 3.3 0.2 - - - -
131B GLU* 3.2 28.6 + - + +
132B ILE* 3.3 11.3 + - + +
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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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83B LEU* 3.7 29.8 - - + -
86B TYR* 3.4 33.5 - - + +
126B PHE* 3.3 8.9 + - + +
127B GLU* 3.1 1.7 - - - -
128B GLN* 1.3 78.0 - - - +
130B LYS* 1.3 63.8 + - - +
132B ILE* 3.1 7.9 + - + +
133B LEU* 3.0 38.3 + - + +
151B ILE* 4.1 29.6 - - + +
154B ILE* 3.8 36.8 - - + -
155B THR* 4.6 4.7 - - - +
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Residues in contact with LYS 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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127B GLU 3.9 10.1 + - - +
128B GLN 3.3 0.6 - - - -
129B LEU* 1.3 79.1 - - - +
131B GLU* 1.3 57.6 + - - +
133B LEU* 3.2 2.3 + - - +
134B GLN* 2.9 63.3 + - - +
147B ILE* 4.2 18.2 - - + -
148B ASN* 5.0 6.3 + - - +
151B ILE* 3.7 28.5 - - + +
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Residues in contact with GLU 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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70B ASN* 2.5 38.8 + - - +
72B LEU* 3.7 21.1 + - + +
127B GLU 4.9 1.0 + - - +
128B GLN* 3.2 26.3 + - - +
130B LYS* 1.3 78.1 - - - +
132B ILE* 1.3 64.6 + - + +
134B GLN* 3.9 12.2 - - - +
135B GLU* 3.0 26.3 + - - +
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Residues in contact with ILE 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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71B PHE* 4.3 12.6 - - + -
72B LEU* 4.2 22.0 - - + +
79B PRO* 3.8 12.7 - - - +
82B ALA* 4.1 11.7 - - + +
83B LEU* 3.7 35.4 - - + +
86B TYR* 3.7 41.3 - - + -
128B GLN* 3.6 17.3 - - + +
129B LEU* 3.1 9.3 + - - +
131B GLU* 1.3 78.7 - - + +
133B LEU* 1.3 58.0 - - - +
135B GLU* 3.5 2.6 + - - +
136B GLY 3.0 23.0 + - - -
142B PHE* 3.6 6.1 - - + -
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Residues in contact with LEU 133 (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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83B LEU* 4.6 3.8 - - + -
129B LEU* 3.0 34.4 + - + +
130B LYS 3.6 2.2 - - - +
132B ILE* 1.3 75.5 - - - +
134B GLN* 1.3 59.3 + - - +
136B GLY* 3.8 0.3 - - - -
137B GLU* 2.9 31.0 + - - +
142B PHE* 3.8 15.2 - - + -
144B PHE* 3.7 14.5 - - + -
147B ILE* 3.5 27.4 - - + -
150B THR* 3.9 22.0 - - + -
151B ILE* 3.9 21.8 - - + +
154B ILE* 4.4 3.4 - - + -
180B LEU* 3.8 28.7 - - + -
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Residues in contact with GLN 134 (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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130B LYS* 2.9 54.4 + - - +
131B GLU* 3.9 12.0 - - - +
133B LEU* 1.3 75.9 - - - +
135B GLU* 1.3 57.2 + - - +
137B GLU* 3.4 12.9 + - - +
138B LYS* 2.8 31.9 + - - +
147B ILE* 4.0 17.9 - - + +
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Residues in contact with GLU 135 (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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72B LEU* 3.8 30.0 - - + +
77B PHE* 4.5 16.9 - - + +
79B PRO* 3.8 4.5 - - + -
131B GLU 3.0 19.3 + - - +
132B ILE 3.6 4.9 - - - +
134B GLN* 1.3 75.1 - - - +
136B GLY* 1.3 56.6 + - - +
138B LYS* 3.2 25.8 + - - +
139B GLN* 2.8 70.3 + - - +
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Residues in contact with GLY 136 (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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79B PRO* 3.5 17.8 - - - +
132B ILE 3.0 11.7 + - - -
133B LEU 3.4 0.2 + - - -
135B GLU* 1.3 71.4 - - - +
137B GLU* 1.3 61.8 + - - +
139B GLN 3.4 0.5 + - - -
140B GLY 3.1 3.8 + - - -
141B VAL* 2.8 35.7 + - - +
142B PHE* 3.4 26.2 - - - -
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Residues in contact with GLU 137 (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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133B LEU 2.9 17.4 + - - +
134B GLN* 3.6 11.4 - - - +
136B GLY* 1.3 72.5 - - - +
138B LYS* 1.3 69.2 + - - +
140B GLY* 3.1 13.0 + - - -
142B PHE* 3.6 18.1 - - - +
143B HIS* 5.8 0.2 - - - -
144B PHE* 3.5 45.4 + - + +
147B ILE* 5.4 1.9 - - - +
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Residues in contact with LYS 138 (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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134B GLN 2.8 19.0 + - - +
135B GLU* 3.5 30.7 + - - +
137B GLU* 1.3 77.1 - - - +
139B GLN* 1.3 63.6 + - - +
140B GLY* 3.4 1.4 + - - -
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Residues in contact with GLN 139 (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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77B PHE* 2.8 27.6 + - - +
79B PRO* 3.4 23.9 - - + +
135B GLU* 2.8 41.8 + - - +
136B GLY 4.0 3.8 - - - +
137B GLU 3.2 0.2 - - - -
138B LYS* 1.3 81.2 - - + +
140B GLY* 1.3 59.3 + - - +
141B VAL* 3.4 6.7 + - + +
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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