Contacts of the helix formed by residues 126 - 141 (chain A) in PDB entry 3CJE
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 PRO 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A PRO 4.9 0.4 - - - +
125A ASP* 1.3 92.7 - - + +
127A ILE* 1.3 66.7 + - - +
128A GLU* 3.6 25.4 - - - +
129A ALA* 3.0 25.6 + - + +
130A GLN* 3.2 11.3 + - - +
172A GOL 4.9 2.0 - - - +
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Residues in contact with ILE 127 (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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125A ASP 3.5 0.6 + - - -
126A PRO* 1.3 71.1 - - - +
128A GLU* 1.3 60.6 + - - +
130A GLN* 3.1 14.3 + - + +
131A GLN* 2.8 54.5 + - + +
172A GOL 4.1 29.1 - - - -
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Residues in contact with GLU 128 (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 PRO* 3.6 17.1 - - + +
127A ILE* 1.3 88.8 + - + +
129A ALA* 1.3 57.0 + - - +
131A GLN* 3.5 14.6 + - - +
132A ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 5.0 4.7 - - - +
85A LYS* 5.2 3.1 - - + +
86A VAL* 3.4 26.4 - - + +
125A ASP* 4.5 3.6 - - + -
126A PRO* 3.0 28.4 + - + +
128A GLU* 1.3 76.6 - - - +
130A GLN* 1.3 61.1 + - - +
132A ALA* 3.3 8.3 + - - +
133A LEU 3.1 21.8 + - - -
171A GOL 5.4 10.1 - - - +
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Residues in contact with GLN 130 (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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86A VAL* 4.4 6.1 - - + -
121A LEU* 3.6 31.5 - - + +
123A SER* 3.6 25.1 + - - +
125A ASP* 2.9 26.5 + - + +
126A PRO 3.2 10.4 + - - +
127A ILE* 3.1 14.4 + - + +
129A ALA* 1.3 74.3 - - - +
131A GLN* 1.3 64.9 + - + +
133A LEU* 3.2 6.4 + - - +
134A ILE* 3.0 29.9 + - + +
172A GOL 2.9 26.5 + - - -
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Residues in contact with GLN 131 (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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127A ILE* 2.8 37.6 + - + +
128A GLU* 3.8 15.5 - - - +
130A GLN* 1.3 78.0 - - + +
132A ALA* 1.3 55.5 + - - +
134A ILE* 3.2 11.4 + - + +
135A GLU* 2.9 38.7 + - + +
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Residues in contact with ALA 132 (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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84A LEU* 4.2 8.9 - - + +
128A GLU 3.0 14.9 + - - +
129A ALA* 3.5 12.1 - - - +
131A GLN* 1.3 75.6 - - - +
133A LEU* 1.3 57.9 + - - +
135A GLU* 3.4 6.7 + - - +
136A ALA* 2.9 30.9 + - - +
171A GOL 6.1 1.8 - - - +
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Residues in contact with LEU 133 (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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77A ILE* 3.8 25.4 - - + +
80A PHE* 3.6 33.0 - - + +
81A ALA* 3.6 19.3 - - + +
84A LEU* 3.9 11.9 - - + +
86A VAL* 3.9 29.6 - - + -
88A VAL* 4.0 17.5 - - + -
121A LEU* 4.6 7.6 - - + -
129A ALA 3.1 13.6 + - - +
130A GLN 3.5 8.3 - - - +
131A GLN 3.2 0.4 - - - -
132A ALA* 1.3 76.9 - - - +
134A ILE* 1.3 59.1 + - + +
136A ALA* 3.3 1.0 + - - +
137A ALA* 2.8 30.3 + - - +
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Residues in contact with ILE 134 (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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77A ILE* 5.1 4.9 - - + -
119A ILE* 3.8 49.1 - - + +
121A LEU* 4.6 11.4 - - + -
130A GLN* 3.0 19.9 + - + +
131A GLN* 3.2 12.8 + - + +
133A LEU* 1.3 77.6 - - + +
135A GLU* 1.3 58.4 + - - +
137A ALA* 3.2 7.6 + - + +
138A LYS* 2.8 48.3 + - + +
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Residues in contact with GLU 135 (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 GLN* 2.9 24.7 + - + +
132A ALA* 3.7 7.2 - - - +
134A ILE* 1.3 77.3 - - - +
136A ALA* 1.3 61.9 + - - +
138A LYS* 2.3 50.4 + - - +
139A LYS* 3.2 47.1 + - - +
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Residues in contact with ALA 136 (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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80A PHE* 3.4 18.9 - - + -
84A LEU* 3.5 25.4 - - + -
132A ALA 2.9 18.2 + - - +
133A LEU 3.7 1.3 - - - +
135A GLU* 1.3 75.6 - - - +
137A ALA* 1.3 57.8 + - - +
139A LYS* 3.2 7.9 + - - +
140A GLY 2.9 24.4 + - - -
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Residues in contact with ALA 137 (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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73A VAL* 4.4 7.4 - - + +
76A GLN* 3.7 25.2 - - + +
77A ILE* 3.8 27.8 - - + +
80A PHE* 3.9 3.7 - - + -
133A LEU 2.8 17.4 + - - +
134A ILE* 3.5 6.3 - - + +
136A ALA* 1.3 77.2 - - - +
138A LYS* 1.3 57.1 + - - +
140A GLY 3.3 0.9 + - - -
141A CYS* 2.9 33.2 + - - +
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Residues in contact with LYS 138 (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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73A VAL* 6.3 0.2 - - - -
134A ILE* 2.8 32.3 + - + +
135A GLU* 2.3 45.3 + - - +
137A ALA* 1.3 76.2 - - - +
139A LYS* 1.3 65.2 + - + +
141A CYS* 3.4 7.7 + - - +
144A GLU* 3.6 42.8 - - - +
145A GLN* 3.1 16.3 - - - +
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Residues in contact with LYS 139 (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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135A GLU* 3.2 37.8 + - - +
136A ALA* 3.9 6.0 - - - +
138A LYS* 1.3 81.1 - - + +
140A GLY* 1.3 60.0 + - - +
141A CYS 3.3 0.2 - - - -
145A GLN* 3.5 28.7 - - - +
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Residues in contact with GLY 140 (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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76A GLN* 3.4 24.6 + - - +
80A PHE* 4.2 11.2 - - - -
136A ALA 2.9 15.6 + - - -
137A ALA 3.6 1.8 - - - -
139A LYS* 1.3 77.7 - - - +
141A CYS* 1.3 58.3 + - - +
142A PHE* 3.1 18.7 + - - -
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Residues in contact with CYS 141 (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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69A LEU* 4.7 0.7 - - - -
72A CYS* 3.1 36.1 - - - +
73A VAL* 4.0 12.3 - - + -
76A GLN* 3.7 12.3 - - + -
137A ALA 2.9 17.3 + - - +
138A LYS 3.6 6.0 - - - +
139A LYS 3.3 1.0 - - - -
140A GLY* 1.3 76.1 - - - +
142A PHE* 1.3 65.2 + - - +
143A LEU* 3.2 2.9 + - - -
144A GLU* 3.4 34.5 - - + -
145A GLN* 3.0 25.2 + - - +
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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