Contacts of the helix formed by residues 122 - 137 (chain I) in PDB entry 4LLL
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 GLU 122 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120I SER* 3.8 10.3 - - - -
121I GLU* 1.3 81.1 - - - +
123I GLU* 1.3 56.6 + - - +
125I GLU* 5.3 0.3 - - - +
126I GLN* 3.7 19.4 + - - +
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Residues in contact with GLU 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I LEU* 4.1 13.0 - - + -
120I SER* 2.7 25.6 + - - +
122I GLU* 1.3 80.2 - - - +
124I ASN* 1.3 55.2 + - - -
125I GLU 3.1 10.9 + - - -
126I GLN* 4.7 3.4 - - - -
127I MET* 3.4 28.3 + - + +
5J TYR* 4.1 0.2 + - - -
130J ASN* 4.6 15.3 - - + -
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Residues in contact with ASN 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I VAL* 3.6 39.5 - - + +
119I LEU* 4.6 1.6 - - + +
120I SER 2.7 16.2 + - - +
121I GLU* 3.5 25.8 + - - +
123I GLU* 1.3 69.9 - - - +
125I GLU* 1.3 57.0 + - - +
127I MET* 6.3 0.2 - - - -
128I LYS* 5.0 1.4 - - - +
5J TYR* 2.6 29.3 + - - -
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Residues in contact with GLU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I GLU* 3.9 19.3 + - - +
122I GLU 5.3 0.4 - - - +
123I GLU 3.1 0.2 - - - -
124I ASN* 1.3 78.1 - - - +
126I GLN* 1.3 69.2 + - - +
127I MET 3.2 1.5 + - - -
128I LYS* 3.7 12.0 + - - +
129I ALA* 3.7 11.6 + - - +
5J TYR* 4.7 0.2 - - - -
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Residues in contact with GLN 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I GLU 3.7 19.0 + - - +
123I GLU* 3.6 4.6 + - - +
125I GLU* 1.3 81.1 - - - +
127I MET* 1.3 56.6 + - - +
129I ALA* 3.4 5.0 + - - +
130I ASN* 2.9 30.0 + - + +
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Residues in contact with MET 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I GLU* 3.4 14.8 + - + +
124I ASN* 6.3 0.2 - - - -
125I GLU 3.2 0.8 - - - -
126I GLN* 1.3 76.9 - - - +
128I LYS* 1.3 54.1 + - - +
131I LEU* 2.3 49.0 + - + +
5J TYR* 4.0 24.5 - - + +
9J PHE* 4.8 20.0 - - + -
127J MET* 3.1 48.6 - - + +
130J ASN* 3.9 26.5 - - + +
131J LEU* 4.5 12.8 - - - +
134J MET* 5.4 5.8 - - + -
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Residues in contact with LYS 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I ASN 5.0 2.2 - - - +
125I GLU* 3.7 9.4 + - - +
126I GLN 3.4 0.6 - - - -
127I MET* 1.3 78.8 - - - +
129I ALA* 1.3 57.3 + - - +
131I LEU* 3.6 6.6 - - - +
132I THR* 3.0 33.7 + - - -
2J GLU* 4.1 19.7 - - + +
3J PHE 5.5 0.7 - - - +
5J TYR* 3.9 22.6 + - + +
8J LEU* 4.0 15.8 - - + +
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Residues in contact with ALA 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I GLU 3.7 9.0 + - - +
126I GLN* 3.4 9.4 + - - +
128I LYS* 1.3 77.5 - - - +
130I ASN* 1.3 64.5 + - - +
132I THR* 3.4 16.5 + - - -
133I LYS* 3.8 6.8 + - - +
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Residues in contact with ASN 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I GLN* 2.9 15.3 + - + +
129I ALA* 1.3 76.3 - - - +
131I LEU* 1.3 61.8 + - - +
132I THR 3.3 0.9 + - - -
133I LYS* 3.5 13.1 + - - +
134I MET* 3.8 8.8 + - - +
127J MET* 3.1 29.2 - - + -
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Residues in contact with LEU 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I MET* 2.3 44.4 + - + +
128I LYS* 3.6 8.3 - - - +
130I ASN* 1.3 69.5 - - - +
132I THR* 1.3 63.1 + - - +
134I MET* 3.5 15.2 + - - +
135I LEU* 3.5 7.8 + - - +
5J TYR* 6.2 0.2 - - + -
8J LEU* 4.5 17.3 - - + -
9J PHE* 6.2 4.3 - - + -
12J ILE* 3.7 15.3 - - + +
127J MET* 3.6 8.5 - - + +
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Residues in contact with THR 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I LYS 3.0 21.1 + - - -
129I ALA* 3.7 8.2 - - - +
130I ASN 3.2 0.6 - - - -
131I LEU* 1.3 75.1 - - - +
133I LYS* 1.3 69.4 + - - +
135I LEU* 2.9 11.3 + - - +
136I SER* 2.9 22.7 + - - -
2J GLU* 4.2 14.6 - - - +
8J LEU* 5.1 7.1 - - - +
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Residues in contact with LYS 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I ALA 3.8 5.6 + - - +
130I ASN* 3.5 9.5 + - - +
131I LEU 3.5 0.4 - - - -
132I THR* 1.3 80.5 - - - +
134I MET* 1.3 62.4 + - - +
136I SER* 3.0 20.1 + - - -
137I SER 3.0 5.7 + - - -
118J GLN* 3.0 26.6 + - + +
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Residues in contact with MET 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I ASN 3.8 6.9 + - - +
131I LEU* 3.5 12.5 + - - +
132I THR 3.2 0.8 - - - -
133I LYS* 1.3 77.3 - - - +
135I LEU* 1.3 59.2 + - - +
137I SER* 2.5 23.2 + - - -
138I LEU* 3.4 11.4 - - - +
12J ILE* 4.3 11.0 - - + -
115J LEU* 4.5 19.4 - - + +
118J GLN* 3.6 19.4 - - + +
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Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I GLN* 5.4 6.1 - - - +
131I LEU 3.5 5.2 + - - +
132I THR* 2.9 11.9 + - - +
134I MET* 1.3 76.2 - - - +
136I SER* 1.3 67.3 + - - +
137I SER 3.0 1.6 - - - -
138I LEU* 2.9 29.9 + - + +
7J TYR* 5.0 11.4 - - + +
8J LEU* 4.7 8.3 - - + +
11J MET* 3.7 39.7 - - + +
12J ILE* 3.8 30.2 - - + +
15J GLU* 4.5 7.2 - - + -
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Residues in contact with SER 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I THR* 2.9 15.8 + - - -
133I LYS* 3.0 14.8 + - - -
135I LEU* 1.3 76.0 - - - +
137I SER* 1.3 57.1 + - - +
138I LEU* 2.9 6.8 + - - -
139I GLN* 4.0 9.2 + - - +
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Residues in contact with SER 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I LYS 3.0 4.6 + - - -
134I MET 2.5 20.4 + - - -
136I SER* 1.3 75.3 - - - +
138I LEU* 1.3 72.3 + - - +
139I GLN 3.8 2.4 + - - -
114J THR* 5.6 7.6 - - - +
115J LEU* 4.3 2.6 - - - +
118J GLN* 2.8 35.7 + - - +
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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