Contacts of the helix formed by residues 120 - 137 (chain C) 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 SER 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C GLN 4.1 0.6 + - - -
119C LEU* 1.3 72.9 - - - +
121C GLU* 1.3 59.2 + - - +
122C GLU* 3.3 6.7 - - - -
123C GLU* 2.8 25.3 + - - +
124C ASN* 2.7 31.2 + - - +
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU 3.8 1.3 + - - -
120C SER* 1.3 74.4 - - - +
122C GLU* 1.3 51.7 + - - +
124C ASN* 4.6 3.6 - - - -
125C GLU* 2.5 47.1 + - + +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER* 3.3 5.6 - - - -
121C GLU* 1.3 77.6 - - - +
123C GLU* 1.3 57.4 + - - +
125C GLU* 3.6 4.8 - - - +
126C GLN* 3.0 25.6 + - - +
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Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLN 3.7 6.9 - - - +
119C LEU* 3.6 22.0 - - + +
120C SER* 2.8 44.5 + - - +
122C GLU* 1.3 77.4 - - - +
124C ASN* 1.3 58.2 + - - +
125C GLU 3.4 0.7 - - - -
126C GLN* 3.6 8.6 + - - +
127C MET* 3.0 26.5 + - - +
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Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C VAL* 5.1 6.3 - - + +
119C LEU* 3.3 28.7 - - + +
120C SER 2.7 22.5 + - - +
121C GLU* 4.3 3.4 - - - +
123C GLU* 1.3 72.4 - - - +
125C GLU* 1.3 55.7 + - - +
126C GLN 3.1 1.1 - - - -
127C MET* 3.7 0.2 - - - +
128C LYS* 2.7 38.2 + - - +
5D TYR* 3.3 19.3 + - + +
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLU* 2.5 32.5 + - + +
122C GLU* 3.6 6.7 - - - +
124C ASN* 1.3 73.2 - - - +
126C GLN* 1.3 63.7 - - - +
128C LYS* 3.8 6.4 - - - +
129C ALA* 3.1 22.9 + - - +
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Residues in contact with GLN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLU 3.0 19.0 + - - +
123C GLU* 3.7 9.6 - - - +
124C ASN 3.1 0.2 - - - -
125C GLU* 1.3 78.0 - - - +
127C MET* 1.3 57.2 + - - +
129C ALA* 3.2 6.3 + - - +
130C ASN* 2.9 40.7 + - - +
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Residues in contact with MET 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 3.8 11.0 - - + -
123C GLU 3.0 19.1 + - - +
124C ASN 3.0 3.3 + - - +
126C GLN* 1.3 72.3 - - - +
128C LYS* 1.3 66.9 + - - +
129C ALA 3.1 1.1 - - - -
130C ASN* 3.7 9.9 - - - +
131C LEU* 3.0 43.5 + - + +
5D TYR* 4.5 4.7 - - + +
9D PHE* 4.2 4.0 - - + -
127D MET* 3.2 15.3 - - + +
130D ASN* 4.2 8.1 - - + -
131D LEU* 2.9 39.7 - - + -
134D MET* 3.2 40.8 - - + -
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN 2.7 21.1 + - - +
125C GLU* 3.8 6.7 - - - +
127C MET* 1.3 73.7 - - - +
129C ALA* 1.3 62.8 + - - +
131C LEU* 3.4 6.8 + - - +
132C THR* 2.8 29.1 + - - +
3D PHE 5.2 9.4 - - - +
5D TYR* 4.4 21.0 + - + +
8D LEU* 4.4 9.1 - - + +
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU 3.1 12.1 + - - +
126C GLN* 3.4 11.2 - - - +
128C LYS* 1.3 81.1 - - - +
130C ASN* 1.3 58.9 + - - +
132C THR* 3.3 8.8 + - - -
133C LYS* 3.0 26.0 + - - +
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Residues in contact with ASN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLN* 2.9 27.7 + - - +
127C MET* 3.7 5.1 - - - +
128C LYS 3.3 0.2 - - - -
129C ALA* 1.3 76.4 - - - +
131C LEU* 1.3 53.8 + - - +
133C LYS* 3.0 9.7 + - - +
134C MET* 2.5 43.6 + - + +
123D GLU* 5.6 10.4 + - - +
127D MET* 3.8 28.1 - - + +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 3.8 34.1 - - + -
127C MET* 3.0 42.1 + - + +
128C LYS* 3.7 5.4 - - - +
130C ASN* 1.3 75.3 - - - +
132C THR* 1.3 53.6 + - - +
134C MET* 3.6 5.3 - - - +
135C LEU* 2.7 35.2 + - - +
5D TYR* 4.9 7.9 - - + -
8D LEU* 4.1 24.7 - - + -
9D PHE* 3.5 26.9 - - + -
12D ILE* 3.9 11.0 - - + +
127D MET* 3.8 20.2 - - + -
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C LYS* 2.8 18.7 + - - +
129C ALA* 3.5 9.4 + - - -
130C ASN 3.2 0.2 - - - -
131C LEU* 1.3 75.8 - - - +
133C LYS* 1.3 63.3 + - - +
135C LEU* 3.3 5.6 + - + +
136C SER* 3.1 19.9 + - - -
3D PHE* 5.7 8.2 + - + +
8D LEU* 3.9 19.9 - - + +
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Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA 3.0 13.2 + - - +
130C ASN* 3.0 12.4 + - - +
132C THR* 1.3 74.1 - - - +
134C MET* 1.3 64.8 + - + +
136C SER* 3.1 21.5 + - - -
137C SER* 3.2 10.6 + - - -
118D GLN* 5.9 6.3 - - + -
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Residues in contact with MET 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TYR* 4.1 27.8 - - + -
9C PHE* 3.4 34.5 - - + -
130C ASN* 2.5 25.0 + - + +
131C LEU* 3.6 11.7 - - - +
133C LYS* 1.3 73.6 - - + +
135C LEU* 1.3 61.6 + - - +
137C SER* 3.1 24.5 - - - +
138C LEU* 3.6 11.9 - - - +
12D ILE* 5.0 4.7 - - + -
115D LEU* 3.9 26.1 - - + +
118D GLN* 5.6 7.2 - - + -
127D MET* 3.3 30.5 - - - +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 6.3 1.8 - - - +
131C LEU 2.7 19.9 + - - +
132C THR* 3.6 8.3 - - + +
133C LYS 3.2 0.4 - - - -
134C MET* 1.3 73.0 - - - +
136C SER* 1.3 66.1 + - - +
137C SER 3.1 0.2 - - - -
138C LEU* 3.1 19.1 + - + +
139C GLN 3.8 15.3 - - - +
7D TYR* 5.1 7.9 - - + +
8D LEU* 4.1 17.7 - - + +
11D MET* 3.5 37.5 - - + +
12D ILE* 3.7 23.8 - - + +
15D GLU* 5.4 5.2 - - + -
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Residues in contact with SER 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C THR 3.1 11.2 + - - -
133C LYS* 3.1 15.3 + - - -
135C LEU* 1.3 77.6 - - - +
137C SER* 1.3 57.7 + - - +
138C LEU 3.0 5.5 + - - -
139C GLN* 3.3 12.2 + - - +
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Residues in contact with SER 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LYS 3.2 13.2 + - - -
134C MET* 3.1 17.3 + - - +
135C LEU 3.1 0.6 - - - -
136C SER* 1.3 77.8 - - - +
138C LEU* 1.3 60.8 + - - +
139C GLN 3.6 0.6 + - - -
114D THR* 4.8 19.4 + - - +
115D LEU* 4.0 18.8 - - - +
118D GLN* 5.4 7.4 - - - +
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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