Contacts of the helix formed by residues 126 - 139 (chain M) 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 GLN 126 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125M GLU* 1.3 77.9 - - - +
127M MET* 1.3 62.3 + - + +
129M ALA* 3.5 6.6 + - - +
130M ASN* 2.9 25.8 + - - +
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Residues in contact with MET 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M GLU 4.3 2.0 - - - +
126M GLN* 1.3 77.4 - - + +
128M LYS* 1.3 55.8 + - - +
130M ASN* 3.0 3.8 + - + +
131M LEU* 2.6 42.7 + - + +
126O GLN 4.5 0.4 - - - +
127O MET* 3.3 52.0 - - + +
130O ASN* 3.6 18.2 - - + -
131O LEU* 4.2 15.3 - - + +
134O MET* 4.3 26.0 - - + -
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Residues in contact with LYS 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M GLU* 3.2 45.3 + - + +
127M MET* 1.3 79.4 - - - +
129M ALA* 1.3 70.3 + - - +
131M LEU* 4.0 4.3 - - - +
132M THR* 3.2 40.3 + - + +
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Residues in contact with ALA 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M GLU 3.0 17.9 + - - +
126M GLN* 3.6 8.3 - - - +
127M MET 3.2 0.2 - - - -
128M LYS* 1.3 86.3 - - - +
130M ASN* 1.3 64.5 + - - +
132M THR* 3.3 15.6 + - - -
133M LYS* 3.6 10.7 + - - +
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Residues in contact with ASN 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M GLN 2.9 18.9 + - - +
127M MET* 3.0 9.6 + - + +
129M ALA* 1.3 77.6 - - - +
131M LEU* 1.3 62.2 + - - +
133M LYS* 3.1 16.8 + - - +
134M MET* 3.1 26.8 + - + +
119O LEU* 5.2 10.5 - - + -
123O GLU 5.8 1.1 - - - +
127O MET* 4.3 22.0 - - + -
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Residues in contact with LEU 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M PHE* 6.6 0.4 - - + -
127M MET* 2.6 23.5 + - + +
128M LYS* 4.0 5.4 - - - +
130M ASN* 1.3 74.1 - - - +
132M THR* 1.3 62.6 + - + +
134M MET* 3.5 9.3 + - - +
135M LEU* 3.2 24.1 + - - +
8O LEU* 4.3 25.0 - - + +
9O PHE* 5.7 4.3 - - + -
12O ILE* 5.6 2.4 - - - +
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Residues in contact with THR 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M LYS* 3.2 26.4 + - + +
129M ALA* 3.3 10.7 + - - -
130M ASN 3.3 0.2 - - - -
131M LEU* 1.3 76.8 - - + +
133M LYS* 1.3 61.5 + - - +
135M LEU* 4.2 4.9 - - - +
136M SER* 3.1 28.6 + - - -
8O LEU* 6.4 1.6 - - + -
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Residues in contact with LYS 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M ALA 3.6 10.0 + - - +
130M ASN* 3.1 11.8 + - - +
132M THR* 1.3 79.6 + - - +
134M MET* 1.3 59.7 + - - +
136M SER* 3.5 5.3 + - - -
137M SER* 2.9 28.8 + - - -
118O GLN* 4.6 18.3 - - - +
119O LEU* 5.0 6.7 - - + -
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Residues in contact with MET 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M PHE* 6.2 8.3 - - + -
130M ASN* 3.1 27.6 - - + +
131M LEU* 3.8 7.4 - - - +
132M THR 3.4 0.2 - - - -
133M LYS* 1.3 77.0 - - - +
135M LEU* 1.3 63.8 + - - +
137M SER* 2.9 18.4 + - - -
138M LEU* 3.0 13.5 + - - +
12O ILE* 5.6 6.7 - - + -
115O LEU* 4.2 34.5 - - + +
118O GLN* 4.8 2.9 - - - -
119O LEU* 4.3 18.6 - - + -
124O ASN* 6.0 4.5 - - + -
127O MET* 5.2 10.5 - - + -
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Residues in contact with LEU 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M LEU 3.2 14.7 + - - +
132M THR* 4.2 5.6 - - - +
134M MET* 1.3 78.7 - - - +
136M SER* 1.3 63.5 + - - +
138M LEU* 3.2 8.2 + - - +
139M GLN* 3.0 19.2 + - - -
8O LEU* 5.1 6.3 - - - +
11O MET* 5.6 8.3 - - + +
12O ILE* 4.9 19.4 - - + +
15O GLU* 5.3 3.1 - - - +
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Residues in contact with SER 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132M THR 3.1 20.4 + - - -
133M LYS* 3.6 6.7 - - - -
135M LEU* 1.3 75.4 - - - +
137M SER* 1.3 63.8 + - - +
139M GLN* 3.2 22.8 + - - +
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Residues in contact with SER 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133M LYS 2.9 15.2 + - - -
134M MET* 2.9 13.4 + - - -
136M SER* 1.3 78.1 - - - +
138M LEU* 1.3 58.6 + - - +
139M GLN* 4.5 1.7 - - - +
114O THR 5.3 2.7 - - - -
118O GLN* 4.0 22.4 - - - -
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M MET 3.0 10.5 + - - +
135M LEU* 3.6 7.6 - - - +
136M SER 3.2 0.4 - - - -
137M SER* 1.3 80.5 - - - +
139M GLN* 1.3 70.7 + - - +
15O GLU* 3.4 38.5 - - + +
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Residues in contact with GLN 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M LEU 3.0 13.8 + - - -
136M SER* 3.2 17.3 - - - +
137M SER 4.5 1.8 - - - +
138M LEU* 1.3 84.7 - - - +
15O GLU* 2.9 26.7 - - - +
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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