Contacts of the helix formed by residues 120 - 138 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116O VAL 4.3 2.0 - - - -
117O SER 4.8 2.1 + - - -
118O GLN 4.3 0.6 - - - -
119O LEU* 1.3 72.3 - - - +
121O GLU* 1.3 54.2 + - - +
122O GLU* 3.4 2.2 - - - -
123O GLU* 3.2 16.8 + - - +
124O ASN 2.5 32.9 + - - -
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Residues in contact with GLU 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O VAL* 4.3 11.2 + - + +
119O LEU 3.5 1.2 + - - -
120O SER* 1.3 71.9 - - - +
122O GLU* 1.3 58.4 + - - +
124O ASN* 3.1 8.8 + - - +
125O GLU* 2.9 28.8 + - - +
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Residues in contact with GLU 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O SER* 3.4 2.1 - - - -
121O GLU* 1.3 79.3 - - - +
123O GLU* 1.3 62.3 + - - +
125O GLU* 3.5 13.5 + - - +
126O GLN* 3.5 10.2 + - - +
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Residues in contact with GLU 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119O LEU* 5.7 2.0 - - + -
120O SER* 3.2 19.5 + - - +
122O GLU* 1.3 78.6 - - - +
124O ASN* 1.3 59.3 + - - +
126O GLN* 3.3 9.7 + - + +
127O MET* 3.1 24.9 + - - +
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Residues in contact with ASN 124 (chain O).
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* 6.0 4.9 - - + -
116O VAL* 5.0 10.1 - - + -
119O LEU* 3.5 19.3 - - + +
120O SER 2.5 21.3 + - - +
121O GLU* 3.1 11.4 + - - +
123O GLU* 1.3 71.5 - - - +
125O GLU* 1.3 63.2 + - - +
126O GLN 3.1 0.4 - - - -
127O MET* 3.3 8.3 + - - +
128O LYS* 3.1 23.6 + - - +
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Residues in contact with GLU 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O GLU 2.9 12.4 + - - +
122O GLU* 3.7 11.7 - - - +
123O GLU 3.4 0.2 - - - -
124O ASN* 1.3 76.1 - - - +
126O GLN* 1.3 57.3 + - - +
128O LYS* 3.7 6.7 + - - +
129O ALA* 3.1 26.7 + - - +
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Residues in contact with GLN 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M MET* 4.9 0.4 - - - -
122O GLU 3.5 8.6 + - - +
123O GLU* 3.3 13.9 + - - +
124O ASN 3.1 0.6 - - - -
125O GLU* 1.3 78.5 - - - +
127O MET* 1.3 63.3 + - - +
129O ALA* 3.4 7.0 + - - +
130O ASN* 3.0 24.6 + - - +
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Residues in contact with MET 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M MET* 3.3 32.1 - - + +
130M ASN* 4.3 17.7 - - + -
134M MET* 5.2 10.5 - - + -
123O GLU 3.1 13.8 + - - +
124O ASN* 3.3 11.2 + - - +
126O GLN* 1.3 77.0 - - - +
128O LYS* 1.3 49.3 - - - +
130O ASN 3.1 1.4 + - - -
131O LEU* 2.6 36.6 + - - +
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Residues in contact with LYS 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M SER 6.4 0.2 - - - +
124O ASN 3.1 12.9 + - - +
125O GLU* 3.9 7.0 - - - +
127O MET* 1.3 80.2 - - - +
129O ALA* 1.3 61.6 + - - +
131O LEU* 3.2 9.9 + - - +
132O THR* 3.1 22.7 + - - -
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Residues in contact with ALA 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O GLU 3.1 19.2 + - - +
126O GLN* 3.8 7.6 - - - +
127O MET 3.3 0.2 - - - -
128O LYS* 1.3 76.5 - - - +
130O ASN* 1.3 59.8 + - - +
132O THR* 3.8 7.9 + - - -
133O LYS* 3.8 14.7 + - - +
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Residues in contact with ASN 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M MET* 3.6 23.6 - - + -
126O GLN 3.0 17.3 + - - +
127O MET 3.6 3.6 - - - +
129O ALA* 1.3 73.6 - - - +
131O LEU* 1.3 66.4 + - - +
132O THR 3.2 1.8 - - - -
133O LYS* 3.2 9.6 + - + +
134O MET* 3.1 28.9 + - + +
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Residues in contact with LEU 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M LEU* 6.2 5.8 - - + -
9M PHE* 6.1 9.6 - - + -
127M MET* 4.2 9.6 - - + +
127O MET 2.6 20.3 + - - +
128O LYS* 3.2 12.5 + - - +
130O ASN* 1.3 75.0 - - - +
132O THR* 1.3 59.6 + - - +
134O MET* 3.6 9.1 + - - +
135O LEU* 3.4 22.2 + - - +
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Residues in contact with THR 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M LEU* 6.4 2.0 - - - -
128O LYS 3.1 10.8 + - - -
129O ALA* 3.8 11.4 - - - -
130O ASN 3.2 0.4 - - - -
131O LEU* 1.3 79.5 - - - +
133O LYS* 1.3 57.4 + - - +
135O LEU* 3.5 5.5 + - - +
136O SER* 3.1 28.2 + - - -
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Residues in contact with LYS 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O ALA 3.8 8.8 + - - +
130O ASN* 3.2 13.2 + - - +
132O THR* 1.3 78.0 - - - +
134O MET* 1.3 64.8 + - + +
136O SER* 3.5 7.4 + - - -
137O SER* 3.0 22.7 + - - -
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Residues in contact with MET 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M THR 6.0 3.1 - - - +
127M MET* 4.3 34.1 - - + -
9O PHE* 5.4 21.1 - - + -
130O ASN* 3.1 17.7 + - + +
131O LEU* 3.8 10.1 - - - +
132O THR 3.4 0.2 - - - -
133O LYS* 1.3 77.8 - - + +
135O LEU* 1.3 58.0 + - - +
137O SER* 3.1 10.1 + - - -
138O LEU* 2.9 25.2 + - - +
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Residues in contact with LEU 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M LEU* 5.6 3.1 - - + +
11M MET* 5.6 7.0 - - + -
12M ILE* 5.2 20.8 - - + +
15M GLU* 5.4 0.5 - - - +
131O LEU 3.4 14.1 + - - +
132O THR* 3.9 6.1 - - - +
133O LYS 3.3 0.2 - - - -
134O MET* 1.3 76.6 - - - +
136O SER* 1.3 60.5 + - - +
138O LEU* 2.9 24.2 + - - +
139O GLN 2.9 16.3 + - - +
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Residues in contact with SER 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O THR 3.1 17.3 + - - -
133O LYS* 3.8 7.4 - - - -
134O MET 3.3 0.2 - - - -
135O LEU* 1.3 72.6 - - - +
137O SER* 1.3 61.0 + - - +
139O GLN* 2.8 22.5 + - - +
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Residues in contact with SER 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M THR* 5.0 13.2 - - - -
133O LYS 3.0 14.5 + - - -
134O MET* 3.1 15.7 + - - -
136O SER* 1.3 76.6 - - - +
138O LEU* 1.3 59.1 + - - +
139O GLN* 3.1 3.9 + - - +
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Residues in contact with LEU 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ILE* 5.6 5.6 - - - +
15M GLU* 4.1 30.6 - - + +
16M MET* 5.9 4.5 - - + -
134O MET 2.9 11.4 + - - +
135O LEU* 2.9 15.1 + - - +
137O SER* 1.3 74.5 - - - +
139O GLN* 1.3 70.5 + - - +
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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