Contacts of the helix formed by residues 120 - 139 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D GLN 4.0 1.0 + - - -
119D LEU* 1.3 73.9 - - - +
121D GLU* 1.3 60.9 + - - +
122D GLU* 2.9 7.0 - - - -
123D GLU* 2.8 25.0 + - - +
124D ASN* 2.6 33.0 + - - +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU 4.1 0.2 + - - -
120D SER* 1.3 71.3 - - - +
122D GLU* 1.3 56.6 + - - +
124D ASN* 4.8 3.0 - - - +
125D GLU* 3.1 26.4 + - - +
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER* 2.9 6.5 - - - -
121D GLU* 1.3 79.0 - - - +
123D GLU* 1.3 60.0 + - - +
125D GLU* 3.5 4.2 + - - +
126D GLN* 2.9 30.5 + - - +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASN* 5.6 10.0 + - - +
119D LEU* 4.2 6.3 - - + -
120D SER* 2.8 34.5 + - - +
122D GLU* 1.3 71.2 - - - +
124D ASN* 1.3 55.2 + - - +
126D GLN* 3.0 8.6 + - - +
127D MET* 2.7 35.7 + - - +
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Residues in contact with ASN 124 (chain D).
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* 3.7 16.1 + - - +
116D VAL* 4.8 14.8 - - + -
119D LEU* 3.3 25.3 - - + +
120D SER 2.6 16.4 + - - +
121D GLU* 4.8 2.5 - - - +
123D GLU* 1.3 73.3 - - - +
125D GLU* 1.3 57.5 + - - +
127D MET* 3.1 3.7 + - - +
128D LYS* 2.8 34.6 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLU 3.1 22.5 + - - +
122D GLU* 3.7 5.6 - - - +
123D GLU 3.3 0.4 - - - -
124D ASN* 1.3 77.6 - - - +
126D GLN* 1.3 57.8 + - - +
128D LYS* 4.0 4.2 - - - +
129D ALA* 3.0 30.7 + - - +
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Residues in contact with GLN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLU 2.9 18.8 + - - +
123D GLU* 3.0 7.2 + - - +
125D GLU* 1.3 77.6 - - - +
127D MET* 1.3 62.0 + - - +
129D ALA* 3.4 7.0 + - - +
130D ASN* 3.1 24.4 + - - +
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Residues in contact with MET 127 (chain D).
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* 3.9 12.6 - - - +
127C MET* 3.2 49.1 - - + +
130C ASN* 3.8 22.2 - - + +
131C LEU* 3.8 11.9 - - + -
134C MET* 3.3 32.1 - - - +
123D GLU 2.7 19.8 + - - +
124D ASN* 3.7 4.5 - - - +
126D GLN* 1.3 70.5 - - - +
128D LYS* 1.3 63.8 + - - +
129D ALA 3.2 0.2 + - - -
130D ASN* 3.2 4.1 + - - -
131D LEU* 2.4 52.2 + - + +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLU 6.3 0.9 - - - +
3C PHE 5.4 7.6 - - - +
5C TYR* 4.3 17.9 - - + +
124D ASN 2.8 19.6 + - - +
125D GLU* 4.1 3.8 - - - +
127D MET* 1.3 76.2 - - - +
129D ALA* 1.3 56.0 + - - +
131D LEU* 3.7 6.1 - - - +
132D THR* 2.6 36.7 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLU 3.0 21.9 + - - +
126D GLN* 3.4 7.4 - - - +
128D LYS* 1.3 80.0 - - - +
130D ASN* 1.3 61.9 + - - +
132D THR* 3.4 7.4 + - - -
133D LYS* 3.2 18.2 + - - +
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Residues in contact with ASN 130 (chain D).
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* 4.2 24.5 - - + +
123C GLU* 6.0 1.3 - - - +
127C MET* 4.2 13.9 - - - -
126D GLN 3.1 13.8 + - - +
127D MET* 3.9 3.6 - - - +
129D ALA* 1.3 79.8 - - - +
131D LEU* 1.3 58.1 + - - +
133D LYS* 3.2 18.3 - - - +
134D MET* 3.1 24.6 - - - +
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Residues in contact with LEU 131 (chain D).
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* 4.4 14.1 - - + -
8C LEU* 4.7 13.7 - - + -
9C PHE* 3.7 34.3 - - + -
12C ILE* 3.5 21.9 - - + +
127C MET* 2.9 40.2 - - + -
9D PHE* 5.1 0.9 - - + -
127D MET* 2.4 63.6 + - + +
128D LYS* 3.7 5.6 - - - +
130D ASN* 1.3 72.7 - - - +
132D THR* 1.3 65.3 + - - +
133D LYS 3.1 0.9 - - - -
134D MET* 3.3 4.5 + - - +
135D LEU* 3.2 17.7 + - - +
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Residues in contact with THR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 5.2 17.0 - - + -
8C LEU* 5.7 4.5 - - - +
128D LYS* 2.6 24.6 + - - +
129D ALA* 3.5 8.2 + - - -
131D LEU* 1.3 75.2 - - - +
133D LYS* 1.3 63.4 + - - +
135D LEU* 3.3 8.3 + - + +
136D SER* 3.1 21.3 + - - -
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Residues in contact with LYS 133 (chain D).
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* 5.5 15.1 + - + -
119C LEU* 6.0 1.3 - - + -
129D ALA 3.2 10.2 + - - +
130D ASN* 3.2 16.2 - - - +
132D THR* 1.3 79.4 - - - +
134D MET* 1.3 64.1 + - + +
136D SER* 3.1 21.8 + - - -
137D SER* 3.5 6.1 + - - -
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Residues in contact with MET 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ILE* 4.6 6.5 - - + -
115C LEU* 4.1 26.1 - - + +
118C GLN* 5.2 9.0 - - + +
119C LEU* 3.9 21.1 - - + -
127C MET* 3.2 44.9 - - + -
5D TYR* 3.8 32.3 - - + -
9D PHE* 4.3 12.8 - - + -
130D ASN 3.1 15.0 + - - +
131D LEU 3.3 6.2 + - - +
133D LYS* 1.3 76.0 - - + +
135D LEU* 1.3 62.3 + - - +
137D SER* 3.1 22.5 + - - -
138D LEU* 3.2 14.1 - - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 5.4 1.6 - - - +
11C MET* 5.5 6.5 - - + -
12C ILE* 3.6 26.1 - - + +
15C GLU* 5.4 2.7 - - + +
131D LEU 3.2 7.0 + - - +
132D THR* 3.7 11.2 - - + +
133D LYS 3.2 0.4 - - - -
134D MET* 1.3 75.3 - - - +
136D SER* 1.3 66.5 + - - +
138D LEU* 3.3 12.0 + - - +
139D GLN* 2.9 27.7 + - + +
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Residues in contact with SER 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D THR* 3.1 12.2 + - - -
133D LYS* 3.1 14.4 + - - -
135D LEU* 1.3 77.0 - - - +
137D SER* 1.3 63.4 + - - +
139D GLN* 3.4 20.4 + - - +
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C THR* 5.1 9.4 - - - +
115C LEU* 4.6 7.1 - - - +
118C GLN* 4.3 21.1 + - - -
133D LYS 3.5 4.5 + - - -
134D MET* 3.1 12.4 + - - -
135D LEU 3.2 0.4 - - - -
136D SER* 1.3 78.0 - - - +
138D LEU* 1.3 74.2 + - - +
139D GLN 4.1 3.3 - - - +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ILE* 4.2 25.8 - - + +
15C GLU* 3.8 25.4 - - + +
16C MET* 4.1 31.0 - - + -
19C LYS* 4.9 12.4 - - + +
111C MET* 5.8 5.8 - - + -
115C LEU* 4.5 18.6 - - + -
134D MET* 3.2 21.8 - - + +
135D LEU* 3.3 12.9 + - - +
137D SER* 1.3 85.3 + - - +
139D GLN* 1.3 68.0 + - - +
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Residues in contact with GLN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 4.5 14.9 - - + +
58D GLN* 4.9 15.0 - - - +
135D LEU* 2.9 19.2 + - + +
136D SER* 3.6 16.6 - - - +
137D SER 3.2 3.3 - - - +
138D LEU* 1.3 86.2 - - - +
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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