Contacts of the helix formed by residues 126 - 137 (chain A) in PDB entry 1LB3
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 ASP 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN* 3.4 12.7 + - - +
12A TYR* 3.7 13.5 - - - -
13A SER 4.8 0.5 + - - -
16A VAL* 4.3 8.7 - - + +
76A ARG* 2.9 42.5 + - - -
121A GLY* 2.8 19.8 + - - +
124A ARG* 4.5 7.6 - - + +
125A ALA* 1.3 71.1 - - - +
127A PRO* 1.3 64.2 - - - +
128A HIS* 3.5 3.5 + - - +
129A LEU* 3.1 23.0 + - + +
130A CYS* 3.1 24.6 + - - -
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Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN* 3.9 9.4 - - - +
125A ALA* 3.2 14.8 - - + +
126A ASP* 1.3 84.2 - - - +
128A HIS* 1.3 59.2 + - + +
130A CYS* 3.7 8.3 - - + +
131A ASP* 2.9 31.0 + - - +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.4 25.7 - + - -
75A ASP* 5.8 4.5 - - + -
76A ARG* 3.2 41.8 + - + +
126A ASP* 3.2 2.1 + - - +
127A PRO* 1.3 83.0 - - + +
129A LEU* 1.3 61.7 + - - +
131A ASP* 3.9 8.7 - - - +
132A PHE* 3.0 25.9 + + + +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.7 27.6 - - + -
20A VAL* 4.6 1.1 - - + -
69A LEU* 6.1 0.2 - - + -
72A PHE* 3.6 34.3 - - + -
117A LEU* 3.9 26.9 - - + +
121A GLY* 3.6 28.5 - - - -
126A ASP* 3.1 24.2 + - - +
128A HIS* 1.3 78.4 + - - +
130A CYS* 1.3 64.1 + - - +
132A PHE* 3.2 7.0 + - + +
133A LEU* 3.0 41.7 + - + +
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Residues in contact with CYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A HIS* 3.7 25.3 - - - +
121A GLY* 3.6 6.3 - - - -
122A SER* 3.5 30.5 - - - -
126A ASP 3.1 18.1 + - - +
127A PRO* 3.7 8.3 - - + +
129A LEU* 1.3 82.8 - - - +
131A ASP* 1.3 56.3 + - - +
133A LEU* 3.3 3.4 + - - +
134A GLU* 3.0 32.0 + - - +
720A CD 3.6 24.9 - - - -
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PRO 2.9 17.2 + - - +
128A HIS* 4.0 9.3 - - - +
130A CYS* 1.3 73.9 - - - +
132A PHE* 1.3 59.8 + - - +
134A GLU* 3.5 13.0 + - - +
135A SER* 2.8 44.8 + - - -
715A CD 2.7 28.8 - - - -
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.7 34.3 - - + -
69A LEU* 3.8 20.2 - - + -
72A PHE* 3.6 50.3 - + + -
128A HIS* 3.0 22.8 + + + +
129A LEU* 3.4 5.8 - - + +
131A ASP* 1.3 78.3 + - - +
133A LEU* 1.3 74.3 + - + +
136A HIS* 3.1 41.2 + + - +
137A TYR* 3.5 29.2 - + - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.6 2.9 - - + -
114A LEU* 3.8 31.4 - - + +
117A LEU* 3.8 25.8 - - + -
118A HIS* 3.6 43.7 - - + +
129A LEU* 3.0 25.9 + - + +
130A CYS 3.7 5.4 - - - +
132A PHE* 1.3 88.9 - - + +
134A GLU* 1.3 61.0 + - - +
137A TYR* 2.9 20.0 + - + +
138A LEU* 2.9 33.8 + - + -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A HIS* 4.6 8.9 + - - +
130A CYS* 3.0 17.5 + - - +
131A ASP* 3.5 24.2 + - - +
133A LEU* 1.3 78.4 - - - +
135A SER* 1.3 64.0 + - - +
136A HIS 3.5 0.3 + - - -
138A LEU* 4.1 26.9 + - + +
139A ASP* 4.2 13.0 + - - +
715A CD 3.9 17.4 - - - -
716A CD 3.5 17.4 - - - -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASP* 2.8 40.8 + - - -
133A LEU 3.3 0.2 - - - -
134A GLU* 1.3 78.6 - - - +
136A HIS* 1.3 82.4 + - - +
140A LYS* 5.9 0.5 - - - +
715A CD 3.7 9.0 - - - -
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Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.5 44.2 + - - +
132A PHE* 3.1 38.8 + + - +
135A SER* 1.3 92.0 + - - +
137A TYR* 1.3 74.8 + - + +
140A LYS* 3.7 30.3 + - - +
719A CD 2.4 30.8 - - - -
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A HIS* 3.7 28.9 - - - -
65A GLY* 2.7 32.9 + - - -
68A ARG* 3.3 21.7 - - - +
69A LEU* 3.3 18.4 + - + +
114A LEU* 3.8 29.2 - - + -
132A PHE* 3.5 32.7 - + - -
133A LEU* 2.9 18.3 + - + +
135A SER 3.8 0.6 - - - -
136A HIS* 1.3 96.3 - - + +
138A LEU* 1.3 66.1 + - + +
139A ASP 3.4 2.0 - - - +
140A LYS* 3.2 7.1 + - - +
141A GLU* 3.0 27.1 + - + +
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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