Contacts of the helix formed by residues 126 - 134 (chain A) in PDB entry 183L
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 TRP 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.1 7.0 - - + -
92A ASP* 4.8 1.3 - - - -
95A ARG* 3.5 57.2 - - - +
121A LEU* 3.5 39.0 - - + -
124A LYS* 3.1 64.8 + - + +
125A ARG* 1.3 69.4 - - - +
127A ASP* 1.3 69.8 + - - +
129A ALA* 3.3 3.3 + - - +
130A ALA* 3.0 24.4 + - - +
153A PHE* 3.6 5.1 - - - +
154A ARG* 3.4 26.6 + - - +
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Residues in contact with ASP 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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125A ARG 3.5 0.2 - - - -
126A TRP* 1.3 78.7 - - - +
128A GLU* 1.3 65.6 + - + +
130A ALA* 3.1 4.4 + - - +
131A VAL* 3.0 27.0 + - - +
154A ARG* 3.5 32.6 + - - +
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Residues in contact with GLU 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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120A MET* 3.6 18.5 - - + +
125A ARG* 3.5 43.7 + - + +
126A TRP 3.3 0.4 - - - -
127A ASP* 1.3 77.7 - - + +
129A ALA* 1.3 64.6 + - - +
131A VAL* 3.3 9.0 + - - +
132A ASN* 3.0 21.8 + - - +
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Residues in contact with ALA 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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117A SER* 4.6 2.0 - - - +
120A MET* 3.8 25.7 - - + -
121A LEU* 4.0 28.9 - - + -
125A ARG 2.9 19.6 + - - +
126A TRP 3.7 4.3 - - - +
128A GLU* 1.3 76.9 - - - +
130A ALA* 1.3 54.5 + - - +
132A ASN* 3.1 3.0 + - - +
133A LEU* 2.7 44.3 + - + +
153A PHE* 6.1 1.1 - - + -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A TRP 3.0 17.6 + - - +
127A ASP 3.4 5.2 - - - +
129A ALA* 1.3 75.9 - - - +
131A VAL* 1.3 65.7 + - + +
133A LEU* 3.5 5.0 + - - +
134A ALA* 3.5 17.8 + - - +
150A ILE* 3.6 33.0 - - + +
153A PHE* 6.1 1.3 - - + +
154A ARG* 3.7 26.9 - - + +
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Residues in contact with VAL 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 ASP 3.0 12.9 + - - +
128A GLU* 3.5 10.8 - - - +
130A ALA* 1.3 80.0 - - + +
132A ASN* 1.3 65.1 + - - +
134A ALA* 3.3 18.0 + - - +
135A LYS* 3.7 24.8 + - - +
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Residues in contact with ASN 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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114A PHE* 5.5 0.7 - - - -
116A ASN* 4.0 11.7 - - - +
117A SER* 2.4 36.8 + - - +
120A MET* 3.9 28.2 - - + +
128A GLU 3.0 13.9 + - - +
129A ALA* 3.1 6.7 + - - +
131A VAL* 1.3 79.3 - - - +
133A LEU* 1.3 65.0 + - - +
134A ALA 3.3 0.2 + - - -
135A LYS* 3.3 31.4 + - - +
136A SER* 5.1 0.5 - - - -
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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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102A MET* 4.4 13.9 - - + -
114A PHE* 3.7 22.2 - - + -
117A SER* 3.6 27.4 - - - +
121A LEU* 4.8 11.0 - - + -
129A ALA* 2.7 29.7 + - + +
130A ALA* 3.9 4.0 - - - +
131A VAL 3.2 0.2 - - - -
132A ASN* 1.3 74.4 - - - +
134A ALA* 1.3 53.8 + - - +
136A SER* 2.6 32.2 + - - -
138A TRP* 3.8 10.5 - - + -
150A ILE* 3.9 26.0 - - + -
153A PHE* 3.7 35.2 - - + -
400A DEN 5.8 2.0 - - + -
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Residues in contact with ALA 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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130A ALA 3.5 9.7 + - - +
131A VAL* 3.3 12.5 + - - +
132A ASN 3.1 0.6 - - - -
133A LEU* 1.3 74.8 - - - +
135A LYS* 1.3 58.6 + - + +
136A SER 3.0 11.1 + - - +
139A TYR* 3.3 52.5 - - + +
140A ASN* 4.7 2.1 + - - +
150A ILE* 3.9 3.5 - - + +
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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