Contacts of the helix formed by residues 124 - 139 (chain B) in PDB entry 3D9L
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 LYS 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B GLN* 5.3 0.2 - - - -
123B PHE* 1.3 78.2 - - - +
125B SER* 1.3 61.9 + - - +
126B GLU* 3.2 28.9 + - + +
127B ILE* 3.0 16.5 + - + +
128B ILE* 3.0 23.9 + - - +
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLN* 3.6 29.4 - - - +
124B LYS* 1.3 72.1 - - - +
126B GLU* 1.3 72.5 + - - +
127B ILE 3.1 0.2 - - - -
128B ILE* 3.7 1.8 - - - +
129B GLN* 3.0 37.2 + - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS* 3.2 36.3 + - + +
125B SER* 1.3 85.3 + - - +
127B ILE* 1.3 60.6 + - + +
130B PRO* 3.2 23.2 - - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 3.8 25.8 - - - +
92B ILE* 3.9 38.4 - - + +
93B ILE* 5.3 1.4 - - - +
123B PHE* 3.9 25.4 - - + -
124B LYS* 3.0 17.3 + - + +
126B GLU* 1.3 83.8 - - + +
128B ILE* 1.3 63.7 + - + +
129B GLN 3.5 0.2 - - - -
130B PRO* 3.4 8.9 - - - +
131B LEU* 3.3 17.5 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 3.7 29.6 - - + +
117B TRP* 3.6 12.3 - - + -
118B GLN* 3.4 53.4 - - + +
123B PHE* 3.4 41.1 - - + +
124B LYS 3.0 9.3 + - - +
127B ILE* 1.3 77.9 - - + +
129B GLN* 1.3 67.9 + - - +
131B LEU* 3.0 18.1 + - + +
132B LEU* 3.0 26.3 + - + +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLN* 3.5 18.7 + - - +
125B SER* 3.0 23.4 + - - +
128B ILE* 1.3 78.2 - - - +
130B PRO* 1.4 60.1 - - + +
132B LEU* 3.3 20.3 + - - +
133B ASP* 2.8 59.7 + - - +
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.1 19.7 - - + -
126B GLU* 3.2 26.7 - - - +
127B ILE 3.4 7.9 - - - +
129B GLN* 1.4 94.8 - - + +
131B LEU* 1.3 56.7 + - - +
133B ASP* 3.7 10.0 - - + +
134B MET* 2.9 35.1 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 3.6 39.3 - - + +
93B ILE* 3.7 25.8 - - + -
96B PHE* 3.8 29.6 - - + -
100B TYR* 2.7 27.5 + - - -
114B LEU* 3.6 28.9 - - + -
127B ILE* 3.3 23.1 - - + +
128B ILE* 3.0 10.8 + - + +
130B PRO* 1.3 74.3 - - - +
132B LEU* 1.3 60.8 + - - +
134B MET* 3.5 7.7 + - - +
135B ALA 3.4 8.7 + - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 4.4 0.9 - - - -
111B VAL* 3.9 22.4 - - + +
114B LEU* 3.7 27.6 - - + -
115B ASN* 3.7 25.1 - - - +
118B GLN* 4.4 5.8 - - - +
128B ILE* 3.0 32.5 + - + +
129B GLN* 3.6 28.9 - - - +
131B LEU* 1.3 73.9 - - - +
133B ASP* 1.3 64.6 + - - +
135B ALA* 3.1 14.8 + - - +
136B ALA* 3.2 13.6 + - - +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLN* 2.8 48.4 + - - +
130B PRO* 3.7 8.9 - - + +
132B LEU* 1.3 77.0 - - - +
134B MET* 1.3 61.5 + - - +
136B ALA* 3.5 5.8 + - - +
137B ALA* 3.1 25.8 + - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.9 33.0 - - - +
96B PHE* 3.9 4.0 - - + -
97B GLN* 3.6 46.0 - - + +
100B TYR* 3.8 19.7 - - + -
130B PRO* 2.9 19.6 + - - +
131B LEU* 3.6 11.7 - - - +
133B ASP* 1.3 77.4 - - - +
135B ALA* 1.3 60.3 - - - +
137B ALA* 3.5 6.4 + - - +
138B LEU* 3.3 26.4 + - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.3 32.9 - - + +
107B LYS* 4.0 15.2 - - + +
111B VAL* 3.7 23.8 - - + -
131B LEU 3.4 1.8 + - - -
132B LEU 3.1 10.9 + - - +
134B MET* 1.3 78.9 - - - +
136B ALA* 1.3 62.6 + - - +
138B LEU* 3.2 22.5 + - - +
139B GLU* 3.7 5.5 + - - +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU 3.2 8.2 + - - +
133B ASP* 3.9 10.3 - - - +
135B ALA* 1.3 77.8 - - - +
137B ALA* 1.3 57.7 + - - +
139B GLU* 2.9 36.8 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP 3.1 18.8 + - - +
134B MET* 4.0 6.3 - - - +
135B ALA 3.3 0.4 - - - -
136B ALA* 1.3 75.8 - - - +
138B LEU* 1.3 59.1 + - - +
139B GLU 3.9 6.0 - - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.5 44.4 - - + +
107B LYS* 3.8 26.9 + - - +
134B MET* 3.3 15.1 + - + +
135B ALA* 3.2 11.6 + - - +
136B ALA 3.1 0.4 - - - -
137B ALA* 1.3 77.8 - - - +
139B GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LYS* 3.6 30.8 + - - +
135B ALA 4.1 5.5 - - - +
136B ALA* 2.9 25.4 + - - +
137B ALA* 3.9 5.5 - - - +
138B LEU* 1.3 82.8 - - - +
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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