Contacts of the helix formed by residues 124 - 134 (chain A) in PDB entry 3SN5
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 ASN 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LYS* 3.7 16.2 + - - +
116A PRO* 5.7 1.3 - - - -
122A THR 3.9 2.0 + - - -
123A GLU* 1.3 71.3 - - - +
125A ILE* 1.3 59.5 + - - +
126A ASN* 3.1 25.1 + - - +
127A ASP* 2.9 39.7 + - + +
128A THR* 3.1 13.6 + - - -
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Residues in contact with ILE 125 (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 PHE* 3.7 33.9 - - + -
114A ILE* 3.9 13.0 - - + +
121A THR* 6.1 2.0 - - + -
123A GLU* 3.5 26.9 + - + +
124A ASN* 1.3 71.1 + - - +
126A ASN* 1.3 58.7 + - + +
128A THR* 3.0 10.5 + - - -
129A PHE* 2.9 50.2 + - + -
260A ARG* 5.0 0.2 - - - +
601A HEM 4.0 10.8 - - - +
1429A K2B 3.4 53.8 - - + -
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Residues in contact with ASN 126 (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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98A LYS* 4.5 16.0 - - - +
124A ASN* 3.1 16.0 + - - +
125A ILE* 1.3 81.7 - - + +
127A ASP* 1.3 56.9 + - - +
129A PHE* 3.4 10.5 + - - +
130A ILE* 3.0 55.8 + - - +
441A ALA 4.9 9.0 - - - +
443A ILE 5.5 2.8 - - - +
445A PRO* 5.4 5.7 - - - +
601A HEM 4.3 12.3 - - - +
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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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124A ASN* 2.9 34.2 + - + +
126A ASN* 1.3 77.6 - - - +
128A THR* 1.4 58.4 + - - +
130A ILE* 3.5 11.0 + - - +
131A LYS* 3.1 43.4 + - - +
127B ASP* 5.5 2.4 - - - +
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Residues in contact with THR 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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123A GLU* 2.8 29.3 + - - +
124A ASN 3.1 11.1 + - - -
125A ILE* 3.0 9.6 + - - -
127A ASP* 1.4 77.8 + - - +
129A PHE* 1.3 54.9 + - + +
131A LYS* 3.6 1.4 + - - +
132A THR* 2.8 34.8 + - - +
256A LEU* 4.5 5.6 - - + -
259A LEU* 4.2 24.2 - - + -
260A ARG* 3.7 29.2 - - + +
263A LEU* 3.5 15.4 - - + +
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Residues in contact with PHE 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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125A ILE* 2.9 39.0 + - + +
126A ASN* 3.8 5.6 - - - +
128A THR* 1.3 73.9 - - - +
130A ILE* 1.4 59.7 + - - +
132A THR* 3.3 3.9 + - - -
133A LEU* 2.9 43.3 + - + +
256A LEU* 3.7 21.1 - - + -
260A ARG* 4.6 5.6 - - - -
282A VAL* 3.9 21.3 - - + -
445A PRO* 3.6 22.9 - - + -
601A HEM 3.5 61.2 - - + -
1429A K2B 3.8 24.0 - - + -
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Residues in contact with ILE 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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126A ASN* 3.0 48.8 + - - +
127A ASP* 3.9 10.5 - - - +
128A THR 3.4 0.2 - - - -
129A PHE* 1.4 75.9 - - - +
131A LYS* 1.3 65.2 + - + +
132A THR 3.2 1.4 + - - -
134A GLN* 3.3 50.0 + - + +
445A PRO* 5.2 3.8 - - + -
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Residues in contact with LYS 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* 3.1 36.3 + - - +
128A THR 3.8 5.2 - - - +
130A ILE* 1.3 77.6 - - + +
132A THR* 1.4 64.2 + - + +
134A GLN 4.1 4.0 - - - +
137A ALA* 3.6 13.4 + - - +
259A LEU* 4.5 11.2 - - + -
131B LYS* 5.5 11.4 - - - -
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Residues in contact with THR 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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128A THR* 2.8 22.0 + - + +
129A PHE 3.6 2.1 + - - -
130A ILE 3.2 1.0 - - - -
131A LYS* 1.4 80.0 - - + +
133A LEU* 1.3 64.0 + - - +
137A ALA* 3.4 20.9 - - - +
141A LEU* 4.0 12.5 - - - +
255A GLU* 3.6 30.3 - - + +
256A LEU* 3.3 38.8 + - - +
259A LEU* 3.8 20.0 - - + -
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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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129A PHE* 2.9 39.3 + - + +
132A THR* 1.3 82.7 - - - +
134A GLN* 1.3 65.8 + - + +
138A LEU* 3.6 27.4 - - - +
141A LEU* 3.7 25.1 - - + -
187A ILE* 5.3 1.3 - - + -
256A LEU* 4.2 11.2 - - + -
445A PRO* 3.5 20.6 - - + +
446A GLY* 3.9 24.6 - - - +
448A LEU* 4.9 2.6 - - - +
449A PHE* 4.9 6.8 + - + -
601A HEM 3.9 30.7 - - + -
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Residues in contact with GLN 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 ILE* 3.3 42.4 + - + +
131A LYS 4.1 3.5 - - - +
133A LEU* 1.3 86.8 - - - +
135A GLY* 1.3 68.0 + - - +
136A HIS 3.5 0.2 + - - -
137A ALA* 3.4 17.5 + - - +
138A LEU* 3.6 8.2 + - - -
445A PRO* 3.0 34.2 + - - +
447A ARG* 3.5 31.8 + - - +
448A LEU* 4.0 18.7 - - + +
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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