Contacts of the helix formed by residues 125 - 134 (chain A) in PDB entry 3H44
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PHE 5.0 1.3 - - - -
116A LEU* 6.1 0.9 - - + -
123A LYS* 2.7 30.2 + - - +
124A GLU* 1.3 76.0 - - - +
126A GLU* 1.3 63.1 + - - -
127A TYR 3.1 2.9 - - - +
128A SER* 3.4 16.9 + - - +
129A GLN* 2.9 25.0 + - - +
817A GLU* 3.1 29.5 - - - +
821A ASN* 3.5 35.3 + - - +
825A THR* 5.9 0.7 - - + -
826A LYS* 5.8 2.6 - - - +
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Residues in contact with GLU 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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121A TYR* 3.8 32.5 - - + +
123A LYS* 2.7 53.6 + - + +
125A ASN* 1.3 72.0 - - - +
127A TYR* 1.3 56.6 + - - +
129A GLN* 3.7 9.3 + - - +
130A PHE* 2.9 31.6 + - - +
164A ARG* 2.7 39.1 + - + +
412B GLN* 3.6 22.9 + - + +
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Residues in contact with TYR 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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115A PHE* 3.6 39.3 + + + +
125A ASN 3.1 0.6 - - - -
126A GLU* 1.3 81.1 - - - +
128A SER* 1.3 69.3 + - - +
130A PHE* 3.3 2.5 + + - +
131A LEU* 3.0 43.1 + - + +
138A SER* 2.7 35.2 + - - -
151A PHE* 3.3 21.8 - + - +
161A ALA* 4.6 4.0 - - - -
164A ARG* 4.2 25.8 - - + +
165A PHE* 3.6 27.5 - + + -
168A PHE* 3.6 33.7 - + + -
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Residues in contact with SER 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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115A PHE* 5.6 3.6 + - - -
125A ASN* 3.4 16.7 + - - +
127A TYR* 1.3 88.2 - - - +
129A GLN* 1.3 58.5 + - - +
131A LEU* 3.9 6.4 - - - +
132A SER* 3.0 26.9 + - - -
138A SER* 6.4 1.1 - - - -
817A GLU* 3.4 19.5 + - - +
820A PHE* 5.7 7.0 - - - -
821A ASN* 5.5 0.9 - - - +
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Residues in contact with GLN 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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123A LYS* 3.5 28.8 - - - +
125A ASN* 2.9 21.3 + - - +
126A GLU* 3.7 11.1 + - - +
128A SER* 1.3 76.0 + - - +
130A PHE* 1.3 66.2 + - - +
132A SER* 3.5 1.0 - - - -
133A GLU* 2.9 53.0 + - + +
817A GLU* 3.7 31.4 - - + +
412B GLN* 5.8 0.4 - - - +
415B LYS* 5.8 3.8 - - - +
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Residues in contact with PHE 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 GLU* 2.9 22.9 + - - +
127A TYR* 3.7 3.4 - + - +
129A GLN* 1.3 77.4 - - - +
131A LEU* 1.3 70.4 + - + +
133A GLU* 4.8 2.9 - - - -
134A HIS* 2.7 55.1 + + - +
153A VAL* 4.4 3.4 - - + -
157A HIS* 3.9 23.6 - - + -
160A GLY* 3.5 9.9 - - - -
161A ALA* 3.1 44.4 - - + -
164A ARG* 3.4 41.3 - - - +
408B GLU* 3.9 6.5 - - - -
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Residues in contact with LEU 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 TYR* 3.0 34.9 + - + +
128A SER* 3.9 6.1 - - - +
130A PHE* 1.3 80.2 - - + +
132A SER* 1.3 66.2 + - - +
134A HIS* 2.8 14.4 + - - -
136A GLY* 2.9 19.7 + - - -
137A SER* 3.6 22.7 - - - +
138A SER* 3.6 31.2 - - - -
151A PHE* 3.7 11.9 - - + -
152A ASP 3.9 11.9 - - - +
153A VAL* 4.2 5.6 - - + -
161A ALA* 3.9 28.9 - - + -
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Residues in contact with SER 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 SER 3.0 18.8 + - - -
129A GLN 3.5 4.9 - - - -
131A LEU* 1.3 77.7 - - - +
133A GLU* 1.3 61.0 - - - +
134A HIS 3.4 0.3 + - - -
135A ALA 3.6 6.6 + - - -
136A GLY 4.5 6.7 + - - -
813A GLN* 3.2 29.3 + - - -
816A SER* 4.7 4.3 + - - -
817A GLU* 3.5 34.9 + - - +
885A HIS* 5.5 2.8 - - - -
888A ALA* 3.8 0.2 - - - +
892A ARG* 3.7 11.6 + - - +
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Residues in contact with GLU 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 GLN* 2.9 48.9 + - + +
130A PHE* 5.1 1.7 - - - -
132A SER* 1.3 75.1 - - - +
134A HIS* 1.3 77.8 + - + +
135A ALA 3.5 1.1 - - - -
813A GLN* 4.5 5.8 - - - +
881A ALA* 6.3 1.3 - - - -
884A LYS* 3.4 57.6 - - + +
885A HIS* 4.1 25.4 + - + +
888A ALA* 3.8 3.9 - - - +
415B LYS* 5.2 5.2 + - - -
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Residues in contact with HIS 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 PHE* 2.7 50.1 + + - +
131A LEU 2.8 4.0 + - - -
133A GLU* 1.3 101.2 + - + +
135A ALA* 1.3 58.1 + - - +
136A GLY 3.2 3.5 + - - -
153A VAL* 3.7 16.8 - - + +
154A SER* 2.8 36.6 + - - -
157A HIS* 3.2 49.6 + + + -
884A LYS* 4.4 17.6 - - + +
888A ALA* 4.6 1.1 - - - +
891A ILE* 5.1 2.5 - - - -
458B GLU* 6.1 2.0 - - - +
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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