Contacts of the helix formed by residues 126 - 139 (chain A) in PDB entry 1IAX
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 GLY 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ALA 2.8 9.1 + - - +
125A GLY* 1.3 75.0 - - - +
127A ALA* 1.3 66.5 + - - -
130A ALA 3.1 10.7 + - - -
286A ARG* 3.4 19.2 + - - -
287A VAL 3.9 4.0 - - - -
288A GLY* 3.0 28.6 - - - +
500A PLP 3.4 12.6 - - - -
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Residues in contact with ALA 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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126A GLY* 1.3 71.2 - - - -
128A THR* 1.3 57.6 + - - +
130A ALA* 3.9 8.1 - - - -
131A ASN* 2.7 44.7 + - - +
237A ASP* 4.6 1.1 - - - +
239A ILE* 3.9 13.0 - - + -
273A VAL* 4.5 9.2 - - + -
274A TYR 4.6 0.7 - - - -
275A SER* 4.0 9.2 + - - -
500A PLP 3.0 47.7 + - + +
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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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125A GLY 3.8 6.3 - - - -
127A ALA* 1.3 80.3 - - - +
129A GLY* 1.3 62.7 + - - +
131A ASN* 3.5 2.6 + - - +
132A GLU* 3.2 20.4 + - - +
152A TYR* 5.4 0.9 + - - -
154A ALA* 5.8 0.3 - - - +
157A ARG* 4.0 14.2 + - - +
158A ASP* 3.3 29.2 + - - +
286A ARG* 4.2 2.1 + - - -
500A PLP 3.1 21.1 + - - -
92B TYR* 5.4 1.4 + - - -
306B SER* 3.8 20.4 - - - +
307B PHE* 3.4 27.4 - - + -
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Residues in contact with GLY 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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124A ALA* 3.8 5.8 - - - -
125A GLY* 2.9 29.8 + - - -
126A GLY 4.0 0.2 - - - -
128A THR* 1.3 72.7 - - - +
130A ALA* 1.3 64.5 - - - +
132A GLU* 3.4 1.5 + - - +
133A THR* 2.8 32.3 + - - -
307B PHE* 4.3 18.6 - - - -
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Residues in contact with ALA 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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124A ALA* 3.4 14.1 - - + +
126A GLY 3.1 14.3 + - - +
127A ALA* 3.1 10.1 + - - +
129A GLY* 1.3 75.4 - - - +
131A ASN* 1.3 57.9 + - - +
134A ILE* 2.9 30.8 + - - +
273A VAL* 3.6 20.2 - - + -
289A ILE 3.9 12.3 - - - +
290A ILE* 3.4 25.2 - - + +
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Residues in contact with ASN 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 ALA* 2.7 30.5 + - - +
128A THR 3.7 4.8 - - - +
130A ALA* 1.3 70.3 - - - +
132A GLU* 1.3 67.0 + - - +
134A ILE* 3.1 21.0 - - - +
135A ILE* 3.2 12.8 + - - +
155A PHE* 3.7 18.6 - - - -
158A ASP* 4.4 8.5 + - + -
159A LEU* 3.7 16.6 - - + -
203A ILE* 4.1 9.0 - - - +
237A ASP* 2.7 28.8 + - - +
273A VAL* 3.4 14.0 - - - +
500A PLP 3.8 13.1 + - - -
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Residues in contact with GLU 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 3.2 6.9 + - - +
129A GLY* 4.0 3.4 - - - +
131A ASN* 1.3 77.7 - - - +
133A THR* 1.3 59.5 + - - +
135A ILE* 3.4 4.4 + - - +
136A PHE* 3.0 53.9 + - + -
158A ASP 3.4 22.8 + - - +
162A ARG* 2.4 61.9 + - - +
163A THR* 3.7 8.8 - - + +
162B ARG* 4.6 3.3 + - - -
307B PHE* 3.0 30.6 - - + +
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Residues in contact with THR 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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124A ALA* 5.0 4.3 - - + +
129A GLY* 2.8 19.7 + - - -
130A ALA 3.8 2.7 - - - -
132A GLU* 1.3 75.0 + - - +
134A ILE* 1.3 67.0 + - - +
135A ILE 3.0 2.2 - - - -
136A PHE* 3.0 10.0 + - - +
137A CYS* 2.9 23.5 + - - -
290A ILE* 3.8 16.6 - - + -
301A ALA* 4.3 11.9 - - - +
304A MET* 3.4 37.1 + - + +
162B ARG* 3.9 11.4 + - - -
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Residues in contact with ILE 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 2.9 17.4 + - - +
131A ASN* 3.1 22.2 - - - +
133A THR* 1.3 76.7 - - - +
135A ILE* 1.3 65.8 + - + +
137A CYS* 3.7 3.5 + - + +
138A LEU* 3.0 53.0 + - + +
203A ILE* 5.5 2.2 - - + -
235A VAL* 4.0 27.6 - - + -
271A HIS* 4.1 15.9 - - + +
273A VAL* 4.1 7.9 - - + -
290A ILE* 4.0 17.7 - - + +
297A VAL* 3.9 28.9 - - + -
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Residues in contact with ILE 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 ASN 3.2 13.6 + - - +
132A GLU 3.7 6.1 - - - +
133A THR 3.0 0.6 - - - -
134A ILE* 1.3 79.9 - - + +
136A PHE* 1.3 64.2 + - - +
137A CYS 3.0 1.7 + - - -
138A LEU* 4.3 0.9 - - - +
139A ALA* 2.8 34.9 + - + +
145A PHE* 3.7 43.1 - - + -
159A LEU* 3.9 35.7 - - + +
163A THR* 4.2 5.4 - - + -
165A VAL* 3.3 39.0 - - + -
203A ILE* 5.4 3.1 - - + -
235A VAL* 5.3 0.4 - - + -
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Residues in contact with PHE 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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132A GLU* 3.0 49.0 + - + -
133A THR 3.3 7.4 - - - +
135A ILE* 1.3 78.1 - - - +
137A CYS* 1.3 50.6 + - - +
139A ALA 3.8 5.8 - - - +
162A ARG* 3.2 37.2 - - + -
163A THR* 3.9 13.5 - - + -
304A MET* 3.9 14.8 - - + -
13B SER* 2.7 27.9 + - - -
15B LEU* 3.8 28.3 - - + +
136B PHE* 4.2 11.9 - + - -
162B ARG* 3.5 46.9 - - + -
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Residues in contact with CYS 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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133A THR* 2.9 22.6 + - - +
134A ILE* 3.8 8.5 - - - +
135A ILE 3.0 0.2 - - - -
136A PHE* 1.3 78.9 - - - +
138A LEU* 1.3 61.1 + - + +
297A VAL* 4.3 17.5 - - + -
300A CYS* 3.3 35.4 - - - -
301A ALA* 3.8 20.0 - - - -
304A MET* 4.4 2.2 - - - -
12B LEU* 3.8 5.2 - - - +
13B SER* 2.8 25.2 + - - -
16B ALA* 3.6 14.4 - - + +
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Residues in contact with LEU 138 (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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134A ILE* 3.0 32.1 + - + +
135A ILE 3.1 1.6 + - - -
137A CYS* 1.3 79.1 - - + +
139A ALA* 1.3 61.8 + - - +
145A PHE* 3.8 19.5 - - + -
200A LYS* 3.9 14.3 - - - +
233A HIS* 3.2 43.4 - - + +
235A VAL* 3.5 31.6 - - + -
271A HIS* 3.6 16.8 - - + +
297A VAL* 4.1 5.8 - - + -
11B ILE 3.8 10.6 - - - +
12B LEU* 3.7 13.4 - - + -
13B SER* 3.7 11.7 + - - +
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Residues in contact with ALA 139 (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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135A ILE 2.8 21.2 + - - +
136A PHE* 3.8 5.9 - - - +
138A LEU* 1.3 78.2 - - - +
140A ASP* 1.3 61.5 + - - +
141A PRO* 4.7 0.9 - - - +
143A ASP* 3.8 21.1 - - + -
145A PHE* 4.0 15.5 - - + -
163A THR 5.3 0.5 - - - +
165A VAL* 4.0 19.7 - - + +
200A LYS* 3.9 13.2 - - + -
13B SER* 3.5 13.3 - - - +
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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