Contacts of the helix formed by residues 126 - 139 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B ALA* 2.7 11.1 + - - +
125B GLY* 1.3 72.1 - - - -
127B ALA* 1.3 66.8 + - - -
128B THR 3.0 2.7 - - - -
130B ALA 3.0 13.9 + - - -
286B ARG* 3.4 18.8 + - - -
287B VAL 3.9 3.4 - - - -
288B GLY* 3.2 27.3 - - - +
501B PLP 3.4 11.0 - - - -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY* 1.3 69.7 - - - -
128B THR* 1.3 66.8 + - - +
130B ALA* 3.7 8.2 - - - +
131B ASN* 2.8 35.8 + - - +
237B ASP* 5.1 0.2 - - - +
239B ILE* 3.1 36.6 - - + -
273B VAL* 4.7 6.3 - - + -
274B TYR 4.5 2.2 - - - +
275B SER* 4.0 7.7 - - - -
501B PLP 2.7 26.8 + - + +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 5.5 0.3 + - - -
306A SER* 4.0 18.5 + - - +
307A PHE* 3.3 31.0 - - + -
125B GLY 3.7 7.9 - - - -
127B ALA* 1.3 81.7 - - - +
129B GLY* 1.3 57.5 + - - +
131B ASN* 3.5 3.3 - - - +
132B GLU* 3.1 24.1 + - - +
152B TYR* 4.9 4.4 + - - -
157B ARG* 3.9 12.8 + - - +
158B ASP* 3.4 29.1 + - - +
286B ARG* 4.0 4.7 + - - -
501B PLP 2.8 20.5 + - - -
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 4.1 17.0 - - - -
124B ALA* 3.6 6.5 - - - -
125B GLY* 2.9 27.0 + - - -
126B GLY 3.8 0.4 - - - -
128B THR* 1.3 73.8 - - - +
130B ALA* 1.3 60.0 + - - +
132B GLU* 4.1 2.9 - - - +
133B THR* 2.8 36.5 + - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ALA* 3.3 13.3 - - + +
126B GLY 3.0 16.5 + - - +
127B ALA* 3.2 6.3 + - - +
129B GLY* 1.3 75.0 - - - +
131B ASN* 1.3 59.0 + - - +
134B ILE* 2.9 29.8 + - - +
273B VAL* 3.8 14.8 - - + -
289B ILE 3.7 16.8 - - - +
290B ILE* 3.4 28.7 - - + +
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA* 2.8 30.8 + - - +
128B THR 3.5 3.4 - - - +
130B ALA* 1.3 77.3 - - - +
132B GLU* 1.3 64.1 + - - +
133B THR 3.1 0.2 + - - -
134B ILE* 3.1 10.5 - - - +
135B ILE* 3.1 26.0 + - - +
152B TYR* 4.7 6.7 - - - -
155B PHE* 3.7 15.5 - - - -
158B ASP* 4.3 12.5 + - + -
159B LEU* 3.5 21.8 - - + -
203B ILE* 4.4 3.1 - - - +
237B ASP* 2.8 28.9 + - - +
273B VAL* 3.3 15.4 - - - +
501B PLP 4.8 0.4 - - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 4.3 6.9 + - - -
307A PHE* 3.4 30.3 - - + +
128B THR 3.1 5.8 + - - +
129B GLY* 4.1 3.3 - - - +
131B ASN* 1.3 78.8 - - - +
133B THR* 1.3 58.2 + - - +
135B ILE* 3.5 4.8 + - - +
136B PHE* 3.0 49.6 + - + -
158B ASP 3.5 24.5 + - - +
162B ARG* 2.6 56.8 + - + +
163B THR* 3.8 8.3 - - + +
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 4.1 12.6 + - - -
123B MET 6.1 0.7 - - - +
124B ALA* 4.9 3.6 - - + +
129B GLY* 2.8 24.8 + - - -
130B ALA 3.7 2.5 - - - -
132B GLU* 1.3 76.3 + - - +
134B ILE* 1.3 68.4 + - - +
136B PHE* 3.0 12.1 + - - +
137B CYS* 2.9 20.9 + - - +
290B ILE* 3.6 19.1 - - + -
301B ALA* 4.0 16.4 - - + +
304B MET* 3.9 30.6 + - + +
305B SER* 5.8 1.1 - - - -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 2.9 18.9 + - - +
131B ASN* 3.1 19.7 - - - +
133B THR* 1.3 73.5 - - - +
135B ILE* 1.3 75.8 + - + +
137B CYS* 3.0 15.0 + - + +
138B LEU* 3.0 33.1 + - + +
203B ILE* 5.4 1.3 - - + -
235B VAL* 4.1 27.4 - - + -
271B HIS* 3.9 20.4 - - + -
272B ILE 5.9 0.2 - - - +
273B VAL* 4.4 7.6 - - + -
290B ILE* 4.0 20.2 - - + +
292B SER* 5.0 0.2 - - - +
297B VAL* 3.9 28.7 - - + -
301B ALA* 5.7 0.2 - - + -
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASN 3.1 16.2 + - - +
132B GLU 3.8 4.3 - - - +
134B ILE* 1.3 90.8 - - + +
136B PHE* 1.3 63.8 + - - +
137B CYS 2.9 1.6 + - - -
138B LEU* 2.9 11.8 + - - +
139B ALA* 3.0 18.1 + - + +
145B PHE* 4.3 35.4 - - + -
159B LEU* 3.7 48.9 - - + +
163B THR* 3.9 8.3 - - + -
165B VAL* 3.5 31.2 - - + -
203B ILE* 5.1 3.8 - - + -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 2.7 26.5 + - - -
15A LEU* 4.0 28.7 - - + +
136A PHE* 4.2 13.0 - + - -
162A ARG* 3.7 42.8 - - + -
132B GLU* 3.0 47.4 + - + -
133B THR* 3.0 9.3 + - - +
135B ILE* 1.3 76.9 - - - +
137B CYS* 1.3 52.3 + - - +
139B ALA 4.0 5.9 - - - +
162B ARG* 3.2 37.0 - - + -
163B THR* 3.7 16.4 - - + +
304B MET* 3.5 17.5 - - + -
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Residues in contact with CYS 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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12A LEU* 3.9 2.1 - - - +
13A SER* 3.3 13.5 + - - -
16A ALA* 3.2 23.3 - - + +
133B THR* 2.9 15.0 + - - +
134B ILE* 3.3 13.5 - - - +
135B ILE 2.9 0.4 - - - -
136B PHE* 1.3 76.8 - - - +
138B LEU* 1.3 68.8 + - + +
297B VAL* 4.4 11.4 - - + -
300B CYS* 3.5 36.1 - - - -
301B ALA* 3.7 21.3 - - - -
304B MET* 3.9 9.4 - - - -
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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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11A ILE 4.1 6.6 - - - +
12A LEU* 3.7 3.8 - - + +
13A SER* 4.0 7.5 + - - +
134B ILE* 3.0 20.1 + - + +
135B ILE 2.9 3.0 + - - +
137B CYS* 1.3 88.5 - - + +
139B ALA* 1.3 62.1 + - - +
145B PHE* 4.3 13.5 - - + -
200B LYS* 3.2 23.9 - - - +
233B HIS* 3.6 38.8 - - + +
235B VAL* 3.8 16.2 - - + -
271B HIS* 3.2 31.2 - - + +
297B VAL* 3.6 24.7 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.6 9.3 - - - -
135B ILE* 3.0 14.4 + - + +
136B PHE* 4.0 5.7 - - - +
138B LEU* 1.3 80.2 - - - +
140B ASP* 1.3 65.3 + - - +
141B PRO* 4.8 0.7 - - - +
143B ASP* 3.9 15.7 - - + -
145B PHE* 4.0 23.8 - - + -
163B THR* 5.1 1.6 - - - +
165B VAL* 3.3 27.1 - - + +
200B LYS* 4.1 3.4 - - + -
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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
------------------------------------------------------------
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