Contacts of the helix formed by residues 129 - 137 (chain B) in PDB entry 1A4I
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 SER 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A SER 3.6 2.2 - - - +
130A ILE* 4.2 22.4 - - - -
133A GLY* 3.3 14.7 + - - -
134A ARG* 4.0 19.5 + - - +
137A ARG* 6.3 0.2 - - - -
139A ASP* 4.5 8.7 + - - -
112B GLU* 5.5 0.7 + - - -
116B ASN* 2.8 30.6 + - - +
127B LEU 3.6 2.1 + - - -
128B THR* 1.4 71.3 - - - +
130B ILE* 1.4 56.0 + - - +
132B ALA* 3.3 6.2 + - - -
133B GLY 2.9 23.9 + - - -
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Residues in contact with ILE 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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129A SER* 4.0 14.2 - - - -
130A ILE* 3.2 40.4 - - + +
116B ASN* 4.6 2.4 + - - +
120B PRO* 3.6 35.4 - - + -
128B THR* 3.3 3.6 + - - +
129B SER* 1.4 75.2 - - - +
131B ASN* 1.3 62.6 + - - +
133B GLY* 3.2 1.9 + - - -
134B ARG* 3.0 49.2 + - - +
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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
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120B PRO* 4.8 6.6 - - + +
123B ASP* 3.5 11.4 - - + +
126B GLY* 3.1 21.1 + - - +
128B THR* 3.2 21.5 + - - +
130B ILE* 1.3 76.0 - - - +
132B ALA* 1.3 59.7 + - - +
134B ARG* 3.2 11.7 + - - +
135B LEU* 2.9 29.2 + - - +
143B CYS* 3.3 9.5 - - - +
144B PHE* 2.4 61.8 + - - +
146B PRO* 4.9 0.6 - - - +
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Residues in contact with ALA 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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133A GLY* 4.1 4.0 - - - -
137A ARG* 3.7 44.7 + - + +
126B GLY 4.3 6.5 + - - +
127B LEU* 5.1 2.5 - - - +
128B THR 2.9 17.1 + - - +
129B SER* 3.6 8.7 - - - +
131B ASN* 1.3 80.4 - - - +
133B GLY* 1.3 55.9 + - - +
135B LEU* 3.5 3.2 + - - +
136B ALA* 2.8 32.3 + - - +
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Residues in contact with GLY 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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129A SER* 3.5 16.8 + - - -
132A ALA* 4.1 4.6 - - - +
133A GLY* 3.4 26.8 - - - -
129B SER 2.9 10.5 + - - -
130B ILE 3.2 0.9 + - - -
132B ALA* 1.3 73.7 - - - +
134B ARG* 1.3 64.0 + - - +
136B ALA* 3.6 2.1 + - - -
137B ARG* 3.2 29.3 + - - +
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Residues in contact with ARG 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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112A GLU* 4.2 10.3 + - - +
116A ASN* 5.9 1.6 - - - +
129A SER* 3.7 15.9 + - - +
120B PRO* 4.0 24.2 + - - +
121B GLU* 5.0 3.6 - - - +
130B ILE* 3.0 36.0 + - - +
131B ASN* 3.6 12.8 + - - +
133B GLY* 1.3 72.6 - - - +
135B LEU* 1.3 66.8 + - - +
137B ARG* 3.2 3.3 + - - -
138B GLY 3.2 5.7 + - - -
139B ASP* 2.9 53.5 + - + +
142B ASP* 5.4 9.8 + - - -
143B CYS* 4.0 17.1 - - + +
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Residues in contact with LEU 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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137A ARG* 3.8 6.7 - - - +
126B GLY 5.8 0.2 - - - +
131B ASN* 2.9 18.5 + - - +
132B ALA* 3.7 4.7 - - - +
134B ARG* 1.3 78.0 - - - +
136B ALA* 1.3 60.7 + - - +
137B ARG 3.1 1.0 + - - -
138B GLY* 3.2 10.6 + - - -
140B LEU* 3.5 34.0 - - + +
143B CYS* 3.9 16.5 - - - -
144B PHE 4.5 5.4 - - - +
145B ILE* 4.6 6.7 - - + -
146B PRO* 4.0 16.4 - - + -
180B PRO* 3.7 32.8 - - + +
183B ASP* 3.6 18.0 - - + +
184B LEU* 4.1 8.1 - - + +
187B TRP* 3.5 9.9 - - - -
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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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136A ALA* 3.5 28.7 - - + -
137A ARG* 4.2 0.2 - - - +
179A ALA* 4.3 2.9 - - - +
183A ASP* 5.8 0.2 - - - +
132B ALA 2.8 23.2 + - - +
133B GLY* 4.0 4.5 - - - +
134B ARG 3.2 0.4 - - - -
135B LEU* 1.3 71.6 - - - +
137B ARG* 1.3 78.0 + - - +
138B GLY 3.4 0.4 - - - -
182B HIS* 5.8 1.0 - - - -
183B ASP* 3.4 24.7 + - - +
186B LEU* 5.3 1.7 - - - +
187B TRP* 3.5 14.1 + - - -
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Residues in contact with ARG 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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112A GLU* 5.8 0.7 - - - +
132A ALA* 3.9 32.8 + - + +
135A LEU* 3.8 9.9 - - - +
136A ALA* 4.2 0.2 - - - +
146A PRO* 5.7 1.0 - - - +
175A LYS* 3.6 53.5 + - + +
179A ALA* 3.7 21.6 - - - +
180A PRO* 3.5 30.2 - - - +
183A ASP* 2.8 31.9 + - - -
133B GLY 3.2 17.0 + - - +
134B ARG* 3.2 6.2 + - - +
135B LEU 3.2 0.6 - - - -
136B ALA* 1.3 105.0 + - + +
138B GLY* 1.3 59.7 + - - +
139B ASP* 3.6 1.1 - - - +
187B TRP* 3.8 15.0 - - - -
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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