Contacts of the helix formed by residues 1128 - 1137 (chain B) in PDB entry 1DIA
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 THR1128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1115B ILE* 3.1 32.3 - - + +
1116B ASN* 3.7 10.1 - - - -
1118B ILE* 3.8 21.1 - - + +
1120B PRO* 4.6 5.1 - - - +
1123B ASP* 2.7 37.7 + - + +
1127B LEU* 1.3 82.4 - - - +
1129B SER* 1.3 60.2 + - - +
1130B ILE* 4.1 7.9 + - - +
1131B ASN* 3.2 16.3 + - - +
1132B ALA* 2.9 25.5 + - - +
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Residues in contact with SER1129 (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 2.1 - - - +
130A ILE* 4.3 22.9 - - - -
133A GLY* 3.3 14.3 + - - -
134A ARG* 4.1 18.6 + - - +
139A ASP* 4.9 6.1 + - - -
1112B GLU* 5.5 0.9 + - - -
1116B ASN* 2.8 28.8 + - - -
1127B LEU 3.6 1.7 + - - -
1128B THR* 1.3 72.1 - - - +
1130B ILE* 1.3 53.8 + - - +
1132B ALA* 3.3 6.2 + - - -
1133B GLY* 2.7 30.1 + - - -
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Residues in contact with ILE1130 (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* 3.9 16.1 - - - -
130A ILE* 3.5 37.7 - - + +
1116B ASN* 4.6 1.7 + - - +
1120B PRO* 3.5 40.6 - - + -
1128B THR* 3.3 3.9 - - - +
1129B SER* 1.3 76.8 - - - +
1131B ASN* 1.3 62.8 + - - +
1133B GLY* 3.4 1.4 + - - -
1134B ARG* 3.1 44.1 + - - +
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Residues in contact with ASN1131 (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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1120B PRO* 4.5 6.6 - - + +
1123B ASP* 3.6 7.9 - - + +
1126B GLY* 3.1 28.9 + - - -
1128B THR* 3.2 20.4 + - - +
1129B SER 3.3 0.4 - - - -
1130B ILE* 1.3 78.9 - - - +
1132B ALA* 1.3 67.6 + - - +
1134B ARG* 3.2 10.3 + - - +
1135B LEU* 3.0 23.0 + - - +
1143B CYS* 3.6 6.9 - - - +
1144B PHE* 2.6 56.8 + - - +
1146B PRO* 4.9 0.8 - - - +
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Residues in contact with ALA1132 (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* 4.2 4.3 - - - +
136A ALA* 5.2 0.2 - - - -
137A ARG* 3.7 45.9 + - + +
1126B GLY 4.6 5.6 + - - +
1127B LEU* 4.9 4.0 - - - +
1128B THR 2.9 18.5 + - - +
1129B SER* 3.6 8.3 - - - +
1131B ASN* 1.3 80.3 - - - +
1133B GLY* 1.3 56.7 + - - +
1135B LEU* 4.6 2.0 - - - -
1136B ALA* 2.9 32.6 + - - +
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Residues in contact with GLY1133 (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* 3.4 19.3 + - - -
132A ALA* 4.1 4.4 - - - +
133A GLY* 3.4 23.5 - - - -
1129B SER 2.7 13.3 + - - -
1130B ILE 3.4 1.3 + - - -
1131B ASN 3.1 0.2 - - - -
1132B ALA* 1.3 75.7 - - - +
1134B ARG* 1.3 58.8 + - - +
1136B ALA* 4.1 1.6 - - - +
1137B ARG* 3.4 29.1 + - - +
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Residues in contact with ARG1134 (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* 4.5 5.9 + - - +
116A ASN* 5.5 3.6 - - - +
129A SER* 3.9 13.8 + - - +
1120B PRO* 3.9 27.3 + - - +
1121B GLU* 5.0 3.4 - - - +
1130B ILE* 3.1 35.2 + - - +
1131B ASN* 3.2 10.2 + - - +
1133B GLY* 1.3 75.5 - - - +
1135B LEU* 1.3 63.6 + - - +
1137B ARG 3.2 2.6 + - - -
1138B GLY 3.2 5.9 + - - -
1139B ASP* 2.9 52.8 + - + +
1142B ASP* 4.8 13.8 + - - -
1143B CYS* 3.9 21.7 - - + +
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Residues in contact with LEU1135 (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 7.4 - - - +
1126B GLY 5.8 0.2 - - - +
1131B ASN* 3.0 16.5 + - - +
1132B ALA* 3.9 3.4 - - - +
1134B ARG* 1.3 77.4 - - - +
1136B ALA* 1.3 60.8 + - - +
1138B GLY 3.4 7.8 + - - -
1140B LEU* 3.5 32.3 - - + +
1143B CYS* 3.8 17.6 - - - -
1144B PHE 4.5 5.4 - - - +
1145B ILE* 4.6 6.1 - - + -
1146B PRO* 4.1 16.2 - - + -
1180B PRO* 3.6 33.2 - - + +
1183B ASP* 3.5 19.9 - - + +
1184B LEU* 3.9 10.5 - - + -
1187B TRP* 3.5 11.8 - - - -
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Residues in contact with ALA1136 (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* 3.6 27.1 - - + -
179A ALA* 4.6 2.3 - - - +
183A ASP* 5.8 0.2 - - - +
1132B ALA 2.9 18.8 + - - +
1133B GLY* 4.1 4.3 - - - +
1134B ARG 3.3 0.2 - - - -
1135B LEU* 1.3 77.5 - - - +
1137B ARG* 1.3 77.0 + - - +
1182B HIS* 5.7 1.2 - - - -
1183B ASP* 3.3 24.9 + - - +
1186B LEU* 5.0 2.9 - - - +
1187B TRP* 3.2 17.3 + - - -
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Residues in contact with ARG1137 (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* 5.5 0.7 - - - +
132A ALA* 3.8 34.6 + - + +
135A LEU* 4.0 7.1 - - - +
136A ALA* 4.2 0.2 - - - +
146A PRO* 6.0 0.2 - - - +
175A LYS* 3.6 52.5 + - + +
179A ALA* 3.6 32.1 - - - +
180A PRO* 3.6 22.6 - - - +
183A ASP* 2.7 32.7 + - - -
1133B GLY 3.4 17.9 + - - +
1134B ARG* 3.2 5.5 + - - +
1135B LEU 3.2 0.6 - - - -
1136B ALA* 1.3 100.6 + - - +
1138B GLY* 1.3 59.1 + - - +
1139B ASP* 3.7 2.7 - - - +
1187B TRP* 3.7 15.1 - - - -
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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