Contacts of the helix formed by residues 1253 - 1261 (chain B) in PDB entry 2BOA
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 SER1253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1144B ASN* 3.3 29.6 - - - +
1145B ARG* 5.1 2.7 - - - -
1147B TRP* 3.7 4.2 - - - +
1149B ALA* 4.5 0.3 - - - +
1207B GLY* 5.2 1.6 - - - -
1243B THR* 5.6 4.2 - - - +
1250B ALA* 3.9 13.2 + - - -
1251B SER 3.3 0.4 - - - -
1252B GLY* 1.3 81.1 - - - +
1254B SER* 1.3 66.6 + - - +
1255B ILE* 4.3 7.5 - - - +
1256B ASP* 3.5 28.7 + - - +
1257B TRP 3.1 18.2 + - - -
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Residues in contact with SER1254 (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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1068B ILE* 4.9 0.7 - - - -
1144B ASN* 3.2 13.0 + - - -
1147B TRP* 3.5 35.4 - - - -
1192B PHE* 3.4 25.1 - - - -
1194B ASP* 3.0 24.6 + - - +
1253B SER* 1.3 73.8 - - - +
1255B ILE* 1.3 65.6 + - - +
1257B TRP* 3.2 9.2 + - - +
1258B ALA* 2.8 27.0 + - - +
1268B THR* 5.2 0.3 + - - -
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Residues in contact with ILE1255 (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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1192B PHE* 4.0 13.2 - - + -
1194B ASP* 4.3 1.6 - - + -
1204B TYR* 3.8 27.6 - - - -
1205B PRO* 3.8 4.6 - - + +
1243B THR* 3.7 22.7 - - + +
1253B SER* 4.3 8.5 - - - +
1254B SER* 1.3 86.3 + - - +
1256B ASP* 1.3 68.4 - - - +
1258B ALA* 4.0 7.4 - - - -
1259B TYR* 3.0 26.9 + - - +
1266B ALA* 3.4 16.0 - - + +
1267B PHE 3.4 28.0 - - - +
1268B THR* 3.4 27.4 - - - +
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Residues in contact with ASP1256 (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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1149B ALA* 3.7 13.0 - - + -
1205B PRO* 3.5 18.5 - - - +
1206B TYR* 3.6 11.8 - - - -
1207B GLY* 2.7 35.1 + - - -
1208B TYR* 2.8 26.2 + - + +
1250B ALA 4.2 0.2 - - - +
1253B SER* 3.4 22.3 + - - +
1254B SER 3.3 0.2 - - - -
1255B ILE* 1.3 80.4 - - - +
1257B TRP* 1.3 65.1 + - - +
1259B TYR* 4.1 2.3 - - - +
1260B ASP* 3.1 30.8 + - - +
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Residues in contact with TRP1257 (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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1147B TRP* 3.6 39.3 - + + -
1148B ASN* 3.6 36.2 - - + +
1149B ALA* 3.5 11.0 - - + +
1180B VAL* 3.9 28.7 - - + +
1183B ILE* 3.6 45.3 - - + -
1184B GLN* 3.8 26.2 - - + +
1192B PHE* 4.6 1.3 - + - -
1253B SER 3.1 13.1 + - - +
1254B SER 3.3 10.8 - - - +
1256B ASP* 1.3 76.0 - - - +
1258B ALA* 1.3 80.6 + - + +
1260B ASP* 3.6 0.6 + - - -
1261B ASN* 2.7 67.2 + - + +
1263B ILE* 4.3 3.8 - - + -
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Residues in contact with ALA1258 (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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1192B PHE* 3.8 35.9 - - + -
1254B SER 2.8 16.2 + - - +
1255B ILE* 3.5 7.4 - - - +
1256B ASP 3.2 0.2 - - - -
1257B TRP* 1.3 83.7 - - + +
1259B TYR* 1.3 64.0 + - - +
1261B ASN 3.0 10.6 + - - -
1263B ILE* 3.0 36.0 + - + +
1266B ALA* 4.2 4.0 - - + -
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Residues in contact with TYR1259 (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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1205B PRO* 3.5 21.1 - - + -
1206B TYR* 3.2 33.4 - + - -
1213B ALA* 3.7 16.6 - - + -
1214B PRO* 3.3 16.3 - - + +
1215B ASP* 2.8 56.5 + - + -
1219B LEU* 4.0 7.6 - - + -
1255B ILE 3.0 17.3 + - - +
1256B ASP 4.1 2.7 - - - +
1258B ALA* 1.3 75.1 - - - +
1260B ASP* 1.3 59.6 + - - +
1262B GLY* 3.3 13.7 + - - -
1263B ILE 3.3 13.8 + - - +
1264B LYS* 3.4 28.9 - - - -
1266B ALA* 4.2 1.3 - - + +
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Residues in contact with ASP1260 (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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1148B ASN 5.4 1.7 - - - +
1149B ALA* 4.2 7.7 - - + +
1206B TYR* 2.5 35.9 + - - -
1208B TYR* 3.0 28.4 + - - -
1256B ASP 3.1 18.1 + - - +
1257B TRP* 3.8 5.6 - - - +
1259B TYR* 1.3 76.6 - - - +
1261B ASN* 1.3 64.6 + - - +
1262B GLY 3.3 2.9 + - - -
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Residues in contact with ASN1261 (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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1148B ASN 4.8 3.2 + - - -
1183B ILE* 6.2 0.4 - - + -
1184B GLN* 3.2 25.3 + - + +
1257B TRP* 2.7 66.8 + - + +
1258B ALA* 3.0 7.0 + - - +
1260B ASP* 1.3 82.6 - - - +
1262B GLY* 1.3 59.6 + - - +
1263B ILE* 3.6 8.3 + - + +
1C NAG 5.5 5.4 + - - -
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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
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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