Contacts of the helix formed by residues 1253 - 1261 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144A ASN* 3.3 28.3 - - - -
1145A ARG* 5.0 2.9 - - - -
1147A TRP* 3.7 1.7 - - - +
1207A GLY* 5.4 1.4 - - - -
1243A THR* 5.7 4.9 - - - +
1250A ALA* 4.6 7.1 + - - -
1251A SER 3.3 3.3 + - - -
1252A GLY* 1.3 79.9 - - - +
1254A SER* 1.3 67.2 + - - +
1255A ILE* 3.9 10.7 - - - +
1256A ASP* 3.6 30.2 + - - +
1257A TRP* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068A ILE* 4.8 2.2 - - - -
1144A ASN* 3.2 11.1 + - - -
1147A TRP* 3.5 36.0 - - - -
1192A PHE* 3.6 19.8 - - - -
1194A ASP* 2.9 34.3 + - - +
1253A SER* 1.3 75.0 - - - +
1255A ILE* 1.3 66.3 + - - +
1257A TRP* 3.3 6.4 + - - +
1258A ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192A PHE* 4.1 9.0 - - + -
1194A ASP* 3.8 7.2 - - + -
1204A TYR* 4.0 24.2 - - - -
1205A PRO* 3.9 5.0 - - + +
1243A THR* 3.6 22.9 - - + +
1253A SER* 3.9 11.9 - - - +
1254A SER* 1.3 86.8 + - - +
1256A ASP* 1.3 68.0 + - - +
1258A ALA* 4.2 6.1 - - - -
1259A TYR* 3.0 24.8 + - - +
1266A ALA* 3.3 16.2 - - + +
1267A PHE 3.6 26.0 - - - +
1268A THR* 3.3 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149A ALA* 4.1 5.8 - - + -
1205A PRO* 3.6 19.8 - - - +
1206A TYR* 3.7 10.2 - - + -
1207A GLY* 2.7 33.3 + - - -
1208A TYR* 3.2 33.3 + - + +
1250A ALA 4.3 0.9 - - - +
1252A GLY 5.7 0.2 + - - -
1253A SER* 3.5 21.8 + - - +
1254A SER 3.3 0.2 - - - -
1255A ILE* 1.3 80.8 - - - +
1257A TRP* 1.3 66.6 + - - +
1259A TYR* 3.3 5.2 + - - +
1260A ASP* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A TRP* 3.8 34.8 - + + -
1148A ASN* 3.3 42.9 - - - +
1149A ALA* 3.6 11.2 - - + +
1171A ASN* 5.0 0.2 - - - +
1180A VAL* 3.7 39.9 - - + +
1183A ILE* 3.6 39.9 - - + -
1184A GLN* 3.9 11.1 - - + +
1192A PHE* 4.8 1.1 - + - -
1253A SER 3.2 12.0 + - - +
1254A SER 3.5 7.4 - - - +
1256A ASP* 1.3 78.7 - - - +
1258A ALA* 1.3 91.4 + - + +
1260A ASP* 3.3 2.7 + - - -
1261A ASN* 3.0 62.4 + - + +
1263A ILE* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192A PHE* 3.6 40.8 - - + -
1254A SER 3.0 16.1 + - - +
1255A ILE 3.6 6.5 - - - +
1256A ASP 3.2 0.2 - - - -
1257A TRP* 1.3 88.6 - - + +
1259A TYR* 1.3 59.6 + - - +
1261A ASN* 3.3 6.8 + - - +
1262A GLY 3.5 0.2 + - - -
1263A ILE* 3.0 35.9 + - + +
1266A ALA* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205A PRO* 3.5 28.3 - - + -
1206A TYR* 3.3 33.0 - + + -
1213A ALA* 3.4 22.0 - - + -
1214A PRO* 3.4 11.9 - - + +
1215A ASP* 3.0 39.0 + - - +
1219A LEU* 4.1 9.4 - - + -
1255A ILE 3.0 9.1 + - - +
1256A ASP* 3.7 4.3 - - - +
1258A ALA* 1.3 71.2 - - - +
1260A ASP* 1.3 55.8 + - - +
1261A ASN 3.1 5.6 + - - -
1262A GLY* 3.2 8.7 + - - -
1263A ILE 3.3 9.0 + - - +
1264A LYS* 3.1 41.1 - - + -
1266A ALA* 4.1 1.5 - - + +
1404A GOL 2.7 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1148A ASN 5.8 1.8 - - - +
1149A ALA* 4.4 8.6 - - + +
1150A SER 5.4 0.3 + - - -
1206A TYR* 2.9 28.8 + - - -
1208A TYR* 3.2 29.4 + - - -
1256A ASP 2.9 17.8 + - - +
1257A TRP* 3.8 6.7 - - - +
1259A TYR* 1.3 75.7 - - - +
1261A ASN* 1.3 64.0 + - - +
1262A GLY 3.4 1.8 + - - -
1404A GOL 4.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1148A ASN 5.0 1.4 - - - +
1183A ILE* 6.1 0.7 - - + -
1184A GLN* 3.2 27.5 + - + +
1257A TRP* 3.0 61.0 + - + +
1258A ALA* 3.3 4.4 + - - +
1259A TYR 3.1 0.8 - - - -
1260A ASP* 1.3 84.3 - - - +
1262A GLY* 1.3 58.5 + - - +
1263A ILE* 3.4 8.9 + - + +
1401A NAG 5.3 7.8 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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