Contacts of the helix formed by residues 1215 - 1232 (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 ASP1215 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213B ALA* 5.0 0.2 - - - -
1214B PRO* 1.3 79.2 - - - +
1216B ALA* 1.3 63.4 + - - +
1217B GLU 3.2 3.8 + - - -
1218B GLU* 3.4 7.0 + - + +
1219B LEU* 3.1 29.7 + - + +
1259B TYR* 2.8 41.8 + - + +
1264B LYS* 3.5 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B TYR* 3.8 24.5 + - + +
1205B PRO 5.3 0.2 - - - +
1212B LYS* 3.9 31.0 - - + +
1213B ALA* 3.0 22.2 + - + +
1214B PRO 3.4 2.0 + - - -
1215B ASP* 1.3 77.2 - - - +
1217B GLU* 1.3 56.8 + - - +
1219B LEU* 4.6 1.3 - - - -
1220B ASP* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214B PRO 5.1 1.3 + - - +
1215B ASP 3.3 1.0 - - - -
1216B ALA* 1.3 74.6 - - - +
1218B GLU* 1.3 65.3 + - - +
1220B ASP* 3.5 5.5 + - - +
1221B LYS* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215B ASP* 3.4 9.4 + - + +
1217B GLU* 1.3 79.0 + - - +
1219B LEU* 1.3 63.5 + - + +
1221B LYS* 3.2 7.7 + - + +
1222B VAL* 3.0 28.9 + - + +
1264B LYS* 2.8 35.4 + - - -
1265B PHE* 3.4 20.8 - - + -
1303B HIS* 2.9 33.0 + - + +
1307B ASN* 4.1 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B TYR* 4.0 24.0 - - + -
1205B PRO* 4.0 24.5 - - + +
1213B ALA* 5.5 0.7 - - + -
1215B ASP* 3.1 26.6 + - + +
1216B ALA* 4.0 1.1 - - - +
1218B GLU* 1.3 77.2 - - + +
1220B ASP* 1.3 57.5 + - - +
1222B VAL* 4.6 0.2 - - - -
1223B ALA* 3.0 30.1 + - - +
1259B TYR* 4.0 17.0 - - + -
1264B LYS* 3.5 28.0 - - + +
1265B PHE* 3.7 29.4 - - + -
1266B ALA 4.5 2.0 - - - +
1267B PHE* 3.4 19.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B TYR* 2.7 37.4 + - - +
1216B ALA 2.9 14.8 + - - +
1217B GLU* 3.9 5.4 - - - +
1218B GLU 3.2 0.2 - - - -
1219B LEU* 1.3 74.4 - - - +
1221B LYS* 1.3 59.7 + - - +
1223B ALA* 4.1 1.2 - - - +
1224B ARG* 3.0 48.9 + - - +
1240B VAL* 4.2 9.0 - - - +
1241B GLY* 4.0 10.2 - - - -
1242B PRO* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1217B GLU 3.2 14.2 + - - +
1218B GLU* 3.2 10.3 + - - +
1220B ASP* 1.3 74.7 - - - +
1222B VAL* 1.3 66.0 + - - +
1224B ARG* 3.3 7.7 + - - +
1225B LEU* 3.0 40.1 + - + +
1303B HIS* 4.5 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1218B GLU* 3.0 20.3 + - + +
1219B LEU* 4.0 4.5 - - - +
1221B LYS* 1.3 74.1 - - + +
1223B ALA* 1.3 66.9 + - - +
1225B LEU* 3.2 7.6 + - - +
1226B ALA* 3.0 21.7 + - - +
1265B PHE* 4.7 4.9 - - + -
1267B PHE* 4.0 18.2 - - + -
1299B THR* 4.8 3.6 - - + +
1300B ILE* 4.1 28.9 - - + +
1303B HIS* 3.6 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202B LEU* 3.4 22.7 - - + +
1204B TYR* 4.4 4.7 - - + -
1219B LEU 3.0 21.2 + - - +
1220B ASP* 4.1 2.7 - - - +
1222B VAL* 1.3 75.2 - - - +
1224B ARG* 1.3 53.5 + - - +
1226B ALA* 3.2 3.6 + - - -
1227B ALA* 2.8 32.4 + - - +
1240B VAL* 3.3 25.6 - - + -
1267B PHE* 3.8 17.2 - - + -
1300B ILE* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220B ASP* 3.0 44.7 + - - +
1221B LYS* 3.3 8.1 - - - +
1222B VAL 3.2 0.4 - - - -
1223B ALA* 1.3 76.5 - - - +
1225B LEU* 1.3 58.1 + - + +
1227B ALA* 3.4 5.8 + - + +
1228B LYS* 3.0 32.5 + - + +
1240B VAL* 4.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221B LYS* 3.0 34.8 + - + +
1222B VAL* 3.2 5.6 + - - +
1224B ARG* 1.3 75.9 - - + +
1226B ALA* 1.3 60.2 - - - +
1228B LYS* 3.5 18.9 - - + +
1229B ALA* 2.9 29.3 + - - +
1299B THR* 4.1 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202B LEU* 3.9 14.6 - - + -
1222B VAL 3.0 13.1 + - - +
1223B ALA 3.5 8.3 - - - +
1225B LEU* 1.3 76.0 - - - +
1227B ALA* 1.3 59.7 + - - +
1229B ALA* 4.3 0.2 - - - -
1230B LEU* 2.9 31.4 + - - +
1296B GLY* 3.6 28.1 - - - +
1299B THR* 4.1 14.5 - - - +
1300B ILE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202B LEU* 3.9 7.0 - - + +
1223B ALA 2.8 9.5 + - - +
1224B ARG 3.6 5.4 - - - +
1226B ALA* 1.3 76.6 - - - +
1228B LYS* 1.3 56.3 + - - +
1230B LEU* 3.4 8.8 + - - +
1231B ALA* 2.9 31.3 + - - +
1236B THR 4.8 0.3 - - - +
1238B TYR* 4.0 22.6 + - + +
1240B VAL* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224B ARG* 3.0 16.8 + - + +
1225B LEU* 3.5 23.8 - - + +
1227B ALA* 1.3 75.5 - - - +
1229B ALA* 1.3 62.2 + - - +
1231B ALA* 3.4 7.4 + - - +
1232B SER* 3.3 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225B LEU 2.9 21.7 + - - +
1226B ALA 3.8 2.9 - - - +
1227B ALA 3.3 0.2 - - - -
1228B LYS* 1.3 73.2 - - - +
1230B LEU* 1.3 62.5 + - - +
1232B SER* 2.6 28.1 + - - -
1295B LEU* 3.6 23.0 - - + +
1299B THR* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226B ALA 2.9 17.7 + - - +
1227B ALA* 3.4 6.7 - - - +
1229B ALA* 1.3 77.1 - - - +
1231B ALA* 1.3 63.8 + - - +
1232B SER 3.1 1.6 + - - -
1233B VAL* 3.4 10.0 + - - +
1234B SER 4.6 1.0 + - - -
1236B THR* 3.8 10.9 + - - +
1238B TYR* 3.5 47.8 - - + +
1269B PHE* 4.0 17.5 - - + -
1292B GLU* 3.4 57.6 - - + +
1293B THR* 3.9 16.6 - - - +
1295B LEU* 4.4 1.5 - - - +
1296B GLY* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227B ALA 2.9 17.7 + - - +
1228B LYS* 3.6 9.0 - - - +
1229B ALA 3.3 0.2 - - - -
1230B LEU* 1.3 76.2 - - - +
1232B SER* 1.3 56.0 + - - +
1233B VAL 3.3 0.2 - - - -
1235B GLY* 2.7 35.3 + - - -
1236B THR 3.2 27.1 - - - +
1237B GLU* 5.1 7.2 - - + -
1238B TYR 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228B LYS 3.3 9.2 + - - -
1229B ALA* 2.6 22.1 + - - -
1230B LEU 3.1 0.6 - - - -
1231B ALA* 1.3 78.1 - - - +
1233B VAL* 1.3 62.3 + - - +
1235B GLY 4.6 0.2 - - - -
1295B LEU* 3.7 12.5 - - - +
----------------------------------------------------------
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