Contacts of the helix formed by residues 1215 - 1235 (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 ASP1215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1214A PRO* 1.3 81.1 - - - +
1216A ALA* 1.3 64.0 + - - +
1217A GLU* 3.2 3.6 - - - -
1218A GLU* 3.0 25.1 + - + +
1219A LEU* 2.9 34.1 + - + +
1259A TYR* 3.0 23.1 + - + +
1264A LYS* 3.4 37.3 + - + +
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Residues in contact with ALA1216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A TYR* 4.1 16.4 - - + +
1205A PRO 5.3 0.7 - - - +
1212A LYS* 5.0 15.5 - - + +
1213A ALA* 3.2 29.0 + - + +
1214A PRO 3.4 1.6 + - - -
1215A ASP* 1.3 74.8 - - - +
1217A GLU* 1.3 53.1 + - - +
1219A LEU* 3.8 10.0 - - - +
1220A ASP* 2.8 37.5 + - - +
1242A PRO* 6.1 1.3 - - + -
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Residues in contact with GLU1217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214A PRO 5.0 2.8 + - - +
1215A ASP* 3.2 1.3 - - - -
1216A ALA* 1.3 78.2 - - - +
1218A GLU* 1.3 61.1 + - - +
1220A ASP* 3.5 6.1 + - - +
1221A LYS* 3.2 34.1 + - + +
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Residues in contact with GLU1218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215A ASP* 3.0 30.4 + - + +
1217A GLU* 1.3 75.3 - - - +
1219A LEU* 1.3 66.8 + - + +
1221A LYS* 3.3 7.6 + - - +
1222A VAL* 3.1 28.1 + - - +
1264A LYS* 4.3 10.4 + - - +
1265A PHE* 3.4 26.7 - - + -
1303A HIS* 3.1 31.1 + - + +
1307A ASN* 3.9 10.4 - - - +
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Residues in contact with LEU1219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A TYR* 3.9 32.1 - - + -
1205A PRO* 4.3 7.9 - - + -
1213A ALA* 4.5 3.6 - - + -
1215A ASP* 2.9 32.4 + - + +
1216A ALA* 3.9 6.3 - - - +
1218A GLU* 1.3 75.0 - - - +
1220A ASP* 1.3 57.5 + - - +
1222A VAL* 3.4 1.5 + - - -
1223A ALA* 3.0 31.5 + - - +
1259A TYR* 4.1 21.8 - - + -
1264A LYS 3.3 22.0 - - - +
1265A PHE* 3.9 17.3 - - + -
1266A ALA 4.4 2.7 - - - +
1267A PHE* 3.6 28.5 - - + -
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Residues in contact with ASP1220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A TYR* 2.3 35.1 + - - +
1216A ALA 2.8 20.0 + - - +
1217A GLU* 3.6 7.4 - - - +
1219A LEU* 1.3 77.3 - - - +
1221A LYS* 1.3 58.7 + - + +
1223A ALA* 3.8 1.2 - - - +
1224A ARG* 2.7 73.0 + - - +
1240A VAL* 4.2 3.0 - - - +
1241A GLY* 4.6 1.6 - - - -
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Residues in contact with LYS1221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217A GLU* 3.2 22.4 + - + +
1218A GLU* 3.3 6.5 + - - +
1220A ASP* 1.3 79.5 - - + +
1222A VAL* 1.3 66.9 + - + +
1224A ARG* 3.6 8.6 + - - +
1225A LEU* 3.1 23.7 + - - +
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Residues in contact with VAL1222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1218A GLU* 3.1 19.1 + - + +
1219A LEU* 3.9 4.0 - - - +
1221A LYS* 1.3 74.8 - - + +
1223A ALA* 1.3 55.2 + - - +
1225A LEU* 3.2 5.5 + - - +
1226A ALA* 2.7 33.1 + - - +
1265A PHE* 5.4 1.8 - - + -
1267A PHE* 4.0 14.4 - - + -
1299A THR* 4.7 4.2 - - + +
1300A ILE* 3.9 37.0 - - + +
1303A HIS* 3.4 47.6 - - + +
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Residues in contact with ALA1223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A LEU* 3.5 27.2 - - + +
1204A TYR* 4.3 7.4 - - + -
1219A LEU 3.0 17.7 + - - +
1220A ASP 3.8 0.4 - - - +
1222A VAL* 1.3 74.4 - - - +
1224A ARG* 1.3 58.7 + - - +
1226A ALA* 4.2 1.8 - - - -
1227A ALA* 2.8 32.6 + - - +
1240A VAL* 3.6 23.3 - - + -
1267A PHE* 4.2 11.6 - - + -
1300A ILE* 5.7 0.9 - - - -
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Residues in contact with ARG1224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220A ASP* 2.7 50.1 + - - +
1221A LYS* 3.8 8.5 - - - +
1223A ALA* 1.3 75.8 - - - +
1225A LEU* 1.3 57.0 + - - +
1227A ALA* 3.8 2.5 - - - +
1228A LYS* 3.0 40.9 + - + +
1240A VAL* 4.1 34.9 + - + +
1241A GLY* 5.7 0.2 - - - -
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Residues in contact with LEU1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221A LYS 3.1 18.4 + - - +
1222A VAL* 3.8 4.0 - - - +
1224A ARG* 1.3 72.9 - - - +
1226A ALA* 1.3 65.7 + - - +
1228A LYS* 4.2 22.6 - - + +
1229A ALA* 3.0 26.4 + - + +
1299A THR* 4.2 16.9 - - + +
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Residues in contact with ALA1226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A LEU* 3.8 15.9 - - + -
1222A VAL 2.7 20.7 + - - +
1223A ALA* 3.7 4.9 - - - +
1225A LEU* 1.3 74.2 - - - +
1227A ALA* 1.3 56.6 + - - +
1229A ALA* 3.5 0.5 + - - +
1230A LEU* 2.9 29.5 + - - +
1269A PHE* 5.6 0.2 - - - -
1296A GLY* 3.5 30.1 - - - +
1299A THR* 4.0 13.6 - - - +
1300A ILE* 3.9 13.7 - - + -
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Residues in contact with ALA1227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A LEU* 4.0 7.7 - - + +
1223A ALA 2.8 17.0 + - - +
1224A ARG 3.8 4.0 - - - +
1226A ALA* 1.3 74.0 - - - +
1228A LYS* 1.3 60.8 + - + +
1230A LEU* 3.2 9.4 + - - +
1231A ALA* 2.9 29.9 + - - +
1236A THR 4.8 1.0 - - - +
1238A TYR* 4.0 28.2 + - + +
1240A VAL* 3.9 18.2 - - + -
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Residues in contact with LYS1228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224A ARG* 3.0 31.2 + - + +
1225A LEU* 3.8 24.7 - - + +
1227A ALA* 1.3 74.7 - - + +
1229A ALA* 1.3 62.4 + - - +
1231A ALA* 3.4 10.2 - - - +
1232A SER* 3.3 17.8 + - - -
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Residues in contact with ALA1229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225A LEU* 3.0 25.1 + - + +
1226A ALA 3.8 3.4 - - - +
1228A LYS* 1.3 73.8 - - - +
1230A LEU* 1.3 65.6 + - - +
1232A SER* 3.2 25.8 + - - -
1295A LEU* 3.8 23.2 - - + +
1299A THR* 3.8 17.7 - - - +
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Residues in contact with LEU1230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226A ALA 2.9 17.8 + - - +
1227A ALA* 3.2 6.7 + - - +
1229A ALA* 1.3 75.6 - - - +
1231A ALA* 1.3 63.3 + - - +
1232A SER 3.3 0.5 + - - -
1233A VAL* 3.4 10.6 + - - +
1234A SER 4.4 1.4 + - - -
1236A THR* 3.8 9.3 - - - +
1238A TYR* 3.4 41.7 - - + -
1269A PHE* 3.7 31.0 - - + -
1292A GLU* 3.3 51.3 - - + +
1293A THR* 3.8 20.0 - - - +
1296A GLY* 4.4 3.9 - - - +
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Residues in contact with ALA1231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1227A ALA 2.9 11.5 + - - +
1228A LYS* 3.4 14.1 - - - +
1229A ALA 3.2 0.2 - - - -
1230A LEU* 1.3 71.8 - - - +
1232A SER* 1.3 62.7 + - - +
1233A VAL 2.9 2.8 + - - -
1235A GLY* 2.8 31.9 + - - -
1236A THR 3.5 27.6 - - - +
1237A GLU* 5.4 4.0 - - + -
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Residues in contact with SER1232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228A LYS 3.3 7.2 + - - -
1229A ALA* 3.2 20.8 + - - -
1230A LEU 3.2 0.4 - - - -
1231A ALA* 1.3 78.9 - - - +
1233A VAL* 1.3 63.2 + - - +
1235A GLY 5.0 0.3 + - - -
1295A LEU* 3.8 14.4 - - - +
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Residues in contact with VAL1233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230A LEU 3.9 8.3 - - - +
1231A ALA 2.9 1.8 + - - -
1232A SER* 1.3 81.0 - - - +
1234A SER* 1.3 66.9 + - - +
1288A PRO* 5.2 2.7 - - + +
1291A GLU* 4.1 13.0 - - + +
1292A GLU* 3.7 33.0 - - + +
1295A LEU* 3.7 30.5 - - + -
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Residues in contact with SER1234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A LEU 4.4 1.4 + - - -
1231A ALA 3.4 1.0 + - - -
1233A VAL* 1.3 84.5 + - - +
1235A GLY* 1.3 61.3 + - - +
1236A THR* 3.7 18.2 - - - -
1272A ARG* 4.0 11.9 + - - -
1288A PRO* 4.9 6.4 + - - +
1292A GLU* 3.9 8.0 + - - -
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Residues in contact with GLY1235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231A ALA* 2.8 19.2 + - - -
1234A SER* 1.3 78.7 - - - +
1236A THR* 1.3 65.3 + - - +
1237A GLU* 3.3 17.5 + - - +
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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
------------------------------------------------------------
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