Contacts of the helix formed by residues 1222 - 1243 (chain A) in PDB entry 5IMX
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 ALA1222 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220A SER 3.2 6.3 + - - +
1221A LEU* 1.3 75.8 - - - +
1223A MET* 1.3 66.1 + - - +
1224A LEU* 3.2 6.3 - - + +
1225A ASP* 2.8 31.4 + - - +
1226A LEU* 3.4 9.4 + - - +
1393A ILE 5.3 4.3 - - - +
1397A LEU* 4.0 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222A ALA* 1.3 75.2 - - - +
1224A LEU* 1.3 63.1 + - - +
1226A LEU* 3.1 14.5 + - - +
1227A LEU* 3.0 26.5 + - + +
1323A PHE* 3.4 33.9 - - + -
1353A ASN* 4.0 6.3 - - + +
1354A CYS* 5.2 0.2 - - - -
1355A PRO* 3.8 18.6 - - + -
1392A VAL* 3.5 22.4 - - + +
1393A ILE* 3.7 20.5 + - - +
1395A THR* 3.5 46.3 + - + +
1396A ALA 4.4 3.1 - - - +
1397A LEU* 4.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222A ALA* 3.2 5.1 - - + +
1223A MET* 1.3 79.9 - - - +
1225A ASP* 1.3 60.3 + - - +
1227A LEU* 3.1 2.8 + - + +
1228A HIS* 2.9 59.7 + - + +
1387A THR* 4.1 24.5 - - + +
1393A ILE* 3.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220A SER 4.2 2.5 - - - +
1221A LEU* 3.7 17.8 - - + -
1222A ALA* 2.8 38.0 + - - +
1224A LEU* 1.3 74.7 - - - +
1226A LEU* 1.3 67.3 + - - +
1228A HIS* 3.6 9.5 + - - +
1229A VAL* 3.2 28.1 + - - +
1262A PRO* 5.0 6.8 - - - +
1264A ARG* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A LEU* 3.7 29.8 - - + -
1221A LEU* 4.1 12.1 - - + -
1222A ALA 3.8 9.6 - - - +
1223A MET* 3.1 11.2 + - - +
1225A ASP* 1.3 83.7 - - - +
1227A LEU* 1.3 60.6 + - - +
1229A VAL* 3.5 6.0 + - + +
1230A ALA* 3.1 22.2 + - - +
1322A ILE* 3.8 25.2 - - + +
1323A PHE* 3.7 36.3 - - + -
1325A LEU* 3.9 11.7 - - + -
1397A LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223A MET 3.0 16.0 + - - +
1224A LEU* 3.1 6.9 + - - +
1226A LEU* 1.3 76.2 - - - +
1228A HIS* 1.3 56.7 + - - +
1230A ALA* 3.4 6.3 + - + +
1231A ARG* 2.7 36.4 + - - +
1319A LEU* 6.1 0.7 - - + -
1323A PHE* 3.8 21.1 - - + -
1358A VAL* 4.2 10.3 - - + -
1361A ILE* 6.0 0.7 - - + -
1383A ILE* 3.9 17.7 - - + +
1386A CYS* 3.7 48.2 - - + +
1387A THR* 3.9 16.4 - - + +
1392A VAL* 4.0 8.1 - - + -
1393A ILE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A LEU* 2.9 56.5 + - + +
1225A ASP* 3.8 8.6 + - - +
1227A LEU* 1.3 77.6 - - - +
1229A VAL* 1.3 52.0 + - - +
1231A ARG* 3.3 34.1 + - - +
1232A ASP* 2.8 43.1 + - - +
1264A ARG* 5.8 4.3 - - + +
1387A THR* 4.6 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A LEU* 3.7 30.7 - - + -
1207A PHE* 5.7 3.1 - - + -
1208A LEU* 6.2 1.1 - - + -
1225A ASP 3.2 15.2 + - - +
1226A LEU* 3.7 10.5 - - + +
1227A LEU 3.5 0.2 - - - -
1228A HIS* 1.3 70.6 - - - +
1230A ALA* 1.3 66.6 + - - +
1232A ASP* 3.1 4.4 + - - +
1233A ILE* 2.9 26.9 + - + +
1257A LEU* 4.2 22.4 - - + -
1264A ARG* 4.6 14.1 - - + -
1266A ALA* 4.1 15.9 - - + -
1322A ILE* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226A LEU 3.1 10.7 + - - +
1227A LEU* 3.4 13.5 - - + +
1229A VAL* 1.3 78.1 - - - +
1231A ARG* 1.3 63.5 + - - +
1233A ILE* 3.5 1.7 + - - -
1234A ALA* 3.0 25.1 + - - +
1315A PHE* 3.6 8.9 - - + -
1319A LEU* 3.9 28.5 - - + -
1322A ILE* 4.0 12.5 - - + +
1323A PHE* 4.7 2.9 - - + -
1383A ILE* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A ASN* 5.6 0.4 + - - +
1227A LEU 2.7 21.2 + - - +
1228A HIS* 3.6 38.3 + - + +
1230A ALA* 1.3 75.5 - - - +
1232A ASP* 1.3 93.6 + - - +
1235A CYS* 3.1 23.7 + - + +
1380A LEU* 3.4 20.6 - - + +
1383A ILE* 3.7 19.9 - - + +
1384A GLU* 3.4 33.8 + - - -
1387A THR* 5.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A ASN* 3.2 37.6 + - - +
1228A HIS* 2.8 28.2 + - - +
1229A VAL* 3.1 5.6 + - - +
1231A ARG* 1.3 110.9 + - - +
1233A ILE* 1.3 64.6 + - - +
1235A CYS* 3.3 1.8 + - - -
1236A GLY 3.1 16.3 + - - -
1264A ARG 4.2 4.5 - - - +
1265A VAL* 3.5 11.8 - - - +
1266A ALA* 2.8 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A ASN* 5.1 0.4 - - - +
1204A LEU* 5.3 0.2 - - + -
1229A VAL* 2.9 20.6 + - + +
1230A ALA* 4.0 3.4 - - - +
1232A ASP* 1.3 71.9 - - - +
1234A ALA* 1.3 55.2 + - - +
1236A GLY* 3.1 4.0 + - - -
1237A CYS* 2.7 45.7 + - - -
1250A ILE* 4.7 2.9 - - + -
1255A CYS* 3.9 26.2 - - + -
1266A ALA* 3.6 34.8 - - + +
1267A LYS* 3.8 16.6 - - - +
1268A ILE* 4.1 11.2 - - + +
1315A PHE* 4.1 4.7 - - + -
1318A LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230A ALA 3.0 18.8 + - - +
1233A ILE* 1.3 76.8 - - - +
1235A CYS* 1.3 53.2 + - - +
1237A CYS* 3.5 7.4 - - - +
1238A GLN* 2.7 34.5 + - - +
1315A PHE* 3.7 20.5 - - + -
1376A PHE* 4.1 6.3 - - + +
1379A ILE* 4.5 9.4 - - + -
1380A LEU* 3.7 23.6 - - + +
1383A ILE* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176A HIS* 3.6 28.8 + - - -
1177A GLN* 4.6 7.6 - - - -
1178A ASN* 3.6 8.7 - - - +
1231A ARG* 3.1 20.1 + - + +
1232A ASP* 3.6 5.8 - - - +
1233A ILE 3.2 0.2 - - - -
1234A ALA* 1.3 75.1 - - - +
1236A GLY* 1.3 63.0 + - - +
1238A GLN* 3.3 5.4 + - - +
1239A TYR* 3.0 18.0 + - - +
1380A LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176A HIS* 3.8 18.0 - - - -
1178A ASN* 4.1 11.9 - - - -
1179A ILE* 4.3 3.9 - - - +
1232A ASP 3.1 7.3 + - - -
1233A ILE 3.1 6.1 + - - -
1235A CYS* 1.3 78.1 - - - +
1237A CYS* 1.3 59.2 + - - +
1239A TYR* 3.3 4.5 + - - +
1240A LEU* 3.0 25.8 + - - +
1268A ILE* 3.9 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233A ILE* 2.7 34.6 + - - +
1234A ALA 3.5 1.1 - - - +
1236A GLY* 1.3 70.1 - - - +
1238A GLN* 1.3 57.2 + - - +
1240A LEU* 3.2 10.5 + - - +
1241A GLU* 2.8 29.6 + - - +
1250A ILE* 3.8 36.1 - - - -
1268A ILE* 4.2 3.8 - - - -
1311A ASP* 5.9 0.9 - - - -
1315A PHE* 4.5 1.6 - - - -
1376A PHE* 3.3 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234A ALA 2.7 20.7 + - - +
1235A CYS* 3.7 7.4 - - - +
1236A GLY 3.2 0.4 - - - -
1237A CYS* 1.3 70.8 - - - +
1239A TYR* 1.3 65.1 + - - +
1241A GLU* 3.4 11.0 + - - +
1242A GLU* 3.0 54.8 + - - +
1376A PHE* 3.7 15.5 - - + +
1377A ALA* 3.4 39.1 - - - +
1380A LEU* 4.0 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173A LYS 4.2 2.9 + - - -
1174A PHE* 3.2 38.5 - + + -
1175A ASN* 2.8 39.8 + - + +
1176A HIS* 3.6 32.3 - + + -
1179A ILE* 3.5 21.1 - - + -
1235A CYS 3.0 8.4 + - - +
1236A GLY 3.3 6.5 + - - +
1238A GLN* 1.3 76.3 - - - +
1240A LEU* 1.3 64.9 + - + +
1242A GLU* 3.3 10.9 + - - +
1243A ASN* 2.8 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174A PHE* 3.7 32.1 - - + -
1179A ILE* 3.8 17.3 - - + -
1236A GLY 3.0 12.2 + - - +
1237A CYS* 3.2 10.1 + - - +
1239A TYR* 1.3 79.5 - - + +
1241A GLU* 1.3 62.8 + - - +
1243A ASN* 2.9 10.0 + - - -
1245A PHE* 2.9 42.4 + - + +
1247A HIS* 4.2 20.0 - - + -
1268A ILE* 3.8 26.2 - - + -
1271A PHE* 3.8 22.7 - - + -
1311A ASP* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237A CYS 2.8 18.8 + - - +
1238A GLN* 3.7 13.4 + - - +
1240A LEU* 1.3 73.6 - - - +
1242A GLU* 1.3 58.6 + - - +
1244A HIS* 3.0 26.2 + - - -
1245A PHE 4.3 2.9 + - - +
1308A SER* 3.6 33.0 + - - +
1312A THR* 5.2 0.2 + - - -
1375A ASN* 3.5 27.2 + - - +
1376A PHE* 3.0 41.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238A GLN* 3.0 50.8 + - - +
1239A TYR* 3.6 10.9 - - - +
1241A GLU* 1.3 78.6 - - + +
1243A ASN* 1.3 65.7 + - - +
1244A HIS* 3.3 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174A PHE* 4.9 14.1 - - + -
1239A TYR* 2.8 62.1 + - - +
1240A LEU* 2.9 7.3 + - - +
1242A GLU* 1.3 81.2 - - - +
1244A HIS* 1.3 73.3 + - - +
1245A PHE* 3.1 4.2 + - - +
----------------------------------------------------------
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