Contacts of the helix formed by residues 1261 - 1278 (chain A) in PDB entry 2WKM
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 THR1261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1201A VAL* 3.6 19.9 - - - +
1253A GLU* 4.8 2.8 + - - -
1259A LYS* 4.4 6.5 + - + -
1260A PHE* 1.3 81.1 - - - +
1262A THR* 1.3 63.8 + - - +
1263A LYS* 3.1 22.6 + - - +
1264A SER* 2.9 27.3 + - - -
1265A ASP* 3.1 7.4 + - - -
1324A ALA* 5.8 0.2 - - - +
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Residues in contact with THR1262 (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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1192A MET* 6.2 0.4 - - + -
1196A ALA* 3.9 34.3 + - + +
1199A LYS* 5.4 3.8 - - - +
1200A PHE 4.7 4.3 + - - -
1201A VAL* 4.0 14.3 - - - +
1261A THR* 1.3 75.7 - - - +
1263A LYS* 1.3 60.0 + - + +
1265A ASP* 3.0 13.7 + - + +
1266A VAL* 2.9 28.0 + - + +
1329A SER* 6.5 0.7 - - - -
1330A PHE* 4.2 16.2 - - + +
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Residues in contact with LYS1263 (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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1253A GLU* 4.9 0.2 - - - +
1261A THR* 3.1 12.3 + - - +
1262A THR* 1.3 81.3 - - + +
1264A SER* 1.3 56.5 + - - +
1266A VAL* 3.1 23.9 + - + +
1267A TRP 3.2 5.2 + - - -
1324A ALA* 3.2 40.2 - - + +
1325A GLU* 4.2 12.0 + - - +
1327A ARG* 2.6 45.8 + - + +
1328A PRO 3.4 16.7 + - - +
1329A SER* 3.9 8.5 - - - +
1332A GLU* 5.0 1.0 + - - -
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Residues in contact with SER1264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251A ALA* 3.5 17.5 + - - +
1253A GLU* 3.8 6.0 + - - -
1254A SER* 3.4 24.0 + - - -
1260A PHE* 3.7 9.4 - - - +
1261A THR* 2.9 34.7 + - - -
1263A LYS* 1.3 75.8 - - - +
1265A ASP* 1.3 66.0 + - - +
1266A VAL 3.1 0.4 - - - -
1267A TRP* 3.3 3.6 + - - +
1268A SER* 3.1 24.4 + - - -
1327A ARG* 3.7 8.0 - - - +
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Residues in contact with ASP1265 (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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1192A MET* 3.7 12.5 - - + +
1200A PHE 4.3 1.6 - - - +
1201A VAL* 3.7 8.2 - - - +
1202A HIS* 2.8 32.5 + - - +
1203A ARG* 3.1 26.2 + - - -
1205A LEU* 4.0 6.6 + - + +
1261A THR 3.1 14.5 + - - +
1262A THR* 3.0 18.7 - - + +
1264A SER* 1.3 79.0 + - - +
1266A VAL* 1.3 53.6 + - - -
1268A SER* 3.2 8.4 + - - -
1269A PHE* 2.8 28.8 + - - +
1330A PHE* 3.8 15.0 - - + -
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Residues in contact with VAL1266 (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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1262A THR* 2.9 22.9 + - + +
1263A LYS* 3.1 17.9 + - + +
1265A ASP* 1.3 74.3 - - - +
1267A TRP* 1.3 66.1 + - - +
1269A PHE* 3.2 3.7 + - - +
1270A GLY 3.0 17.5 + - - -
1319A CYS* 3.6 31.2 - - + +
1327A ARG* 4.3 8.7 - - + -
1328A PRO* 3.6 28.3 - - + +
1329A SER* 5.0 1.1 - - - -
1330A PHE* 3.6 27.1 - - + +
1333A LEU* 4.0 9.4 - - + -
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Residues in contact with TRP1267 (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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1248A LYS 5.2 0.8 + - - -
1249A TRP 3.5 19.1 + - - -
1250A MET 3.4 13.8 + - - -
1251A ALA* 3.5 19.3 - - + -
1252A LEU* 4.0 19.1 - - + -
1263A LYS 3.2 3.2 + - - -
1264A SER 3.4 10.3 - - - +
1266A VAL* 1.3 79.5 - - - +
1268A SER* 1.3 57.2 + - - +
1270A GLY 2.9 14.7 + - - -
1271A VAL* 3.1 13.5 + - + +
1284A TYR* 4.6 7.2 + - - -
1296A LEU* 3.7 33.6 - - + +
1301A ARG* 3.8 25.8 - - - -
1319A CYS 3.3 13.2 + - - +
1320A TRP* 3.1 54.9 + + + +
1321A HIS 4.2 1.3 - - - -
1322A PRO* 5.1 1.6 - - + -
1327A ARG* 3.5 26.2 - - - +
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Residues in contact with SER1268 (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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1203A ARG 5.5 4.6 + - - -
1204A ASP* 5.9 0.3 - - - -
1205A LEU* 3.8 30.8 + - - +
1249A TRP* 2.6 32.2 + - - +
1250A MET* 4.5 2.3 - - - +
1264A SER 3.1 14.3 + - - -
1265A ASP* 3.5 11.5 + - - -
1267A TRP* 1.3 72.9 - - - +
1269A PHE* 1.3 61.2 + - - +
1271A VAL* 3.0 8.3 + - - +
1272A LEU* 2.8 27.0 + - - +
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Residues in contact with PHE1269 (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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1185A GLY 3.6 25.1 - - - -
1188A VAL* 3.7 21.5 - - + -
1189A ALA* 3.7 20.6 - - + -
1205A LEU* 3.5 15.2 - - + +
1265A ASP 2.8 13.8 + - - +
1266A VAL 3.2 6.9 + - - +
1268A SER* 1.3 76.9 - - - +
1270A GLY* 1.3 57.9 + - - +
1272A LEU* 3.3 12.0 + - + +
1273A LEU* 3.0 43.2 + - + +
1319A CYS* 4.5 6.5 - - - -
1330A PHE* 3.6 16.6 - + + -
1333A LEU* 3.9 25.6 - - + -
1337A ILE* 3.6 30.1 - - + -
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Residues in contact with GLY1270 (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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1266A VAL 3.0 5.9 + - - -
1267A TRP 2.9 10.2 + - - -
1269A PHE* 1.3 77.4 - - - +
1271A VAL* 1.3 62.7 + - - +
1273A LEU* 3.4 9.2 + - - +
1274A TRP* 3.3 14.9 + - - +
1316A MET* 4.1 4.8 - - - +
1319A CYS* 3.8 20.9 - - - -
1320A TRP* 3.2 24.1 - - - -
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Residues in contact with VAL1271 (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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1248A LYS 4.0 17.0 - - - +
1249A TRP* 3.5 35.9 - - + +
1267A TRP* 3.1 28.1 + - + +
1268A SER 3.0 6.6 + - - +
1270A GLY* 1.3 72.5 - - - +
1272A LEU* 1.3 67.3 + - - +
1274A TRP* 3.1 5.9 + - + +
1275A GLU* 2.9 22.3 + - + +
1283A PRO* 4.3 10.8 - - + -
1284A TYR* 4.7 2.0 - - - +
1302A LEU* 4.1 17.5 - - + -
1320A TRP* 3.7 18.2 - - + +
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Residues in contact with LEU1272 (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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1165A LEU* 5.0 2.9 - - + -
1185A GLY* 5.0 0.2 - - - -
1188A VAL* 4.1 22.0 - - + -
1205A LEU* 3.8 24.5 - - + -
1206A ALA* 3.6 29.2 - - - +
1207A ALA* 3.8 11.0 - - + +
1210A CYS* 3.9 11.4 - - - -
1268A SER 2.8 12.7 + - - +
1269A PHE* 3.4 20.6 - - + +
1270A GLY 3.2 0.2 - - - -
1271A VAL* 1.3 77.5 - - - +
1273A LEU* 1.3 65.2 + - - +
1275A GLU* 3.1 18.4 + - - +
1276A LEU* 3.0 39.9 + - + +
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Residues in contact with LEU1273 (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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1182A ILE* 6.2 2.0 - - - -
1185A GLY* 4.3 8.3 - - - -
1269A PHE* 3.0 48.1 + - + +
1270A GLY* 3.5 10.8 - - - +
1271A VAL 3.2 0.2 - - - -
1272A LEU* 1.3 76.8 - - + +
1274A TRP* 1.3 62.8 + - - +
1276A LEU* 2.9 33.3 + - + +
1277A MET* 3.0 17.8 + - - +
1312A LEU* 4.1 31.6 - - + -
1315A VAL* 4.2 17.3 - - + -
1316A MET* 3.7 20.2 - - + +
1319A CYS* 5.4 0.4 - - - -
1337A ILE* 4.2 6.5 - - + -
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Residues in contact with TRP1274 (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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1270A GLY 3.3 9.1 + - - +
1271A VAL 3.1 9.3 + - - +
1273A LEU* 1.3 77.5 - - - +
1275A GLU* 1.3 68.3 + - + +
1277A MET* 3.4 1.3 + - - +
1278A THR* 2.8 51.6 + - + +
1281A ALA* 3.3 30.7 - - + -
1282A PRO 3.7 15.7 - - - -
1283A PRO* 3.7 21.3 - - + -
1284A TYR 5.0 0.4 - - - -
1285A PRO* 5.6 1.8 - - + -
1302A LEU* 3.7 40.9 - - + +
1303A LEU 2.8 30.4 + - - +
1305A PRO* 3.6 17.6 - - + +
1316A MET* 3.5 20.1 - - - +
1320A TRP* 4.4 1.3 - + + -
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Residues in contact with GLU1275 (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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1166A ARG* 4.4 14.7 + - - -
1169A ILE* 3.7 2.1 - - - +
1207A ALA* 2.9 44.8 + - + +
1208A ARG* 4.9 0.9 + - - -
1249A TRP* 3.0 38.3 + - + +
1271A VAL* 2.9 21.4 + - + +
1272A LEU* 3.1 15.3 + - - +
1274A TRP* 1.3 84.6 - - + +
1276A LEU* 1.3 59.9 + - - +
1278A THR* 3.1 6.3 + - - -
1279A ARG 3.0 2.9 + - - -
1280A GLY* 2.7 34.4 + - - +
1281A ALA 4.6 8.8 - - - +
1283A PRO* 5.0 1.5 - - + +
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Residues in contact with LEU1276 (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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1165A LEU* 3.8 27.6 - - + -
1169A ILE* 4.0 15.5 - - + -
1181A LEU* 3.3 39.4 - - + +
1182A ILE* 5.5 0.2 - - - -
1184A PHE* 4.1 8.7 - - + -
1185A GLY* 3.4 36.1 - - - +
1207A ALA* 5.9 0.7 - - + -
1272A LEU* 3.0 27.5 + - + +
1273A LEU* 2.9 17.5 + - + +
1275A GLU* 1.3 77.4 - - + +
1277A MET* 1.3 68.9 + - - +
1279A ARG* 2.9 18.4 + - - -
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Residues in contact with MET1277 (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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1178A VAL* 3.7 39.3 - - + +
1181A LEU* 4.0 21.2 - - + +
1182A ILE* 4.1 9.9 - - + -
1273A LEU* 3.0 14.7 + - - +
1276A LEU* 1.3 84.7 - - - +
1278A THR* 1.3 59.6 + - - +
1279A ARG* 3.2 3.7 - - - +
1305A PRO* 4.0 15.7 - - + +
1307A TYR* 3.9 29.9 + - + +
1308A CYS* 4.0 19.3 - - + -
1309A PRO* 4.2 5.6 - - + -
1312A LEU* 3.6 26.5 - - + -
1316A MET* 3.9 8.3 - - + -
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Residues in contact with THR1278 (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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1274A TRP* 2.8 54.9 + - + +
1275A GLU* 3.1 10.2 + - - -
1277A MET* 1.3 76.1 - - - +
1279A ARG* 1.3 69.4 + - - +
1281A ALA* 3.3 31.7 + - + +
1305A PRO* 3.7 20.4 - - + -
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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