Contacts of the helix formed by residues 1293 - 1313 (chain A) in PDB entry 5W0N
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 SER1293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1166A GLY 5.0 0.4 + - - -
1274A LYS* 4.7 3.6 - - - +
1291A GLY 3.4 3.8 + - - -
1292A LEU* 1.3 73.7 - - - +
1294A ARG* 1.3 64.1 + - - +
1295A LYS* 3.5 8.3 + - - +
1296A MET* 3.2 25.9 + - - +
1297A THR* 2.8 28.3 + - - -
1342A PRO* 5.4 0.9 - - - +
1345A ARG* 4.5 20.3 - - - +
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Residues in contact with ARG1294 (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 LYS* 5.7 0.2 - - - +
1293A SER* 1.3 74.5 - - - +
1295A LYS* 1.3 65.5 + - + +
1297A THR* 3.1 8.6 + - - -
1298A ASN* 3.0 30.5 + - - +
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Residues in contact with LYS1295 (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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1293A SER* 3.4 7.2 + - - +
1294A ARG* 1.3 78.6 - - + +
1296A MET* 1.3 56.8 + - - +
1298A ASN* 3.2 10.9 + - - +
1299A PHE* 2.9 27.9 + - - +
1342A PRO* 4.0 23.5 - - + +
1344A ASP* 3.2 33.4 + - - +
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Residues in contact with MET1296 (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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1160A ILE* 4.8 1.6 - - - -
1165A ARG 4.3 4.9 - - - +
1166A GLY* 3.6 33.0 - - - +
1167A SER* 3.9 17.0 - - - +
1292A LEU* 3.9 5.2 - - + -
1293A SER* 3.2 24.0 + - - +
1295A LYS* 1.3 78.8 - - - +
1297A THR* 1.3 58.2 + - - +
1299A PHE* 3.3 8.3 + - - +
1300A ILE* 2.9 55.0 + - + +
1341A ALA* 4.5 7.6 - - + -
1342A PRO* 3.2 46.8 - - + +
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Residues in contact with THR1297 (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 LYS* 6.1 0.3 - - - +
1275A TYR* 3.9 40.4 + - + +
1276A ILE* 4.2 16.6 + - + +
1292A LEU* 3.7 16.5 + - - +
1293A SER 2.8 22.9 + - - -
1294A ARG* 3.1 7.6 + - - -
1296A MET* 1.3 77.5 - - - +
1298A ASN* 1.3 64.8 + - - +
1300A ILE* 3.4 8.6 + - - +
1301A MET* 3.0 31.4 + - + +
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Residues in contact with ASN1298 (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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1294A ARG* 3.0 22.9 + - - +
1295A LYS* 3.2 10.3 + - - +
1297A THR* 1.3 80.1 - - - +
1299A PHE* 1.3 55.3 + - - +
1301A MET* 3.3 5.8 + - - +
1302A LYS* 2.9 48.3 + - - +
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Residues in contact with PHE1299 (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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1158A CYS 3.6 11.0 - - - -
1160A ILE* 3.6 29.6 - - + -
1295A LYS 2.9 16.5 + - - +
1296A MET* 3.6 6.7 - - - +
1298A ASN* 1.3 76.3 - - - +
1300A ILE* 1.3 61.9 + - - +
1302A LYS* 3.4 10.2 + - + +
1303A ALA* 3.1 20.7 + - + +
1336A THR* 3.6 31.8 - - + +
1339A GLU* 3.8 20.0 - - + -
1340A LEU 3.5 16.6 - - - -
1341A ALA* 3.7 25.4 - - + -
1342A PRO* 3.7 19.5 - - + -
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Residues in contact with ILE1300 (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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1160A ILE* 4.0 28.5 - - + -
1167A SER* 4.9 2.2 - - - -
1168A LEU* 4.5 5.6 - - + -
1173A TYR* 3.9 16.2 - - + +
1276A ILE* 4.2 15.7 - - + -
1292A LEU* 4.1 25.8 - - + -
1296A MET* 2.9 38.2 + - + +
1297A THR* 3.8 4.5 - - - +
1299A PHE* 1.3 77.4 - - - +
1301A MET* 1.3 63.9 + - - +
1303A ALA* 3.1 16.0 + - - +
1304A PHE* 3.1 42.8 + - + -
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Residues in contact with MET1301 (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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1245A TYR* 3.6 23.8 - - + +
1246A THR* 4.9 10.8 - - + +
1251A PHE* 3.9 24.5 - - + -
1275A TYR* 4.3 17.3 - - + +
1276A ILE* 4.5 12.3 - - + -
1297A THR* 3.0 30.9 + - + +
1298A ASN* 3.3 6.7 + - - +
1300A ILE* 1.3 77.0 - - - +
1302A LYS* 1.3 58.2 + - + +
1304A PHE* 3.2 11.6 + - + +
1305A ILE* 2.9 43.0 + - + +
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Residues in contact with LYS1302 (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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985A ILE* 5.8 5.9 - - - +
1298A ASN* 2.9 32.9 + - - +
1299A PHE* 3.8 10.3 - - + +
1301A MET* 1.3 76.3 - - + +
1303A ALA* 1.3 57.6 + - - +
1305A ILE* 3.7 12.1 - - + +
1306A ASN* 2.9 41.9 + - - +
1335A LEU 4.4 0.2 - - - -
1336A THR* 6.5 0.4 - - - -
1337A GLU* 5.5 8.4 + - - +
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Residues in contact with ALA1303 (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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1154A PHE* 3.4 10.5 - - + -
1158A CYS* 3.8 31.4 - - + -
1160A ILE* 4.4 11.0 - - + -
1299A PHE* 3.1 12.6 + - + +
1300A ILE* 3.1 11.3 + - - +
1302A LYS* 1.3 76.7 - - - +
1304A PHE* 1.3 57.5 + - - +
1306A ASN* 3.3 2.6 + - - +
1307A GLY 2.8 25.3 + - - -
1335A LEU* 3.5 15.7 + - - +
1336A THR* 4.7 4.7 - - + +
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Residues in contact with PHE1304 (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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1151A MET* 4.0 36.3 - - + -
1154A PHE* 4.2 15.7 - + - -
1155A THR* 4.6 0.9 - - + -
1160A ILE* 4.3 12.1 - - + -
1173A TYR* 4.2 13.5 - + - -
1176A MET* 4.8 8.7 - - + -
1241A LEU* 4.4 5.4 - - + -
1242A LEU* 3.9 27.6 - - + +
1245A TYR* 4.8 19.1 - + + +
1246A THR* 3.9 17.1 - - + +
1300A ILE* 3.1 46.6 + - + -
1301A MET* 3.2 15.5 + - + +
1303A ALA* 1.3 76.3 - - + +
1305A ILE* 1.3 57.2 + - - +
1307A GLY* 3.2 0.9 + - - -
1308A ARG* 2.8 29.1 + - - +
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Residues in contact with ILE1305 (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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985A ILE* 4.7 23.3 - - + -
987A LEU* 3.8 32.8 - - + -
1246A THR* 4.2 18.2 - - + -
1301A MET* 2.9 32.9 + - + +
1302A LYS* 3.7 11.9 - - + +
1303A ALA 3.3 0.2 - - - -
1304A PHE* 1.3 76.4 - - - +
1306A ASN* 1.3 68.1 + - - +
1308A ARG* 3.1 11.0 + - + +
1309A ARG* 3.1 25.0 + - - +
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Residues in contact with ASN1306 (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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1302A LYS* 2.9 23.1 + - - +
1303A ALA 3.7 0.2 - - - +
1305A ILE* 1.3 79.6 - - - +
1307A GLY* 1.3 58.4 + - - +
1309A ARG* 2.9 40.8 + - - +
1310A VAL* 2.9 32.9 + - - +
1334A VAL 3.5 4.5 + - - +
1335A LEU* 2.8 43.9 + - - +
1336A THR* 4.4 1.0 - - - +
1337A GLU* 3.4 27.3 + - - +
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Residues in contact with GLY1307 (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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1154A PHE* 3.8 15.3 - - - -
1242A LEU* 3.8 7.6 - - - -
1303A ALA 2.8 18.7 + - - -
1304A PHE 3.2 3.8 + - - -
1306A ASN* 1.3 73.8 - - - +
1308A ARG* 1.3 61.0 + - - +
1311A PHE* 2.9 32.7 + - - +
1335A LEU* 3.7 16.7 - - - +
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Residues in contact with ARG1308 (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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987A LEU* 3.5 31.1 + - - +
988A GLU* 2.6 38.4 + - - +
989A PRO* 4.5 1.4 - - - +
990A LEU* 3.5 30.9 - - + +
1239A LEU* 4.2 2.8 - - + +
1242A LEU* 4.1 18.0 - - + +
1243A ARG* 4.5 13.1 - - + +
1246A THR* 3.4 23.8 - - - +
1247A GLU* 2.7 30.6 + - - -
1304A PHE 2.8 13.9 + - - +
1305A ILE* 3.3 12.7 + - - +
1307A GLY* 1.3 73.7 - - - +
1309A ARG* 1.3 60.5 + - - +
1312A GLY* 3.0 27.5 + - - -
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Residues in contact with ARG1309 (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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988A GLU* 3.1 31.2 + - - +
990A LEU* 5.2 0.9 - - - -
1305A ILE* 3.1 14.2 + - - +
1306A ASN* 2.9 46.1 + - - +
1308A ARG* 1.3 81.4 - - - +
1310A VAL* 1.3 62.5 + - - +
1313A ILE* 3.0 56.9 + - + +
1334A VAL* 4.0 19.6 + - - +
1337A GLU* 5.0 4.6 + - - +
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Residues in contact with VAL1310 (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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997A PHE* 4.9 1.0 - - - -
1306A ASN 2.9 16.1 + - - +
1307A GLY 4.0 2.0 - - - +
1309A ARG* 1.3 82.4 - - + +
1311A PHE* 1.3 62.3 + - + +
1313A ILE 4.0 10.9 - - - +
1315A VAL* 6.5 0.2 - - - -
1328A TYR* 4.1 23.6 + - + +
1329A PHE* 3.6 49.3 - - + +
1334A VAL* 3.5 31.9 - - + -
1335A LEU* 3.9 13.7 - - + -
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Residues in contact with PHE1311 (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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997A PHE* 3.6 21.1 - - - -
1001A LEU* 3.7 25.5 - - + +
1004A VAL* 4.4 10.3 - - + -
1150A THR* 5.5 0.4 - - + -
1154A PHE* 4.3 20.2 - + - -
1238A TRP* 3.4 37.0 - + + +
1239A LEU* 4.1 9.0 - - + +
1242A LEU* 3.8 14.4 - - + -
1307A GLY* 2.9 29.6 + - - +
1310A VAL* 1.3 78.9 - - + +
1312A GLY* 1.3 57.8 + - - +
1313A ILE 3.7 0.2 - - - -
1329A PHE* 3.6 51.6 - + + -
1330A PHE* 3.7 25.1 - + - -
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Residues in contact with GLY1312 (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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990A LEU* 4.2 9.9 - - - +
991A PRO* 3.9 11.1 - - - +
993A LEU* 3.6 13.0 - - - +
997A PHE* 5.1 0.2 - - - -
1239A LEU* 3.7 19.9 - - - +
1308A ARG 3.0 18.2 + - - -
1310A VAL 3.4 0.2 - - - -
1311A PHE* 1.3 78.5 - - - +
1313A ILE* 1.3 64.1 + - - +
1314A PRO* 3.4 11.8 - - - +
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Residues in contact with ILE1313 (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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988A GLU* 3.4 28.9 - - + +
989A PRO 4.4 6.7 - - - +
990A LEU* 3.8 16.2 - - + -
991A PRO* 3.7 25.4 - - + -
997A PHE* 4.9 1.1 - - - -
1308A ARG* 5.9 0.2 - - - +
1309A ARG* 3.0 33.6 + - + +
1310A VAL* 4.0 8.9 - - - +
1312A GLY* 1.3 80.5 - - - +
1314A PRO* 1.3 75.3 - - - +
1315A VAL* 3.5 14.9 + - + +
1328A TYR* 4.3 0.5 + - - -
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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
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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