Contacts of the helix formed by residues 1108 - 1129 (chain J) in PDB entry 3F5P
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 SER1108 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107J PRO* 1.3 73.1 - - - +
1109J LEU* 1.3 62.8 + - - +
1110J SER* 3.6 8.8 + - - -
1111J LYS* 3.1 31.4 + - - +
1112J MET* 3.1 31.0 + - - +
1238J PRO* 5.7 0.9 - - - -
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Residues in contact with LEU1109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108J SER* 1.3 74.3 - - - +
1110J SER* 1.3 59.9 + - - +
1112J MET* 3.3 4.5 + - + +
1113J ILE* 2.9 52.1 + - + +
1238J PRO* 3.9 35.9 - - + +
1240J MET* 3.8 24.0 - - + -
1241J LEU* 4.8 7.9 - - + -
1269J GLU* 6.3 2.0 - - + -
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Residues in contact with SER1110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108J SER* 3.3 7.9 + - - -
1109J LEU* 1.3 77.5 - - - +
1111J LYS* 1.3 66.5 + - - +
1113J ILE* 3.6 6.8 + - - +
1114J GLN* 3.2 22.7 + - - +
1269J GLU* 4.4 17.4 + - - +
1271J GLU* 6.0 2.8 - - - +
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Residues in contact with LYS1111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107J PRO* 4.3 10.8 - - + -
1108J SER* 3.1 33.6 + - - +
1110J SER* 1.3 78.7 - - - +
1112J MET* 1.3 61.4 + - - +
1114J GLN* 3.1 24.3 + - + +
1115J MET* 3.2 19.9 + - + +
1147J PHE* 4.7 25.7 - - - +
1271J GLU* 5.2 12.9 + - - +
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Residues in contact with MET1112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107J PRO* 3.6 49.1 - - + +
1108J SER 3.1 15.8 + - - +
1109J LEU* 3.8 6.1 - - + +
1110J SER 3.3 0.2 - - - -
1111J LYS* 1.3 74.9 - - - +
1113J ILE* 1.3 59.7 - - - +
1115J MET* 3.2 9.8 + - - +
1116J ALA* 2.8 29.0 + - - +
1202J LEU* 5.4 0.3 - - - +
1205J ILE* 3.7 34.3 - - + +
1206J ALA* 4.3 11.2 - - - +
1208J LEU* 5.4 0.2 - - + -
1238J PRO* 4.9 12.3 - - + -
1241J LEU* 3.5 35.3 - - + +
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Residues in contact with ILE1113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109J LEU* 2.9 36.4 + - + +
1110J SER* 3.8 7.2 - - - +
1112J MET* 1.3 75.2 - - - +
1114J GLN* 1.3 57.0 + - - +
1116J ALA* 3.1 6.1 + - + +
1117J GLY 2.8 27.2 + - - -
1240J MET* 3.3 41.5 - - + -
1241J LEU* 4.4 7.4 - - + -
1244J LEU* 5.8 0.2 - - + -
1266J ILE* 3.8 29.2 - - + -
1269J GLU* 4.0 28.3 - - + +
1270J MET* 3.6 9.4 - - - +
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Residues in contact with GLN1114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110J SER 3.2 10.1 + - - +
1111J LYS* 3.1 20.1 + - + +
1113J ILE* 1.3 79.2 - - - +
1115J MET* 1.3 60.1 + - + +
1117J GLY 3.5 0.2 + - - -
1118J GLU* 3.1 55.3 + - - +
1147J PHE 6.0 1.8 - - - +
1269J GLU 4.4 2.3 + - - +
1270J MET* 3.2 31.2 - - - +
1271J GLU* 3.0 57.5 + - + +
1274J PHE* 5.1 3.6 - - - +
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Residues in contact with MET1115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087J LEU* 4.1 22.2 - - + -
1090J TYR* 3.7 31.0 - - + +
1091J LEU* 4.6 6.3 - - + -
1094J LEU* 5.9 1.8 - - + -
1107J PRO* 6.1 4.9 - - + -
1111J LYS* 3.2 18.6 + - + +
1112J MET* 3.2 8.8 + - - +
1114J GLN* 1.3 74.7 - - + +
1116J ALA* 1.3 68.3 + - - +
1118J GLU* 3.3 8.9 + - - +
1119J ILE* 3.0 33.0 + - + +
1143J VAL* 5.7 0.7 - - + -
1147J PHE* 5.1 9.6 - - + +
1149J VAL* 4.0 19.7 - - + -
1205J ILE* 4.3 30.3 - - + -
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Residues in contact with ALA1116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112J MET 2.8 17.6 + - - +
1113J ILE* 3.5 10.3 - - + +
1115J MET* 1.3 78.0 - - - +
1117J GLY* 1.3 56.3 + - - +
1119J ILE* 4.8 1.8 - - - -
1120J ALA* 2.9 31.5 + - - +
1198J PHE* 3.4 14.9 - - + -
1202J LEU* 3.6 27.8 - - + -
1205J ILE* 5.0 0.8 - - - +
1241J LEU* 5.0 5.6 - - + -
1244J LEU* 5.4 4.9 - - + -
1262J ILE* 6.0 0.4 - - + -
1266J ILE* 4.3 9.0 - - + -
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Residues in contact with GLY1117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113J ILE 2.8 17.4 + - - -
1114J GLN 4.0 0.4 - - - -
1116J ALA* 1.3 72.9 - - - +
1118J GLU* 1.3 57.4 + - - +
1120J ALA* 3.7 5.4 - - - +
1121J ASP* 2.9 28.9 + - - +
1263J ILE* 4.3 7.2 - - - +
1266J ILE* 3.5 21.0 - - - +
1270J MET* 4.0 13.9 - - - -
1274J PHE* 4.2 4.4 - - - -
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Residues in contact with GLU1118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061J HIS* 3.4 35.4 + - + +
1114J GLN* 3.1 49.1 + - - +
1115J MET* 3.9 3.3 - - - +
1117J GLY* 1.3 75.2 - - - +
1119J ILE* 1.3 64.9 + - - +
1121J ASP* 3.2 1.6 + - - -
1122J GLY* 3.1 19.6 + - - -
1147J PHE 4.3 2.1 - - - +
1148J THR* 3.5 28.2 + - - +
1149J VAL* 2.8 41.0 + - - +
1270J MET* 4.3 3.6 - - + -
1274J PHE* 5.0 0.9 - - + -
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Residues in contact with ILE1119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087J LEU* 3.9 23.8 - - + -
1115J MET* 3.0 20.5 + - + +
1116J ALA* 3.8 2.9 - - - +
1118J GLU* 1.3 77.1 - - - +
1120J ALA* 1.3 63.1 + - - +
1122J GLY 3.5 0.5 + - - -
1123J MET* 3.1 22.7 + - - +
1136J LEU* 4.3 13.7 - - + -
1141J CYS* 3.9 11.0 - - - -
1149J VAL* 3.6 20.0 - - + -
1151J ILE* 3.6 19.6 - - + +
1198J PHE* 3.3 26.0 - - + -
1201J VAL* 3.8 23.8 - - + -
1205J ILE* 4.4 7.6 - - + -
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Residues in contact with ALA1120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116J ALA 2.9 20.1 + - - +
1117J GLY* 3.7 2.7 - - - +
1119J ILE* 1.3 78.4 - - - +
1121J ASP* 1.3 57.2 + - - +
1123J MET 3.3 0.2 + - - -
1124J ALA* 2.8 31.5 + - - +
1198J PHE* 3.7 15.0 - - + -
1259J PHE* 3.6 23.7 - - + +
1262J ILE* 4.5 7.4 - - + -
1263J ILE* 3.7 22.7 - - + -
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Residues in contact with ASP1121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059J CYS* 4.2 2.9 - - - -
1061J HIS* 2.6 32.4 + - + +
1117J GLY 2.9 19.0 + - - +
1118J GLU 3.2 1.0 + - - +
1120J ALA* 1.3 73.5 - - - +
1122J GLY* 1.3 60.0 + - - +
1124J ALA* 3.3 1.9 + - - +
1125J TYR* 3.0 27.5 + - - +
1263J ILE* 3.5 10.6 - - + +
1274J PHE* 4.1 3.8 - - + -
1278J SER* 3.9 7.0 - - - -
1279J PHE* 2.7 29.3 + - - +
1280J TYR* 2.8 34.9 + - - +
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Residues in contact with GLY1122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059J CYS* 4.2 0.9 - - - -
1061J HIS* 3.7 26.7 - - - +
1062J VAL* 4.0 15.6 - - - +
1118J GLU 3.1 10.7 + - - -
1119J ILE 4.0 1.8 - - - -
1121J ASP* 1.3 77.1 - - - +
1123J MET* 1.3 56.9 + - - +
1125J TYR* 3.3 7.1 - - - +
1126J LEU* 2.9 25.6 + - - +
1151J ILE* 4.6 6.5 - - - -
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Residues in contact with MET1123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119J ILE* 3.1 21.6 + - + +
1120J ALA 3.7 2.2 - - - +
1122J GLY* 1.3 74.4 - - - +
1124J ALA* 1.3 61.3 + - - +
1126J LEU* 3.0 10.7 + - + +
1127J ASN* 2.8 34.0 + - - +
1133J HIS* 3.8 24.0 - - + -
1136J LEU* 3.9 25.1 - - + -
1151J ILE* 4.0 19.5 - - + -
1194J ASP* 3.2 37.9 - - + +
1259J PHE* 3.5 38.6 - - + -
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Residues in contact with ALA1124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120J ALA 2.8 17.3 + - - +
1121J ASP 3.6 5.6 - - - +
1123J MET* 1.3 75.3 - - - +
1125J TYR* 1.3 59.7 + - - +
1127J ASN* 3.3 4.8 + - - +
1128J ALA* 2.8 30.8 + - - +
1259J PHE* 3.6 23.0 - - + +
1260J LEU* 4.3 21.8 - - + +
1263J ILE* 4.3 4.0 - - + -
1279J PHE* 4.0 13.7 - - + -
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Residues in contact with TYR1125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056J GLU 3.8 4.5 + - - -
1057J PHE* 3.4 32.5 - + + -
1058J ASN* 2.8 26.9 + - - +
1059J CYS* 3.3 37.0 - - + -
1062J VAL* 4.0 9.6 - - + -
1121J ASP 3.0 13.8 + - - +
1122J GLY 3.3 8.3 - - - +
1124J ALA* 1.3 73.8 - - - +
1126J LEU* 1.3 68.7 + - + +
1128J ALA* 3.3 1.8 + - - +
1129J ASN* 3.1 45.7 + - - -
1279J PHE* 3.6 30.0 - + + -
1284J GLU* 3.8 29.0 + - - -
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Residues in contact with LEU1126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057J PHE* 3.8 41.5 - - + -
1062J VAL* 5.2 2.0 - - + -
1122J GLY 2.9 15.3 + - - +
1123J MET* 3.1 18.2 - - - +
1125J TYR* 1.3 80.1 - - + +
1127J ASN* 1.3 65.3 + - - +
1129J ASN* 3.1 15.1 + - - +
1130J LYS 3.4 0.2 + - - -
1131J PHE* 3.2 46.8 + - + +
1132J VAL 4.5 0.4 - - - -
1133J HIS* 4.2 24.0 - - + +
1151J ILE* 5.3 1.3 - - + -
1154J PHE* 3.8 26.2 - - + -
1157J THR* 4.6 2.2 - - - +
1194J ASP* 5.2 0.2 - - - +
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Residues in contact with ASN1127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123J MET* 2.8 21.6 + - - +
1124J ALA* 3.8 6.5 - - - +
1126J LEU* 1.3 74.8 - - - +
1128J ALA* 1.3 58.0 + - - +
1130J LYS* 3.0 27.7 + - - +
1131J PHE 3.3 19.6 + - - +
1160J ILE* 5.7 0.4 - - - +
1191J THR* 2.8 41.6 + - + +
1194J ASP* 3.7 17.4 + - - -
1195J VAL* 5.4 0.3 - - - +
1259J PHE* 3.5 23.5 + - + -
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Residues in contact with ALA1128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124J ALA 2.8 18.6 + - - +
1125J TYR 3.5 7.6 - - - +
1126J LEU 3.1 0.2 - - - -
1127J ASN* 1.3 77.8 - - - +
1129J ASN* 1.3 62.5 + - - +
1130J LYS* 3.2 9.6 + - - +
1260J LEU* 6.5 0.4 - - + -
1279J PHE* 3.6 26.2 - - + -
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Residues in contact with ASN1129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056J GLU* 4.2 24.2 - - + +
1057J PHE* 5.2 3.1 - - + -
1125J TYR* 3.1 42.1 + - - +
1126J LEU* 3.1 9.3 + - - +
1128J ALA* 1.3 82.5 - - - +
1130J LYS* 1.3 70.3 + - - +
1131J PHE* 3.3 25.6 - - + -
1159J ASP* 4.9 1.0 - - - +
1279J PHE* 5.6 0.2 - - - -
1284J GLU* 4.4 8.8 + - - +
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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