Contacts of the helix formed by residues 1108 - 1129 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106I PRO 3.3 4.0 + - - -
1107I PRO* 1.3 73.9 - - - +
1109I LEU* 1.3 65.1 + - - +
1110I SER* 3.3 9.6 + - - -
1111I LYS* 3.1 35.2 + - - +
1112I MET* 3.1 17.7 + - - +
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Residues in contact with LEU1109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108I SER* 1.3 74.1 - - - +
1110I SER* 1.3 58.9 + - - +
1112I MET* 3.4 3.5 + - - +
1113I ILE* 2.9 48.3 + - + +
1238I PRO* 3.9 34.7 - - + +
1240I MET* 4.0 26.7 - - + -
1241I LEU* 4.7 9.6 - - + -
1269I GLU* 6.4 2.2 - - + -
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Residues in contact with SER1110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108I SER* 3.0 9.0 + - - -
1109I LEU* 1.3 82.5 - - - +
1111I LYS* 1.3 64.8 + - - +
1113I ILE* 3.5 9.1 + - - +
1114I GLN* 3.0 23.0 + - - +
1269I GLU* 4.5 17.4 + - - +
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Residues in contact with LYS1111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107I PRO* 4.3 11.2 - - + -
1108I SER* 3.1 32.6 + - - +
1110I SER* 1.3 79.5 - - - +
1112I MET* 1.3 57.3 + - - +
1114I GLN* 3.1 27.1 + - + +
1115I MET* 3.2 21.4 + - + +
1147I PHE* 6.6 0.2 - - + -
1271I GLU* 4.6 14.4 + - - +
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Residues in contact with MET1112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107I PRO* 3.6 29.8 - - + +
1108I SER 3.1 19.3 + - - +
1109I LEU* 3.8 6.1 - - - +
1111I LYS* 1.3 70.5 - - - +
1113I ILE* 1.3 56.7 + - - +
1114I GLN 3.0 1.3 - - - -
1115I MET* 3.1 8.2 + - - +
1116I ALA* 2.7 36.1 + - - +
1202I LEU* 5.5 0.2 - - - +
1205I ILE* 3.2 37.1 - - + +
1206I ALA* 3.1 37.0 - - + +
1238I PRO* 4.9 11.4 - - + -
1241I LEU* 3.4 29.6 - - + -
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Residues in contact with ILE1113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109I LEU* 2.9 39.9 + - + +
1110I SER* 3.5 7.9 - - - +
1112I MET* 1.3 74.5 - - - +
1114I GLN* 1.3 65.0 + - - +
1116I ALA* 3.1 4.7 + - + +
1117I GLY* 2.8 23.4 + - - -
1240I MET* 3.6 37.2 - - + -
1241I LEU* 4.4 9.2 - - + -
1244I LEU* 5.5 0.4 - - + -
1266I ILE* 4.3 17.5 - - + -
1269I GLU* 3.9 36.1 - - + +
1270I MET* 3.9 12.1 - - - +
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Residues in contact with GLN1114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110I SER 3.0 14.1 + - - +
1111I LYS* 3.1 18.6 - - + +
1112I MET 3.0 0.2 - - - -
1113I ILE* 1.3 77.6 - - - +
1115I MET* 1.3 59.6 + - + +
1118I GLU* 2.9 57.1 + - - +
1147I PHE 6.1 0.4 - - - +
1269I GLU 4.4 1.7 - - - +
1270I MET* 3.3 32.0 - - - +
1271I GLU* 2.9 61.2 + - - +
1274I PHE* 5.1 3.0 - - - +
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Residues in contact with MET1115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087I LEU* 3.9 19.1 - - + -
1090I TYR* 3.7 35.4 - - + +
1091I LEU* 4.6 4.9 - - + -
1094I LEU* 5.5 2.7 - - + -
1107I PRO* 5.7 4.7 - - + -
1111I LYS* 3.2 22.0 + - + +
1112I MET* 3.4 7.6 - - - +
1114I GLN* 1.3 75.4 - - + +
1116I ALA* 1.3 60.0 + - - +
1118I GLU* 3.2 8.7 + - - +
1119I ILE* 2.8 38.0 + - + +
1143I VAL* 5.9 0.7 - - + -
1147I PHE* 5.3 9.0 - - + +
1149I VAL* 3.9 20.0 - - + -
1205I ILE* 3.8 30.1 - - + -
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Residues in contact with ALA1116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112I MET 2.7 17.0 + - - +
1113I ILE* 3.1 16.8 + - + +
1115I MET* 1.3 73.0 - - - +
1117I GLY* 1.3 56.6 + - - +
1119I ILE* 4.7 1.3 - - - -
1120I ALA* 2.9 30.4 + - - +
1198I PHE* 3.5 12.2 - - + -
1202I LEU* 3.6 31.0 - - + -
1205I ILE* 4.7 2.8 - - - +
1241I LEU* 5.0 3.1 - - + -
1244I LEU* 5.3 3.6 - - + -
1262I ILE* 6.3 0.2 - - + -
1266I ILE* 4.4 8.7 - - + -
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Residues in contact with GLY1117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113I ILE 2.8 15.7 + - - -
1116I ALA* 1.3 73.9 - - - +
1118I GLU* 1.3 57.2 + - - +
1120I ALA* 3.7 5.0 - - - +
1121I ASP* 2.8 30.7 + - - +
1263I ILE* 4.3 5.4 - - - +
1266I ILE* 3.7 20.3 - - - +
1270I MET* 3.9 15.3 - - - -
1274I PHE* 4.1 6.1 - - - -
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Residues in contact with GLU1118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061I HIS* 3.4 35.8 + - + +
1114I GLN* 2.9 52.8 + - - +
1115I MET* 3.8 7.1 - - - +
1117I GLY* 1.3 73.0 - - - +
1119I ILE* 1.3 66.3 + - - +
1121I ASP* 3.4 1.4 + - - -
1122I GLY* 3.2 17.3 + - - -
1147I PHE 4.1 3.1 - - - +
1148I THR* 3.5 30.5 + - - +
1149I VAL* 3.0 34.4 + - - +
1270I MET* 4.1 4.3 - - + -
1274I PHE* 4.8 1.2 - - + -
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Residues in contact with ILE1119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087I LEU* 3.8 16.2 - - + -
1115I MET* 2.8 20.0 + - + +
1116I ALA* 3.8 3.4 - - - +
1118I GLU* 1.3 75.4 - - - +
1120I ALA* 1.3 65.0 + - - +
1122I GLY 3.4 1.7 + - - -
1123I MET* 3.2 20.1 + - - +
1136I LEU* 4.4 15.7 - - + -
1141I CYS* 3.7 17.3 - - - -
1149I VAL* 3.8 17.7 - - + -
1151I ILE* 3.7 18.4 - - + +
1198I PHE* 3.6 23.3 - - + -
1201I VAL* 3.7 26.2 - - + -
1202I LEU* 6.6 0.2 - - + -
1205I ILE* 4.5 7.2 - - + -
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Residues in contact with ALA1120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116I ALA 2.9 19.0 + - - +
1117I GLY* 3.7 3.8 - - - +
1119I ILE* 1.3 78.0 - - - +
1121I ASP* 1.3 57.5 + - - +
1123I MET* 2.9 4.2 + - - +
1124I ALA* 2.8 29.5 + - - +
1198I PHE* 3.9 18.6 - - + -
1259I PHE* 3.8 18.9 - - + +
1262I ILE* 4.9 4.7 - - + -
1263I ILE* 3.6 24.2 - - + +
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Residues in contact with ASP1121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059I CYS* 4.2 2.4 - - - -
1061I HIS* 2.8 27.7 + - - +
1117I GLY 2.8 18.2 + - - +
1118I GLU 3.8 0.7 - - - +
1119I ILE 3.2 0.4 - - - -
1120I ALA* 1.3 76.4 - - - +
1122I GLY* 1.3 64.1 + - - +
1124I ALA* 3.3 2.4 + - - +
1125I TYR* 3.1 22.3 + - - +
1263I ILE* 3.4 12.3 - - + +
1274I PHE* 4.0 4.7 - - + -
1278I SER* 3.3 6.7 - - - -
1279I PHE* 2.6 32.3 + - - +
1280I TYR* 2.8 34.8 + - - +
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Residues in contact with GLY1122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059I CYS* 4.5 0.9 - - - -
1061I HIS* 3.8 25.7 - - - +
1062I VAL* 4.0 15.2 - - - +
1118I GLU 3.2 8.5 + - - -
1119I ILE 3.4 3.6 + - - -
1120I ALA 3.2 0.4 - - - -
1121I ASP* 1.3 79.0 - - - +
1123I MET* 1.3 57.4 + - - +
1125I TYR* 3.2 6.9 - - - +
1126I LEU* 3.0 25.6 + - - +
1151I ILE* 4.6 6.5 - - - +
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Residues in contact with MET1123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119I ILE* 3.2 14.7 + - + +
1120I ALA 2.9 8.1 + - - +
1122I GLY* 1.3 75.0 - - - +
1124I ALA* 1.3 60.8 + - - +
1126I LEU* 3.2 9.7 + - + +
1127I ASN* 2.8 35.6 + - - +
1133I HIS* 3.7 23.3 - - + -
1136I LEU* 3.8 28.5 - - + -
1151I ILE* 4.1 16.4 - - + -
1194I ASP* 3.4 33.4 - - + +
1259I PHE* 3.2 44.2 - - + -
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Residues in contact with ALA1124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120I ALA 2.8 12.6 + - - +
1121I ASP 3.7 7.9 - - - +
1123I MET* 1.3 74.7 - - - +
1125I TYR* 1.3 57.1 + - - +
1127I ASN* 3.1 4.6 + - - +
1128I ALA* 2.8 32.4 + - - +
1259I PHE* 3.7 21.3 - - + +
1260I LEU* 3.8 29.8 - - + -
1263I ILE* 4.2 4.9 - - + -
1279I PHE* 3.8 8.9 - - + -
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Residues in contact with TYR1125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056I GLU 3.9 5.4 + - - -
1057I PHE* 3.7 23.8 - + + -
1058I ASN* 3.0 36.5 + - - +
1059I CYS* 3.3 33.4 - - + -
1062I VAL* 4.0 8.7 - - + -
1121I ASP 3.1 12.9 + - - +
1122I GLY 3.2 9.6 - - - +
1124I ALA* 1.3 76.3 - - - +
1126I LEU* 1.3 66.3 + - + +
1128I ALA* 3.3 0.7 + - - +
1129I ASN* 2.9 46.3 + - - -
1279I PHE* 3.5 30.3 - + + -
1284I GLU* 3.4 31.6 + - - -
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Residues in contact with LEU1126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057I PHE* 3.6 45.1 - - + -
1062I VAL* 5.3 2.5 - - + -
1122I GLY 3.0 14.1 + - - +
1123I MET* 3.3 15.9 - - + +
1125I TYR* 1.3 79.3 - - + +
1127I ASN* 1.3 64.7 + - - +
1129I ASN* 3.0 13.8 + - - +
1130I LYS 3.2 0.5 + - - -
1131I PHE* 3.2 33.7 + - + +
1132I VAL 4.6 0.2 - - - -
1133I HIS* 3.9 46.9 - - + +
1151I ILE* 5.5 1.3 - - + -
1154I PHE* 4.1 14.1 - - + -
1157I THR* 4.9 1.8 - - - -
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Residues in contact with ASN1127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123I MET* 2.8 23.3 + - - +
1124I ALA* 3.1 5.4 + - - +
1126I LEU* 1.3 75.2 - - - +
1128I ALA* 1.3 55.1 + - - +
1130I LYS* 2.7 35.5 + - - +
1131I PHE 3.0 22.0 + - - +
1160I ILE* 5.5 1.7 - - - +
1191I THR* 3.1 38.5 + - + +
1194I ASP* 3.7 16.8 + - - -
1259I PHE* 3.3 25.7 - - - -
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Residues in contact with ALA1128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124I ALA 2.8 16.5 + - - +
1125I TYR 3.7 5.2 - - - +
1127I ASN* 1.3 78.8 - - - +
1129I ASN* 1.3 63.3 + - - +
1130I LYS* 3.2 11.7 + - - +
1260I LEU* 6.4 1.3 - - + -
1279I PHE* 3.7 25.1 - - + -
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Residues in contact with ASN1129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056I GLU* 4.8 16.1 - - - +
1057I PHE* 4.9 9.6 - - + -
1125I TYR* 2.9 52.3 + - - +
1126I LEU 3.0 7.9 + - - +
1128I ALA* 1.3 83.1 - - - +
1130I LYS* 1.3 71.1 + - - +
1131I PHE* 3.2 26.0 - - + -
1159I ASP* 5.9 0.2 - - - -
1279I PHE* 5.4 0.8 - - - -
1284I GLU* 4.8 4.9 + - - +
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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