Contacts of the helix formed by residues 1261 - 1278 (chain B) in PDB entry 3EFJ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A THR* 5.8 9.6 - - + +
1201B VAL* 3.6 20.6 - - - +
1253B GLU* 4.6 4.0 + - + +
1259B LYS* 4.2 5.3 + - + -
1260B PHE* 1.3 79.5 - - - +
1262B THR* 1.3 61.9 + - - +
1263B LYS* 3.2 14.7 + - - +
1264B SER* 3.1 35.4 + - - -
1265B ASP* 3.1 5.2 + - - -
1324B ALA* 5.5 1.4 - - - +
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Residues in contact with THR1262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196B ALA* 4.6 31.5 - - + +
1199B LYS* 5.6 4.5 - - - -
1200B PHE 4.8 5.8 - - - +
1201B VAL* 4.2 14.4 - - + -
1261B THR* 1.3 73.9 - - - +
1263B LYS* 1.3 67.5 + - - +
1265B ASP* 3.0 17.5 + - - +
1266B VAL* 2.9 31.3 + - - +
1330B PHE* 3.8 7.2 - - - -
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Residues in contact with LYS1263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261B THR* 3.2 11.1 + - - +
1262B THR* 1.3 84.8 + - - +
1264B SER* 1.3 57.3 + - - +
1266B VAL* 3.4 19.6 + - + +
1267B TRP 3.5 2.1 + - - -
1324B ALA* 3.4 42.4 - - + +
1325B GLU* 4.3 12.6 + - - +
1327B ARG* 2.8 51.1 + - + +
1328B PRO 3.6 17.9 + - - +
1329B SER* 3.7 12.3 - - - +
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Residues in contact with SER1264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250B MET* 5.8 0.2 - - - -
1251B ALA* 3.6 9.4 + - - +
1253B GLU* 4.0 6.3 + - - -
1254B SER* 2.7 27.6 + - - -
1259B LYS 4.4 0.9 - - - -
1260B PHE* 4.0 11.2 - - - -
1261B THR* 3.1 35.5 + - - -
1263B LYS* 1.3 75.3 - - - +
1265B ASP* 1.3 62.7 + - - +
1267B TRP* 3.4 17.0 - - - +
1268B SER* 3.5 10.0 + - - -
1327B ARG* 3.8 8.9 - - - +
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Residues in contact with ASP1265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192B MET* 3.7 25.5 - - + +
1200B PHE 4.4 1.7 - - - +
1201B VAL* 3.6 9.8 - - - +
1202B HIS* 2.9 27.2 + - - +
1203B ARG* 3.1 26.0 + - - -
1205B LEU* 3.9 6.4 + - + +
1260B PHE* 5.9 0.7 - - - -
1261B THR 3.1 12.0 + - - +
1262B THR* 3.0 16.0 + - - +
1264B SER* 1.3 75.2 - - - +
1266B VAL* 1.3 58.9 + - - +
1268B SER* 3.0 9.3 + - - -
1269B PHE* 2.8 28.2 + - - +
1330B PHE* 3.8 6.3 - - + -
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Residues in contact with VAL1266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262B THR* 2.9 20.5 + - - +
1263B LYS* 3.4 17.9 - - + +
1264B SER 3.3 0.2 - - - -
1265B ASP* 1.3 75.4 - - - +
1267B TRP* 1.3 59.9 + - - +
1269B PHE* 3.3 4.3 + - - +
1270B GLY 3.0 17.5 + - - -
1319B CYS* 3.4 35.0 - - + +
1327B ARG* 4.1 8.7 - - + -
1328B PRO* 3.4 29.6 - - + +
1329B SER* 4.9 0.7 - - - -
1330B PHE* 3.6 28.7 - - + +
1333B LEU* 4.1 7.6 - - + -
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Residues in contact with TRP1267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248B LYS 4.9 2.2 + - - -
1249B TRP 3.2 20.5 + - - -
1250B MET 3.3 15.1 + - - -
1251B ALA* 3.6 13.2 - - + -
1252B LEU* 4.0 19.3 - - + -
1263B LYS 3.5 2.0 + - - -
1264B SER 3.4 12.5 + - - +
1265B ASP 3.1 0.2 - - - -
1266B VAL* 1.3 78.9 - - - +
1268B SER* 1.3 62.5 + - - +
1270B GLY 3.0 11.6 + - - -
1271B VAL* 3.1 20.5 + - + +
1284B TYR* 5.0 3.8 + - - -
1296B LEU* 3.9 31.6 - - + +
1301B ARG* 4.1 17.9 - - - -
1319B CYS 3.4 10.9 + - - +
1320B TRP* 3.1 59.0 + + + -
1321B HIS 4.3 1.6 - - - -
1322B PRO 4.8 0.7 - - - -
1327B ARG* 3.2 37.7 - - - +
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Residues in contact with SER1268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203B ARG 5.6 2.6 + - - -
1205B LEU* 3.4 35.2 + - - +
1249B TRP* 2.7 32.3 + - - +
1250B MET* 4.6 2.3 - - - -
1264B SER 3.5 9.2 + - - -
1265B ASP* 3.0 10.7 + - - -
1267B TRP* 1.3 77.1 - - - +
1269B PHE* 1.3 52.3 + - - +
1271B VAL* 3.1 7.6 + - - +
1272B LEU* 2.8 33.3 + - - +
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Residues in contact with PHE1269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185B GLY 3.4 27.1 - - - -
1188B VAL* 3.7 22.2 - - + -
1189B ALA* 3.7 19.7 - - + -
1205B LEU* 3.7 13.6 - - + +
1265B ASP 2.8 11.9 + - - +
1266B VAL 3.3 7.4 - - - +
1268B SER* 1.3 77.3 - - - +
1270B GLY* 1.3 53.0 + - - +
1272B LEU* 2.9 10.6 + - + +
1273B LEU* 2.7 61.5 + - + +
1319B CYS* 4.3 5.4 - - - -
1330B PHE* 3.7 15.9 - + + -
1333B LEU* 3.9 27.4 - - + -
1337B ILE* 3.7 21.1 - - + -
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Residues in contact with GLY1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266B VAL 3.0 7.7 + - - -
1267B TRP 3.0 9.3 + - - -
1269B PHE* 1.3 76.2 - - - +
1271B VAL* 1.3 60.5 + - - +
1273B LEU* 3.3 9.4 + - - +
1274B TRP* 3.1 17.8 + - - +
1316B MET* 3.9 6.1 - - - +
1319B CYS* 3.9 18.8 - - - -
1320B TRP* 3.3 23.4 - - - -
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Residues in contact with VAL1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248B LYS 4.0 19.1 - - - +
1249B TRP* 3.7 29.8 - - + +
1267B TRP* 3.1 25.2 + - + +
1268B SER 3.1 6.5 + - - +
1270B GLY* 1.3 75.5 - - - +
1272B LEU* 1.3 56.6 + - - +
1274B TRP* 3.3 5.0 - - + +
1275B GLU* 3.0 27.1 + - - +
1283B PRO* 4.1 15.3 - - + -
1284B TYR* 4.9 1.1 - - - +
1302B LEU* 4.3 14.1 - - + -
1320B TRP* 3.5 25.4 - - + +
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Residues in contact with LEU1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165B LEU* 5.5 0.7 - - + -
1185B GLY* 4.9 0.2 - - - -
1188B VAL* 4.0 22.9 - - + -
1205B LEU* 3.8 22.0 - - + -
1206B ALA* 3.6 27.4 - - - +
1207B ALA* 3.8 11.7 - - + +
1210B CYS* 3.9 13.2 - - - -
1268B SER 2.8 13.4 + - - +
1269B PHE* 2.9 18.6 + - + +
1271B VAL* 1.3 74.1 - - - +
1273B LEU* 1.3 62.0 + - - +
1275B GLU* 3.0 18.7 + - - +
1276B LEU* 2.9 49.5 + - + +
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Residues in contact with LEU1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181B LEU 5.5 0.7 - - - +
1182B ILE* 5.5 2.5 - - - +
1185B GLY* 3.9 27.6 - - - -
1269B PHE* 2.7 47.0 + - + +
1270B GLY* 3.3 11.0 + - - +
1272B LEU* 1.3 72.8 - - + +
1274B TRP* 1.3 63.1 + - - +
1276B LEU* 3.2 10.7 + - + +
1277B MET* 3.1 28.8 + - - +
1312B LEU* 4.2 22.9 - - + -
1315B VAL* 3.9 24.5 - - + -
1316B MET* 3.7 17.7 - - + -
1337B ILE* 4.1 9.0 - - + -
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Residues in contact with TRP1274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B GLY 3.1 12.3 + - - +
1271B VAL* 3.3 16.4 - - - +
1273B LEU* 1.3 74.7 - - - +
1275B GLU* 1.3 65.5 + - - +
1277B MET* 3.4 2.1 + - - +
1278B THR* 3.0 55.2 + - + +
1281B ALA* 3.3 29.6 - - + -
1282B PRO 4.0 12.3 - - - -
1283B PRO* 3.8 22.2 - - + -
1284B TYR 5.1 0.9 - - - -
1285B PRO* 5.6 2.7 - - + -
1302B LEU* 3.7 36.6 - - + +
1303B LEU* 2.9 27.3 + - + -
1305B PRO* 3.6 20.7 - - + +
1313B TYR* 5.3 0.4 - + - -
1316B MET* 3.7 17.2 - - - +
1320B TRP* 4.3 4.7 - + + -
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Residues in contact with GLU1275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166B ARG* 4.3 13.9 - - - +
1169B ILE* 3.7 2.3 - - - +
1206B ALA* 4.9 0.2 - - - +
1207B ALA* 3.0 40.8 + - + +
1208B ARG* 4.7 1.2 + - - -
1249B TRP* 2.8 44.1 + - + +
1271B VAL 3.0 15.6 + - - +
1272B LEU* 3.1 16.8 - - - +
1274B TRP* 1.3 84.2 - - + +
1276B LEU* 1.3 60.0 + - - +
1278B THR* 3.1 9.7 + - - -
1280B GLY* 2.8 34.4 + - - +
1281B ALA 4.6 7.8 - - - +
1283B PRO* 4.7 4.0 - - + +
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Residues in contact with LEU1276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165B LEU* 3.8 32.8 - - + -
1169B ILE* 4.1 13.2 - - + -
1181B LEU* 3.2 52.8 - - + +
1184B PHE* 4.1 11.0 - - + -
1185B GLY* 3.4 27.6 - - - +
1207B ALA* 5.1 4.7 - - + -
1272B LEU* 2.9 30.4 + - + +
1273B LEU* 3.2 13.9 + - + +
1275B GLU* 1.3 76.3 - - - +
1277B MET* 1.3 60.0 + - - +
1279B ARG* 3.0 15.4 + - - -
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Residues in contact with MET1277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178B VAL* 3.9 17.3 - - + +
1181B LEU* 3.9 28.8 - - + +
1182B ILE* 4.1 11.7 - - + -
1273B LEU* 3.1 16.9 + - - +
1274B TRP 3.4 0.4 + - - +
1276B LEU* 1.3 79.7 - - - +
1278B THR* 1.3 60.8 + - - +
1279B ARG* 3.2 3.5 + - - +
1305B PRO* 3.9 25.6 - - + +
1307B TYR* 3.6 37.1 + - - +
1308B CYS* 4.0 6.1 - - + -
1309B PRO* 3.8 18.8 - - + -
1312B LEU* 3.8 16.6 - - + -
1316B MET* 3.8 15.9 - - + -
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Residues in contact with THR1278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274B TRP* 3.0 50.0 + - + +
1275B GLU* 3.1 12.0 + - - -
1276B LEU 3.3 0.2 - - - -
1277B MET* 1.3 75.6 - - - +
1279B ARG* 1.3 67.6 + - - +
1280B GLY 3.4 0.2 + - - -
1281B ALA* 3.3 31.5 + - + +
1305B PRO* 3.8 18.6 - - + -
1306B GLU 5.6 0.4 - - - +
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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
------------------------------------------------------------
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