Contacts of the helix formed by residues 1266 - 1282 (chain B) in PDB entry 1BRW
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 HIS1266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1245B TYR* 5.4 7.2 + - - -
1264B GLY 3.8 1.6 + - - -
1265B PRO* 1.3 71.8 - - - +
1267B ASP* 1.3 85.8 + - + +
1269B THR* 3.4 4.4 + - - -
1270B GLU* 2.9 46.9 + - - +
1424B ARG* 3.1 40.5 + - - -
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Residues in contact with ASP1267 (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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1241B GLN* 5.0 6.9 + - - -
1242B PRO 4.3 4.3 - - - +
1243B LEU* 3.9 14.7 - - + +
1244B GLY* 3.2 25.6 + - - +
1265B PRO* 3.4 17.7 - - - +
1266B HIS* 1.3 97.1 + - + +
1268B LEU* 1.3 66.3 + - - -
1270B GLU* 4.3 4.5 - - - -
1271B LEU* 3.2 19.4 + - - +
1383B LYS* 4.9 5.2 - - - +
1427B LEU* 3.3 23.4 - - + +
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Residues in contact with LEU1268 (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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1090B THR* 4.1 12.8 - - + +
1091B THR* 3.9 15.7 - - - +
1094B VAL* 4.6 4.3 - - + -
1243B LEU* 3.6 35.7 - - + +
1244B GLY* 4.8 2.5 - - - -
1255B GLU* 4.0 24.0 - - + +
1259B THR* 3.4 27.6 - - + +
1265B PRO* 3.5 19.2 + - + +
1266B HIS 3.3 0.4 - - - -
1267B ASP* 1.3 79.5 + - - +
1269B THR* 1.3 67.2 + - - +
1271B LEU* 3.4 2.4 + - + +
1272B CYS* 3.0 46.1 + - - -
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Residues in contact with THR1269 (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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1259B THR* 3.4 27.6 + - + +
1262B GLY* 6.0 4.4 - - - -
1264B GLY* 4.0 6.9 + - - -
1265B PRO 2.7 23.9 + - - -
1266B HIS* 3.7 4.7 - - - -
1268B LEU* 1.3 75.3 - - - +
1270B GLU* 1.3 65.0 + - - +
1272B CYS* 3.2 6.6 + - - +
1273B LEU* 3.1 37.1 + - + +
1300B ILE* 5.0 13.9 - - + -
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Residues in contact with GLU1270 (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 HIS* 2.9 33.1 + - - +
1267B ASP* 5.1 1.8 - - - -
1269B THR* 1.3 75.5 - - - +
1271B LEU* 1.3 63.3 + - - +
1273B LEU* 3.0 13.6 + - - +
1274B THR* 3.0 28.0 + - - +
1293B ARG* 5.9 4.5 - - - +
1427B LEU* 3.5 31.1 - - + +
1428B ILE* 6.0 0.3 - - - +
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Residues in contact with LEU1271 (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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1091B THR* 3.5 24.5 - - + +
1199B ASP* 3.7 4.9 - - - +
1201B LYS* 3.7 22.2 - - - +
1237B SER* 3.8 16.2 - - - +
1243B LEU* 3.9 15.3 - - + -
1267B ASP 3.2 16.2 + - - +
1268B LEU* 3.8 4.7 - - - +
1269B THR 3.4 0.2 - - - -
1270B GLU* 1.3 79.2 - - - +
1272B CYS* 1.3 61.3 + - - +
1274B THR* 3.4 3.2 + - - -
1275B LEU* 3.1 40.7 + - + +
1427B LEU* 3.5 12.3 - - + +
1428B ILE* 3.8 27.4 - - + -
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Residues in contact with CYS1272 (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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1091B THR* 4.2 18.2 - - - -
1094B VAL* 3.9 33.2 - - + -
1095B LEU* 4.4 14.3 - - + +
1098B LEU* 4.1 15.8 - - + +
1268B LEU* 3.0 44.8 + - - -
1269B THR* 3.2 8.5 + - - +
1271B LEU* 1.3 77.4 - - - +
1273B LEU* 1.3 59.5 + - + +
1276B GLY* 2.9 26.2 + - - -
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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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1098B LEU* 4.5 5.8 - - + -
1269B THR* 3.1 30.0 + - + +
1270B GLU* 3.0 11.3 + - - +
1272B CYS* 1.3 74.1 - - + +
1274B THR* 1.3 66.6 + - - +
1277B SER* 3.1 26.7 + - - -
1293B ARG* 4.4 27.6 - - + +
1296B LEU* 3.8 30.9 - - + +
1297B GLU* 3.7 37.2 - - + +
1300B ILE* 4.4 16.4 - - + -
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Residues in contact with THR1274 (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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1235B VAL* 4.7 9.0 - - + -
1270B GLU* 3.0 20.1 + - - +
1271B LEU* 3.4 10.7 + - - -
1273B LEU* 1.3 76.0 - - - +
1275B LEU* 1.3 62.5 + - + +
1277B SER* 2.9 20.7 + - - -
1278B HIS* 3.2 29.7 + - + +
1293B ARG* 6.4 0.2 - - - +
1428B ILE* 4.0 33.2 - - + +
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Residues in contact with LEU1275 (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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1081B LYS* 4.7 4.9 - - + -
1091B THR* 3.8 24.2 - - + -
1095B LEU* 3.5 16.4 - - + -
1197B VAL* 4.3 15.9 - - + +
1199B ASP* 3.5 38.6 - - + +
1235B VAL* 3.9 37.7 - - + -
1271B LEU* 3.1 25.0 + - + +
1274B THR* 1.3 77.7 - - + +
1276B GLY* 1.3 65.9 + - - +
1278B HIS* 3.4 8.4 + - - +
1279B MET* 3.2 24.6 + - - +
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Residues in contact with GLY1276 (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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1095B LEU* 4.1 2.6 - - - +
1099B VAL* 3.7 20.9 - - - +
1272B CYS 2.9 21.9 + - - -
1275B LEU* 1.3 75.3 - - - +
1277B SER* 1.3 63.6 + - - +
1279B MET* 3.1 8.0 + - - +
1280B VAL* 3.1 26.2 + - - +
1296B LEU* 3.4 9.2 - - - -
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Residues in contact with SER1277 (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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1273B LEU 3.1 15.3 + - - -
1274B THR* 2.9 21.7 + - - -
1276B GLY* 1.3 76.0 - - - +
1278B HIS* 1.3 57.7 + - - +
1280B VAL* 3.2 1.4 + - - -
1281B TYR* 2.9 30.7 + - - +
1289B LEU* 3.7 36.3 + - - +
1292B ALA* 3.7 11.2 - - - +
1293B ARG* 3.8 15.6 - - - +
1296B LEU* 3.5 5.2 - - - +
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Residues in contact with HIS1278 (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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1197B VAL* 4.3 8.5 - - + -
1233B MET* 3.5 32.6 - - + +
1235B VAL* 4.0 25.1 - - + +
1274B THR* 3.2 28.3 + - + -
1275B LEU* 3.4 9.9 + - - +
1276B GLY 3.2 0.2 - - - -
1277B SER* 1.3 81.5 + - - +
1279B MET* 1.3 58.0 + - - +
1281B TYR* 3.9 3.7 - + - +
1282B LEU* 3.1 36.9 + - + +
1289B LEU* 3.9 31.6 - - + +
1431B THR* 4.3 13.5 - - + +
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Residues in contact with MET1279 (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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1079B VAL* 3.7 30.9 - - + +
1080B ASP 4.6 2.5 - - - +
1081B LYS* 3.9 27.1 - - + -
1095B LEU* 3.7 36.1 - - + -
1096B GLY* 5.9 0.2 - - - -
1099B VAL* 4.0 26.5 - - + -
1104B VAL* 4.0 4.1 - - + +
1106B VAL* 4.9 14.6 - - + -
1197B VAL* 3.6 22.7 - - + -
1275B LEU 3.2 13.4 + - - +
1276B GLY 3.1 8.1 + - - +
1278B HIS* 1.3 76.4 - - - +
1280B VAL* 1.3 62.5 + - - +
1282B LEU* 4.1 0.8 - - - +
1283B ALA* 3.2 23.6 + - - +
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Residues in contact with VAL1280 (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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1099B VAL* 4.4 4.9 - - + -
1102B VAL* 3.9 15.3 - - + -
1104B VAL* 3.7 20.4 - - + -
1276B GLY 3.1 13.4 + - - +
1277B SER 3.7 6.1 - - - +
1279B MET* 1.3 76.0 - - - +
1281B TYR* 1.3 58.6 + - - +
1283B ALA 3.1 2.1 + - - -
1284B GLU 3.0 22.5 + - - -
1285B LYS* 3.0 34.8 + - + +
1286B ALA* 3.7 21.3 - - + -
1292B ALA* 4.0 8.1 - - + +
1295B LEU* 4.3 10.5 - - + -
1296B LEU* 4.3 14.8 - - + -
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Residues in contact with TYR1281 (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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1277B SER 2.9 16.7 + - - +
1278B HIS* 3.9 5.8 - + - +
1280B VAL* 1.3 76.9 - - - +
1282B LEU* 1.3 63.1 - - + +
1284B GLU* 2.9 23.4 + - - +
1286B ALA* 3.6 18.8 - - - -
1287B PRO 3.4 24.0 + - - -
1288B SER* 3.7 18.1 - - - +
1289B LEU* 3.8 29.6 - - + -
1292B ALA* 4.6 0.6 - - - +
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Residues in contact with LEU1282 (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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1077B VAL* 3.6 8.3 - - - +
1195B ALA* 4.0 23.6 - - + -
1196B ILE 4.7 0.2 - - - +
1197B VAL* 3.6 24.9 - - + -
1231B ARG* 3.2 49.6 + - + +
1233B MET* 3.8 26.5 - - + -
1278B HIS* 3.1 26.6 + - + +
1279B MET* 4.2 3.4 - - - +
1281B TYR* 1.3 82.6 - - + +
1283B ALA* 1.3 58.5 + - - +
1284B GLU* 3.2 0.9 - - - -
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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
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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